The full dataset viewer is not available (click to read why). Only showing a preview of the rows.
The dataset generation failed
Error code: DatasetGenerationError
Exception: ArrowTypeError
Message: ("Expected bytes, got a 'list' object", 'Conversion failed for column Socs36E with type object')
Traceback: Traceback (most recent call last):
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/packaged_modules/json/json.py", line 137, in _generate_tables
pa_table = paj.read_json(
File "pyarrow/_json.pyx", line 308, in pyarrow._json.read_json
File "pyarrow/error.pxi", line 154, in pyarrow.lib.pyarrow_internal_check_status
File "pyarrow/error.pxi", line 91, in pyarrow.lib.check_status
pyarrow.lib.ArrowInvalid: JSON parse error: Column() changed from object to string in row 0
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1855, in _prepare_split_single
for _, table in generator:
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/packaged_modules/json/json.py", line 167, in _generate_tables
pa_table = pa.Table.from_pandas(df, preserve_index=False)
File "pyarrow/table.pxi", line 3874, in pyarrow.lib.Table.from_pandas
File "/src/services/worker/.venv/lib/python3.9/site-packages/pyarrow/pandas_compat.py", line 611, in dataframe_to_arrays
arrays = [convert_column(c, f)
File "/src/services/worker/.venv/lib/python3.9/site-packages/pyarrow/pandas_compat.py", line 611, in <listcomp>
arrays = [convert_column(c, f)
File "/src/services/worker/.venv/lib/python3.9/site-packages/pyarrow/pandas_compat.py", line 598, in convert_column
raise e
File "/src/services/worker/.venv/lib/python3.9/site-packages/pyarrow/pandas_compat.py", line 592, in convert_column
result = pa.array(col, type=type_, from_pandas=True, safe=safe)
File "pyarrow/array.pxi", line 339, in pyarrow.lib.array
File "pyarrow/array.pxi", line 85, in pyarrow.lib._ndarray_to_array
File "pyarrow/error.pxi", line 91, in pyarrow.lib.check_status
pyarrow.lib.ArrowTypeError: ("Expected bytes, got a 'list' object", 'Conversion failed for column Socs36E with type object')
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1436, in compute_config_parquet_and_info_response
parquet_operations = convert_to_parquet(builder)
File "/src/services/worker/src/worker/job_runners/config/parquet_and_info.py", line 1053, in convert_to_parquet
builder.download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 925, in download_and_prepare
self._download_and_prepare(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1001, in _download_and_prepare
self._prepare_split(split_generator, **prepare_split_kwargs)
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1742, in _prepare_split
for job_id, done, content in self._prepare_split_single(
File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/builder.py", line 1898, in _prepare_split_single
raise DatasetGenerationError("An error occurred while generating the dataset") from e
datasets.exceptions.DatasetGenerationError: An error occurred while generating the datasetNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
updated
list |
|---|
[
{
"content": "You are a protein interaction prediction system. Given a partial protein network in compressed BioPAX format, predict the complete network including missing interactions. Generate the complete network in compressed BioPAX format.",
"role": "system"
},
{
"content": "Complete this network:\n<biopax>\n <proteins>\n <p id=\"zk1127.3\" name=\"ZK1127.3\" uniprot=\"Q23403\"/>\n <p id=\"meg-3\" name=\"meg-3\" uniprot=\"A0A5K4EK08\"/>\n <p id=\"mrg-1\" name=\"mrg-1\" uniprot=\"A8XMR4\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"zk1127.3\" b=\"mrg-1\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"zk1127.3\" b=\"meg-3\" type=\"Affinity Capture-MS\"/>\n <i id=\"3\" a=\"zk1127.3\" b=\"mrg-1\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"zk1127.3\" name=\"ZK1127.3\" uniprot=\"Q23403\"/>\n <p id=\"meg-3\" name=\"meg-3\" uniprot=\"A0A5K4EK08\"/>\n <p id=\"mrg-1\" name=\"mrg-1\" uniprot=\"A8XMR4\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"zk1127.3\" b=\"mrg-1\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"meg-3\" b=\"mrg-1\" type=\"Affinity Capture-MS\"/>\n <i id=\"3\" a=\"zk1127.3\" b=\"meg-3\" type=\"Affinity Capture-MS\"/>\n <i id=\"4\" a=\"zk1127.3\" b=\"mrg-1\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Generate a protein network in compressed BioPAX format with the following properties:\n- Proteins: AdSL, CG15631, CG18528, CG2930, CG4617, Fem-1, Sec10, lva, tRNA:Q:34E\n- Network density: approximately 0.22\n- Hub proteins (highly connected): tRNA:Q:34E, CG18528\n- Total interactions: approximately 8",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"adsl\" name=\"AdSL\" uniprot=\"A0A813C1X1\"/>\n <p id=\"cg15631\" name=\"CG15631\" uniprot=\"A0A0M4E847\"/>\n <p id=\"cg18528\" name=\"CG18528\" uniprot=\"A0A0M5J9N0\"/>\n <p id=\"cg2930\" name=\"CG2930\" uniprot=\"A0A0M3QYT3\"/>\n <p id=\"cg4617\" name=\"CG4617\" uniprot=\"A0A0M4ETT7\"/>\n <p id=\"fem-1\" name=\"Fem-1\" uniprot=\"A0A5P9Q4Z3\"/>\n <p id=\"sec10\" name=\"Sec10\" uniprot=\"L1JK28\"/>\n <p id=\"lva\" name=\"lva\" uniprot=\"A0A836G862\"/>\n <p id=\"trna:q:34e\" name=\"tRNA:Q:34E\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg18528\" b=\"trna:q:34e\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg2930\" b=\"trna:q:34e\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"adsl\" b=\"trna:q:34e\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"sec10\" b=\"trna:q:34e\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"cg15631\" b=\"trna:q:34e\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"cg4617\" b=\"trna:q:34e\" type=\"Two-hybrid\"/>\n <i id=\"7\" a=\"lva\" b=\"trna:q:34e\" type=\"nan\"/>\n <i id=\"8\" a=\"fem-1\" b=\"trna:q:34e\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a known protein network in compressed BioPAX format and a new protein with sequence and structural information, predict which proteins in the network the new protein will interact with. Generate the interactions in compressed BioPAX format.",
"role": "system"
},
{
"content": "Network:\n<biopax>\n <proteins>\n <p id=\"arp3\" name=\"Arp3\" uniprot=\"A0A812UW37\"/>\n <p id=\"cg14478\" name=\"CG14478\" uniprot=\"A0A0M4EIU2\"/>\n <p id=\"cg5144\" name=\"CG5144\" uniprot=\"Q8T8X7\" fullname=\"arginine kinase\"/>\n <p id=\"leash\" name=\"Leash\" uniprot=\"Q9VGU4\"/>\n <p id=\"patronin\" name=\"Patronin\" uniprot=\"B7YZJ1\"/>\n <p id=\"poxm\" name=\"Poxm\" uniprot=\"S7ZK63\" fullname=\"Cytochrome P450 monooxygenase poxM\"/>\n <p id=\"ppn\" name=\"Ppn\" uniprot=\"A0A7L0H3J1\"/>\n <p id=\"rps18\" name=\"RpS18\" uniprot=\"A0A1W0E4X0\"/>\n <p id=\"hale\" name=\"hale\" uniprot=\"Q8T3W6\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg14478\" b=\"cg5144\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg14478\" b=\"patronin\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"arp3\" b=\"cg14478\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg14478\" b=\"hale\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"cg14478\" b=\"rps18\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"cg14478\" b=\"poxm\" type=\"Two-hybrid\"/>\n <i id=\"7\" a=\"cg14478\" b=\"ppn\" type=\"Two-hybrid\"/>\n <i id=\"8\" a=\"cg14478\" b=\"leash\" type=\"Affinity Capture-MS\"/>\n <i id=\"9\" a=\"poxm\" b=\"hale\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>\n\nNew to integrate:\nPROTEIN: CG2540\n UniProt ID: Q9VYK7\n Full Name: glutathione-specific gamma-glutamylcyclotransferase\n Organism: Drosophila melanogaster\n Sequence Length: 311 amino acids\n Sequence: MLDFLTELRSSGSRADQLPGNIYTEFFANVIEEPREHGCKSADQDFTQGFSMLRTFDTENSNQLEPPAATDADVWIFGYGSLVWKTDFPYIDRRRGFVWGFKRRFYQHSIDHRGIPERPGRVVTL...HALLHEISGILEEEQLAEQAHQLEKLLERCQKPGGREWLIYAALQAKNKS\n AlphaFold Structure: Available\n Structure Coverage: residues 1-311\n Function: Catalyzes the cleavage of glutathione into 5-oxo-L-proline and a Cys-Gly dipeptide. Acts specifically on glutathione, but not on other gamma-glutamyl peptides\n\nPredict for CG2540:",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"arp3\" name=\"Arp3\" uniprot=\"A0A812UW37\"/>\n <p id=\"cg14478\" name=\"CG14478\" uniprot=\"A0A0M4EIU2\"/>\n <p id=\"cg2540\" name=\"CG2540\" uniprot=\"Q9VYK7\" fullname=\"glutathione-specific gamma-glutamylcyclotransferase\"/>\n <p id=\"cg5144\" name=\"CG5144\" uniprot=\"Q8T8X7\" fullname=\"arginine kinase\"/>\n <p id=\"leash\" name=\"Leash\" uniprot=\"Q9VGU4\"/>\n <p id=\"patronin\" name=\"Patronin\" uniprot=\"B7YZJ1\"/>\n <p id=\"poxm\" name=\"Poxm\" uniprot=\"S7ZK63\" fullname=\"Cytochrome P450 monooxygenase poxM\"/>\n <p id=\"ppn\" name=\"Ppn\" uniprot=\"A0A7L0H3J1\"/>\n <p id=\"rps18\" name=\"RpS18\" uniprot=\"A0A1W0E4X0\"/>\n <p id=\"hale\" name=\"hale\" uniprot=\"Q8T3W6\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg14478\" b=\"cg2540\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Generate a protein network in compressed BioPAX format with the following properties:\n- Proteins: AkhR, CCAP, CCAP-R, CG5890\n- Network density: approximately 0.50\n- Hub proteins (highly connected): CCAP, CG5890\n- Total interactions: approximately 3",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"akhr\" name=\"AkhR\" uniprot=\"Q9VM96\"/>\n <p id=\"ccap\" name=\"CCAP\" uniprot=\"A0A1E1G7R6\"/>\n <p id=\"ccap-r\" name=\"CCAP-R\" uniprot=\"A0A8J2HPF7\"/>\n <p id=\"cg5890\" name=\"CG5890\" uniprot=\"A0A0M5J5D5\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"ccap\" b=\"cg5890\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"akhr\" b=\"ccap\" type=\"Biochemical Activity\"/>\n <i id=\"3\" a=\"ccap\" b=\"ccap-r\" type=\"Biochemical Activity\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Generate a protein network with the following properties:\n- Proteins: Bcl9l, CTNNB1, Shank3, Yap1\n- Network density: approximately 0.67\n- Hub proteins (highly connected): Bcl9l, CTNNB1\n- Total interactions: approximately 4",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"bcl9l\" name=\"Bcl9l\" uniprot=\"A0A7K4VGS7\"/>\n <p id=\"ctnnb1\" name=\"CTNNB1\" uniprot=\"R9WTP6\"/>\n <p id=\"shank3\" name=\"Shank3\" uniprot=\"A0A8B0M4P3\"/>\n <p id=\"yap1\" name=\"Yap1\" uniprot=\"A0A0S7F1Z1\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"bcl9l\" b=\"ctnnb1\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"bcl9l\" b=\"ctnnb1\" type=\"Reconstituted Complex\"/>\n <i id=\"3\" a=\"bcl9l\" b=\"yap1\" type=\"Co-fractionation\"/>\n <i id=\"4\" a=\"bcl9l\" b=\"shank3\" type=\"Proximity Label-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a partial protein network in compressed BioPAX format, predict the complete network including missing interactions. Generate the complete network in compressed BioPAX format.",
"role": "system"
},
{
"content": "Complete this network:\n<biopax>\n <proteins>\n <p id=\"cg12620\" name=\"CG12620\" uniprot=\"Q4V424\"/>\n <p id=\"cg34159\" name=\"CG34159\" uniprot=\"Q9VL29\"/>\n <p id=\"nop17l\" name=\"Nop17l\" uniprot=\"A0A812VCN9\"/>\n <p id=\"pp1-13c\" name=\"Pp1-13C\" uniprot=\"A0A0A9VX68\" fullname=\"protein-serine/threonine phosphatase\"/>\n <p id=\"pp1-87b\" name=\"Pp1-87B\" uniprot=\"A0A812X3N9\"/>\n <p id=\"pp1alpha-96a\" name=\"Pp1alpha-96A\" uniprot=\"A0A0B4KHS9\" fullname=\"Serine/threonine-protein phosphatase\"/>\n <p id=\"flw\" name=\"flw\" uniprot=\"A0A4D6K293\" fullname=\"Serine/threonine-protein phosphatase\"/>\n <p id=\"mei-s332\" name=\"mei-S332\" uniprot=\"A0A0B4LG47\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg12620\" b=\"nop17l\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"nop17l\" b=\"mei-s332\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"pp1-87b\" b=\"flw\" type=\"Affinity Capture-MS\"/>\n <i id=\"4\" a=\"nop17l\" b=\"flw\" type=\"Phenotypic Enhancement\"/>\n <i id=\"5\" a=\"nop17l\" b=\"flw\" type=\"Phenotypic Suppression\"/>\n <i id=\"6\" a=\"nop17l\" b=\"pp1-87b\" type=\"Phenotypic Suppression\"/>\n <i id=\"7\" a=\"pp1-87b\" b=\"pp1alpha-96a\" type=\"Phenotypic Suppression\"/>\n <i id=\"8\" a=\"pp1-87b\" b=\"flw\" type=\"Phenotypic Suppression\"/>\n <i id=\"9\" a=\"nop17l\" b=\"flw\" type=\"Affinity Capture-Western\"/>\n <i id=\"10\" a=\"nop17l\" b=\"pp1-13c\" type=\"Affinity Capture-Western\"/>\n <i id=\"11\" a=\"nop17l\" b=\"pp1-87b\" type=\"Affinity Capture-Western\"/>\n <i id=\"12\" a=\"nop17l\" b=\"flw\" type=\"Two-hybrid\"/>\n <i id=\"13\" a=\"nop17l\" b=\"pp1-13c\" type=\"Two-hybrid\"/>\n <i id=\"14\" a=\"cg34159\" b=\"nop17l\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg12620\" name=\"CG12620\" uniprot=\"Q4V424\"/>\n <p id=\"cg34159\" name=\"CG34159\" uniprot=\"Q9VL29\"/>\n <p id=\"nop17l\" name=\"Nop17l\" uniprot=\"A0A812VCN9\"/>\n <p id=\"pp1-13c\" name=\"Pp1-13C\" uniprot=\"A0A0A9VX68\" fullname=\"protein-serine/threonine phosphatase\"/>\n <p id=\"pp1-87b\" name=\"Pp1-87B\" uniprot=\"A0A812X3N9\"/>\n <p id=\"pp1alpha-96a\" name=\"Pp1alpha-96A\" uniprot=\"A0A0B4KHS9\" fullname=\"Serine/threonine-protein phosphatase\"/>\n <p id=\"flw\" name=\"flw\" uniprot=\"A0A4D6K293\" fullname=\"Serine/threonine-protein phosphatase\"/>\n <p id=\"mei-s332\" name=\"mei-S332\" uniprot=\"A0A0B4LG47\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg12620\" b=\"nop17l\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg12620\" b=\"pp1-87b\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"nop17l\" b=\"pp1-87b\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"nop17l\" b=\"pp1alpha-96a\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"cg12620\" b=\"flw\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"nop17l\" b=\"mei-s332\" type=\"Two-hybrid\"/>\n <i id=\"7\" a=\"pp1-87b\" b=\"flw\" type=\"Affinity Capture-MS\"/>\n <i id=\"8\" a=\"cg12620\" b=\"pp1-87b\" type=\"Affinity Capture-MS\"/>\n <i id=\"9\" a=\"nop17l\" b=\"flw\" type=\"Phenotypic Enhancement\"/>\n <i id=\"10\" a=\"nop17l\" b=\"flw\" type=\"Phenotypic Suppression\"/>\n <i id=\"11\" a=\"nop17l\" b=\"pp1-87b\" type=\"Phenotypic Enhancement\"/>\n <i id=\"12\" a=\"nop17l\" b=\"pp1-87b\" type=\"Phenotypic Suppression\"/>\n <i id=\"13\" a=\"pp1-87b\" b=\"pp1alpha-96a\" type=\"Phenotypic Suppression\"/>\n <i id=\"14\" a=\"pp1-87b\" b=\"flw\" type=\"Phenotypic Suppression\"/>\n <i id=\"15\" a=\"nop17l\" b=\"pp1alpha-96a\" type=\"Affinity Capture-Western\"/>\n <i id=\"16\" a=\"nop17l\" b=\"flw\" type=\"Affinity Capture-Western\"/>\n <i id=\"17\" a=\"nop17l\" b=\"pp1-13c\" type=\"Affinity Capture-Western\"/>\n <i id=\"18\" a=\"nop17l\" b=\"pp1-87b\" type=\"Affinity Capture-Western\"/>\n <i id=\"19\" a=\"nop17l\" b=\"flw\" type=\"Two-hybrid\"/>\n <i id=\"20\" a=\"nop17l\" b=\"pp1-13c\" type=\"Two-hybrid\"/>\n <i id=\"21\" a=\"cg34159\" b=\"nop17l\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Generate a protein network with the following properties:\n- Proteins: K01C8.1, elks-1, glh-1, klp-11\n- Network density: approximately 0.67\n- Hub proteins (highly connected): K01C8.1, glh-1\n- Total interactions: approximately 4",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"k01c8.1\" name=\"K01C8.1\" uniprot=\"Q21080\" fullname=\"L-serine deaminase\"/>\n <p id=\"elks-1\" name=\"elks-1\" uniprot=\"A8XZ97\"/>\n <p id=\"glh-1\" name=\"glh-1\" uniprot=\"A0A2S2R9X9\"/>\n <p id=\"klp-11\" name=\"klp-11\" uniprot=\"A8WJH6\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"k01c8.1\" b=\"klp-11\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"k01c8.1\" b=\"glh-1\" type=\"Affinity Capture-MS\"/>\n <i id=\"3\" a=\"k01c8.1\" b=\"elks-1\" type=\"Proximity Label-MS\"/>\n <i id=\"4\" a=\"elks-1\" b=\"glh-1\" type=\"Proximity Label-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Complete this partial protein network in compressed BioPAX format:\n<biopax>\n <proteins>\n <p id=\"bubr1\" name=\"BubR1\" uniprot=\"F8WLE2\"/>\n <p id=\"cg11380\" name=\"CG11380\" uniprot=\"A0A0M4ER81\"/>\n <p id=\"cg13476\" name=\"CG13476\" uniprot=\"Q7KUL3\"/>\n <p id=\"cg15087\" name=\"CG15087\" uniprot=\"Q8MSY4\" fullname=\"Vacuolar protein sorting-associated protein 51 homolog\"/>\n <p id=\"cg3501\" name=\"CG3501\" uniprot=\"A0A0A1WL39\"/>\n <p id=\"dpy-30l1\" name=\"Dpy-30L1\" uniprot=\"Q9VKQ9\" fullname=\"Protein dpy-30 homolog\"/>\n <p id=\"mtf-1\" name=\"MTF-1\" uniprot=\"Q9YGM3\"/>\n <p id=\"utx\" name=\"Utx\" uniprot=\"Q76NQ3\"/>\n <p id=\"wdr82\" name=\"Wdr82\" uniprot=\"A0A1Y1S5V9\"/>\n <p id=\"ash2\" name=\"ash2\" uniprot=\"O60070\" fullname=\"Set1 complex component ash2\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg11380\" b=\"dpy-30l1\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg13476\" b=\"dpy-30l1\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"dpy-30l1\" b=\"ash2\" type=\"Affinity Capture-MS\"/>\n <i id=\"4\" a=\"dpy-30l1\" b=\"mtf-1\" type=\"Phenotypic Suppression\"/>\n <i id=\"5\" a=\"dpy-30l1\" b=\"wdr82\" type=\"Affinity Capture-MS\"/>\n <i id=\"6\" a=\"wdr82\" b=\"ash2\" type=\"Affinity Capture-MS\"/>\n <i id=\"7\" a=\"dpy-30l1\" b=\"utx\" type=\"Affinity Capture-MS\"/>\n <i id=\"8\" a=\"utx\" b=\"ash2\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"bubr1\" name=\"BubR1\" uniprot=\"F8WLE2\"/>\n <p id=\"cg11380\" name=\"CG11380\" uniprot=\"A0A0M4ER81\"/>\n <p id=\"cg13476\" name=\"CG13476\" uniprot=\"Q7KUL3\"/>\n <p id=\"cg15087\" name=\"CG15087\" uniprot=\"Q8MSY4\" fullname=\"Vacuolar protein sorting-associated protein 51 homolog\"/>\n <p id=\"cg3501\" name=\"CG3501\" uniprot=\"A0A0A1WL39\"/>\n <p id=\"dpy-30l1\" name=\"Dpy-30L1\" uniprot=\"Q9VKQ9\" fullname=\"Protein dpy-30 homolog\"/>\n <p id=\"mtf-1\" name=\"MTF-1\" uniprot=\"Q9YGM3\"/>\n <p id=\"utx\" name=\"Utx\" uniprot=\"Q76NQ3\"/>\n <p id=\"wdr82\" name=\"Wdr82\" uniprot=\"A0A1Y1S5V9\"/>\n <p id=\"ash2\" name=\"ash2\" uniprot=\"O60070\" fullname=\"Set1 complex component ash2\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg3501\" b=\"dpy-30l1\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"dpy-30l1\" b=\"mtf-1\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"bubr1\" b=\"dpy-30l1\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg11380\" b=\"dpy-30l1\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"cg13476\" b=\"dpy-30l1\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"dpy-30l1\" b=\"ash2\" type=\"Affinity Capture-MS\"/>\n <i id=\"7\" a=\"dpy-30l1\" b=\"mtf-1\" type=\"Phenotypic Suppression\"/>\n <i id=\"8\" a=\"dpy-30l1\" b=\"wdr82\" type=\"Affinity Capture-MS\"/>\n <i id=\"9\" a=\"wdr82\" b=\"ash2\" type=\"Affinity Capture-MS\"/>\n <i id=\"10\" a=\"dpy-30l1\" b=\"utx\" type=\"Affinity Capture-MS\"/>\n <i id=\"11\" a=\"utx\" b=\"ash2\" type=\"Affinity Capture-MS\"/>\n <i id=\"12\" a=\"cg15087\" b=\"dpy-30l1\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a partial protein network in compressed BioPAX format, predict the complete network including missing interactions. Generate the complete network in compressed BioPAX format.",
"role": "system"
},
{
"content": "Complete this partial protein network in compressed BioPAX format:\n<biopax>\n <proteins>\n <p id=\"cg6910\" name=\"CG6910\" uniprot=\"M9PI33\" fullname=\"Inositol oxygenase\"/>\n <p id=\"hsp60b\" name=\"Hsp60B\" uniprot=\"A0AB39Z0I8\"/>\n <p id=\"sxl\" name=\"Sxl\" uniprot=\"A0A140B9G0\"/>\n <p id=\"tbph\" name=\"TBPH\" uniprot=\"A0A0M4EBH0\"/>\n <p id=\"ci\" name=\"ci\" uniprot=\"D4GNN4\"/>\n <p id=\"lft\" name=\"lft\" uniprot=\"A0A0M4EA86\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg6910\" b=\"tbph\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg6910\" b=\"hsp60b\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg6910\" b=\"sxl\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg6910\" b=\"ci\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg6910\" name=\"CG6910\" uniprot=\"M9PI33\" fullname=\"Inositol oxygenase\"/>\n <p id=\"hsp60b\" name=\"Hsp60B\" uniprot=\"A0AB39Z0I8\"/>\n <p id=\"sxl\" name=\"Sxl\" uniprot=\"A0A140B9G0\"/>\n <p id=\"tbph\" name=\"TBPH\" uniprot=\"A0A0M4EBH0\"/>\n <p id=\"ci\" name=\"ci\" uniprot=\"D4GNN4\"/>\n <p id=\"lft\" name=\"lft\" uniprot=\"A0A0M4EA86\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg6910\" b=\"tbph\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg6910\" b=\"lft\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg6910\" b=\"hsp60b\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg6910\" b=\"sxl\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"cg6910\" b=\"ci\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"sxl\" b=\"ci\" type=\"Affinity Capture-Western\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Complete this partial protein network in compressed BioPAX format:\n<biopax>\n <proteins>\n <p id=\"f15e11.14\" name=\"F15E11.14\" uniprot=\"G5EBF3\"/>\n <p id=\"f26d2.15\" name=\"F26D2.15\" uniprot=\"G5ECL7\"/>\n <p id=\"w09d10.4\" name=\"W09D10.4\" uniprot=\"O18183\" fullname=\"Protein phosphatase\"/>\n <p id=\"y22d7al.10\" name=\"Y22D7AL.10\" uniprot=\"Q965Q1\" fullname=\"10 kDa heat shock protein, mitochondrial\"/>\n <p id=\"clec-65\" name=\"clec-65\" uniprot=\"E3MXH2\"/>\n <p id=\"dao-2\" name=\"dao-2\" uniprot=\"A8XHQ9\"/>\n <p id=\"dsh-1\" name=\"dsh-1\" uniprot=\"A8WUI7\"/>\n <p id=\"eya-1\" name=\"eya-1\" uniprot=\"O17670\" fullname=\"Protein phosphatase eya-1\"/>\n <p id=\"gst-20\" name=\"gst-20\" uniprot=\"A8XYC1\"/>\n <p id=\"wrt-2\" name=\"wrt-2\" uniprot=\"A8XJD5\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"eya-1\" b=\"wrt-2\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"f26d2.15\" b=\"wrt-2\" type=\"Co-fractionation\"/>\n <i id=\"3\" a=\"w09d10.4\" b=\"wrt-2\" type=\"Co-fractionation\"/>\n <i id=\"4\" a=\"f15e11.14\" b=\"wrt-2\" type=\"Co-fractionation\"/>\n <i id=\"5\" a=\"clec-65\" b=\"wrt-2\" type=\"Co-fractionation\"/>\n <i id=\"6\" a=\"f15e11.14\" b=\"dao-2\" type=\"Co-fractionation\"/>\n <i id=\"7\" a=\"dao-2\" b=\"wrt-2\" type=\"Co-fractionation\"/>\n <i id=\"8\" a=\"y22d7al.10\" b=\"wrt-2\" type=\"Co-fractionation\"/>\n <i id=\"9\" a=\"w09d10.4\" b=\"clec-65\" type=\"Co-fractionation\"/>\n </interactions>\n</biopax>",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"f15e11.14\" name=\"F15E11.14\" uniprot=\"G5EBF3\"/>\n <p id=\"f26d2.15\" name=\"F26D2.15\" uniprot=\"G5ECL7\"/>\n <p id=\"w09d10.4\" name=\"W09D10.4\" uniprot=\"O18183\" fullname=\"Protein phosphatase\"/>\n <p id=\"y22d7al.10\" name=\"Y22D7AL.10\" uniprot=\"Q965Q1\" fullname=\"10 kDa heat shock protein, mitochondrial\"/>\n <p id=\"clec-65\" name=\"clec-65\" uniprot=\"E3MXH2\"/>\n <p id=\"dao-2\" name=\"dao-2\" uniprot=\"A8XHQ9\"/>\n <p id=\"dsh-1\" name=\"dsh-1\" uniprot=\"A8WUI7\"/>\n <p id=\"eya-1\" name=\"eya-1\" uniprot=\"O17670\" fullname=\"Protein phosphatase eya-1\"/>\n <p id=\"gst-20\" name=\"gst-20\" uniprot=\"A8XYC1\"/>\n <p id=\"wrt-2\" name=\"wrt-2\" uniprot=\"A8XJD5\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"eya-1\" b=\"wrt-2\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"f26d2.15\" b=\"wrt-2\" type=\"Co-fractionation\"/>\n <i id=\"3\" a=\"w09d10.4\" b=\"wrt-2\" type=\"Co-fractionation\"/>\n <i id=\"4\" a=\"f15e11.14\" b=\"wrt-2\" type=\"Co-fractionation\"/>\n <i id=\"5\" a=\"clec-65\" b=\"wrt-2\" type=\"Co-fractionation\"/>\n <i id=\"6\" a=\"f15e11.14\" b=\"dao-2\" type=\"Co-fractionation\"/>\n <i id=\"7\" a=\"gst-20\" b=\"wrt-2\" type=\"Co-fractionation\"/>\n <i id=\"8\" a=\"dao-2\" b=\"wrt-2\" type=\"Co-fractionation\"/>\n <i id=\"9\" a=\"f15e11.14\" b=\"gst-20\" type=\"Co-fractionation\"/>\n <i id=\"10\" a=\"y22d7al.10\" b=\"wrt-2\" type=\"Co-fractionation\"/>\n <i id=\"11\" a=\"w09d10.4\" b=\"clec-65\" type=\"Co-fractionation\"/>\n <i id=\"12\" a=\"f26d2.15\" b=\"w09d10.4\" type=\"Co-fractionation\"/>\n <i id=\"13\" a=\"dsh-1\" b=\"wrt-2\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a partial protein network in compressed BioPAX format, predict the complete network including missing interactions. Generate the complete network in compressed BioPAX format.",
"role": "system"
},
{
"content": "Complete this network:\n<biopax>\n <proteins>\n <p id=\"cg4911\" name=\"CG4911\" uniprot=\"A0A0M4EJ52\"/>\n <p id=\"nej\" name=\"nej\" uniprot=\"Q0ZIL3\"/>\n <p id=\"skpa\" name=\"skpA\" uniprot=\"E9NN95\"/>\n <p id=\"skpb\" name=\"skpB\" uniprot=\"Q7KJ69\"/>\n <p id=\"vir\" name=\"vir\" uniprot=\"Q3ZSN8\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg4911\" b=\"skpa\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg4911\" b=\"skpb\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg4911\" b=\"nej\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"skpa\" b=\"skpb\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg4911\" name=\"CG4911\" uniprot=\"A0A0M4EJ52\"/>\n <p id=\"nej\" name=\"nej\" uniprot=\"Q0ZIL3\"/>\n <p id=\"skpa\" name=\"skpA\" uniprot=\"E9NN95\"/>\n <p id=\"skpb\" name=\"skpB\" uniprot=\"Q7KJ69\"/>\n <p id=\"vir\" name=\"vir\" uniprot=\"Q3ZSN8\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg4911\" b=\"vir\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg4911\" b=\"skpa\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg4911\" b=\"skpb\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg4911\" b=\"nej\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"skpa\" b=\"skpb\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a known protein network in compressed BioPAX format and a new protein with sequence and structural information, predict which proteins in the network the new protein will interact with. Generate the interactions in compressed BioPAX format.",
"role": "system"
},
{
"content": "Known protein network in compressed BioPAX format:\n<biopax>\n <proteins>\n <p id=\"cg14546\" name=\"CG14546\" uniprot=\"A0A0M4EUI0\"/>\n <p id=\"cg31156\" name=\"CG31156\" uniprot=\"A0A0M4EN79\"/>\n <p id=\"cg4936\" name=\"CG4936\" uniprot=\"A0A0M4F4K4\"/>\n <p id=\"cg7768\" name=\"CG7768\" uniprot=\"Q7K2I4\" fullname=\"Peptidyl-prolyl cis-trans isomerase\"/>\n <p id=\"e(spl)m3-hlh\" name=\"E(spl)m3-HLH\"/>\n <p id=\"med28\" name=\"MED28\" uniprot=\"A0A1Q3ARU1\"/>\n <p id=\"pgam5\" name=\"Pgam5\" uniprot=\"X2JC94\" fullname=\"Serine/threonine-protein phosphatase PGAM5, mitochondrial\"/>\n <p id=\"ras85d\" name=\"Ras85D\" uniprot=\"A0A812RL10\"/>\n <p id=\"sesb\" name=\"sesB\" uniprot=\"Q6PX79\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg4936\" b=\"e(spl)m3-hlh\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg14546\" b=\"cg4936\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg31156\" b=\"cg4936\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg4936\" b=\"med28\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"cg4936\" b=\"cg7768\" type=\"Affinity Capture-MS\"/>\n <i id=\"6\" a=\"cg4936\" b=\"ras85d\" type=\"Phenotypic Enhancement\"/>\n <i id=\"7\" a=\"cg4936\" b=\"sesb\" type=\"Affinity Capture-MS\"/>\n <i id=\"8\" a=\"cg4936\" b=\"pgam5\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>\n\nNew protein to integrate:\nPROTEIN: CG2712\n UniProt ID: A0A0M4F9K4\n Organism: Drosophila busckii\n Sequence Length: 359 amino acids\n Sequence: MSLDKLTQTPMLQPELKQLCRVCNVSSKAALPIFQPHSIDGDGELTTLAALLRLCANLDVLEEENFMPSYMCKDCVDWLKHVYHFRRTAERTDLLLRKRHKHTQARLNAESDEYIFVLEQAYLET...YSSNLIAHKRSHTRNSIKTPRAAPGSVKKRTRKRARKKEKERDSQSELDI\n AlphaFold Structure: Available\n Structure Coverage: residues 1-359\n Function: Belongs to the snail C2H2-type zinc-finger protein family\n\nPredict the interactions for CG2712 in compressed BioPAX format:",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg14546\" name=\"CG14546\" uniprot=\"A0A0M4EUI0\"/>\n <p id=\"cg2712\" name=\"CG2712\" uniprot=\"A0A0M4F9K4\"/>\n <p id=\"cg31156\" name=\"CG31156\" uniprot=\"A0A0M4EN79\"/>\n <p id=\"cg4936\" name=\"CG4936\" uniprot=\"A0A0M4F4K4\"/>\n <p id=\"cg7768\" name=\"CG7768\" uniprot=\"Q7K2I4\" fullname=\"Peptidyl-prolyl cis-trans isomerase\"/>\n <p id=\"e(spl)m3-hlh\" name=\"E(spl)m3-HLH\"/>\n <p id=\"med28\" name=\"MED28\" uniprot=\"A0A1Q3ARU1\"/>\n <p id=\"pgam5\" name=\"Pgam5\" uniprot=\"X2JC94\" fullname=\"Serine/threonine-protein phosphatase PGAM5, mitochondrial\"/>\n <p id=\"ras85d\" name=\"Ras85D\" uniprot=\"A0A812RL10\"/>\n <p id=\"sesb\" name=\"sesB\" uniprot=\"Q6PX79\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg14546\" b=\"cg2712\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg2712\" b=\"cg4936\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a partial protein network in compressed BioPAX format, predict the complete network including missing interactions. Generate the complete network in compressed BioPAX format.",
"role": "system"
},
{
"content": "Complete this partial protein network in compressed BioPAX format:\n<biopax>\n <proteins>\n <p id=\"r09b3.2\" name=\"R09B3.2\" uniprot=\"O45712\"/>\n <p id=\"kin-2\" name=\"kin-2\" uniprot=\"A8XKP2\"/>\n <p id=\"nhr-10\" name=\"nhr-10\" uniprot=\"A8XPJ5\"/>\n <p id=\"nhr-137\" name=\"nhr-137\" uniprot=\"A8XC57\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"kin-2\" b=\"nhr-137\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"r09b3.2\" b=\"nhr-137\" type=\"Co-fractionation\"/>\n </interactions>\n</biopax>",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"r09b3.2\" name=\"R09B3.2\" uniprot=\"O45712\"/>\n <p id=\"kin-2\" name=\"kin-2\" uniprot=\"A8XKP2\"/>\n <p id=\"nhr-10\" name=\"nhr-10\" uniprot=\"A8XPJ5\"/>\n <p id=\"nhr-137\" name=\"nhr-137\" uniprot=\"A8XC57\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"kin-2\" b=\"nhr-137\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"r09b3.2\" b=\"nhr-137\" type=\"Co-fractionation\"/>\n <i id=\"3\" a=\"nhr-10\" b=\"nhr-137\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Predict the protein interaction network:\n\nPROTEIN: CG5147\n UniProt ID: A0A0M3QWY8\n Organism: Drosophila busckii\n Sequence Length: 400 amino acids\n Sequence: MPAKKAAAAAAPVAAAANGMTRLTPARDLTLGGRGGAAANKKVFAPNLNAVRNKNTNVKTSKDFTQPRGGRARGGRGSAAGATRGRGGGGNSTLIQTTGVFSEGAGAVHLRKSTSAAGGGGGSSY...INLGPIQAKLKATPDWVHLFKQQDAAALQQRVAAATAYATTATASAAAAT\n AlphaFold Structure: Available\n Structure Coverage: residues 1-400\n\nPROTEIN: Crk\n UniProt ID: H9XVM7\n Organism: Drosophila melanogaster\n Sequence Length: 184 amino acids\n Sequence: MDTFDVSDRNSWYFGPMSRQDATEVLMNERERGVFLVRDSNSIAGDYVLCVREDTKVSNYIINKVQQQDQIVYRIGDQSFDNLPKLLTFYTLHYLDTTPLKRPACRRVEKVIGKFDFVGSDQDDLPFQRGEVLTIVRKDEDQWWTARNSSGKIGQIPVPYIQQSRQFLWNANKTFDTATLTLGY\n AlphaFold Structure: Available\n Structure Coverage: residues 1-184\n\nPROTEIN: Sin\n UniProt ID: Q848U8\n Organism: Enterococcus faecium\n Sequence Length: 183 amino acids\n Sequence: MKKFGAERIFIEKQSGATITHRPVFQEALDYVRDQDIFIVEAIDRLGRNYDEIIASVNYLKKKNVKLIITSLPIMAEAIGNPLLDKFIKDLIIQILAMIAEQERTESKRRQAQGIKIAKANGVYKGRPKLYSADAKDPQRRLVYKSIVEDLKNGVAIAKIAKDYNVTRQTVYRIKKDSMVNDK\n AlphaFold Structure: Available\n Structure Coverage: residues 1-183\n Function: Belongs to the site-specific recombinase resolvase family\n\nPROTEIN: Sxl\n UniProt ID: A0A140B9G0\n Organism: Drosophila melanogaster\n Sequence Length: 288 amino acids\n Sequence: YAFSPQDTEFSFPSSSSRRGYNDFPGCGGSGGNGGSANNLGGGNMCHLPPMASNNSLNNLCGLSLGSGGSDDLMNDPRASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSFGY...QPLSVRLAEEHGKAKAAHFMSQMGVVPANVPPPPPQPPAHMAAAFNMMHR\n AlphaFold Structure: Available\n Structure Coverage: residues 1-288\n\nPROTEIN: ftz\n UniProt ID: B0FE39\n Organism: Drosophila mauritiana\n Sequence Length: 412 amino acids\n Sequence: MATTNSQSHYSYADNMNMYNMYHPHSLPPTYYDNSGSNAYYQNSSTYQSYQGYYPQESYSESCYYYNNQEQMTTHTVPPVQPTTPPKANKRKAEEDAASIIAAVEERPSTLRALLTNPVKKLKYT...PAYSHSHSHGYGLLNDYPQQQTHQQYDAYPQQYQQQCSYQQHPQDLYHLS\n AlphaFold Structure: Available\n Structure Coverage: residues 1-412",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg5147\" name=\"CG5147\" uniprot=\"A0A0M3QWY8\"/>\n <p id=\"crk\" name=\"Crk\" uniprot=\"H9XVM7\"/>\n <p id=\"sin\" name=\"Sin\" uniprot=\"Q848U8\"/>\n <p id=\"sxl\" name=\"Sxl\" uniprot=\"A0A140B9G0\"/>\n <p id=\"ftz\" name=\"ftz\" uniprot=\"B0FE39\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"sin\" b=\"ftz\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg5147\" b=\"sin\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"sin\" b=\"sxl\" type=\"Affinity Capture-Western\"/>\n <i id=\"4\" a=\"sin\" b=\"sxl\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"crk\" b=\"sin\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Predict the protein interaction network:\n\nPROTEIN: dcr-1\n UniProt ID: A0A0C9QPE9\n Organism: Fopius arisanus\n Sequence Length: 1949 amino acids\n Sequence: MAFPFNDQVYTKSFTPREYQVELLYTAKQRDIIICLGKYTEQTFIVTKLIQEFATGNRIPLVSAQRILYLLDSEESCSLKSSYIEQLTDLKVSVIDSTTQDNDFAHIFTSGHVVVTTSAIFYKFV...GRRVRVTVDVFGKGSFKGIGRNYRIAKCTAAKCALKKLKKMQSSSQRQKI\n AlphaFold Structure: Not available\n\nPROTEIN: elks-1\n UniProt ID: A8XZ97\n Organism: Caenorhabditis briggsae\n Sequence Length: 743 amino acids\n Sequence: MATTSVPAPGVQDYDLMQPGMSRLNLNSLNPSGINLAREYEQLKVEYDTIMEKLNQTMNSIKTFWSPELKRERQMRRDEANRIAHLERMVQSGGIGGNEYGLGSTNEALQLRMELRERDERIRQL...AHPDPTISMNAMASVIPGAPLPAPIIPGTIGHPPQSHQNPHDDDADGIWA\n AlphaFold Structure: Available\n Structure Coverage: residues 1-743\n\nPROTEIN: meg-3\n UniProt ID: A0A5K4EK08\n Organism: Schistosoma mansoni\n Sequence Length: 150 amino acids\n Sequence: YLLCKKEYSIMNRFFWTVTQCTILLVIICNLNTMKATSANSRTHGATSTSTHGATSTAKPAASTPPKAAATSTIKPTVTTPKAAATSTIKPTVTTKPSPAKPAASNTAKPAASTPKKPHDERAVLAAAAVPIVLGVIGEVIGFILQYIAS\n AlphaFold Structure: Available\n Structure Coverage: residues 1-150\n\nPROTEIN: mrt-2\n UniProt ID: A8XHC3\n Organism: Caenorhabditis briggsae\n Sequence Length: 267 amino acids\n Sequence: MELETGQVTVMEMKKENVKELAQILKTVVFKDFGMLYAFETGLKITVDDGAFQQANAFLNSAFFSDYKVREDRIALKLPIKTIYEFLSIPEGNSNSVKFSYSGMFDPLKLLIEESDGCVIRGKFN...RMNPAFALASKLILRVDERGVLSCQFSIDHGECRTSYIEFLTVPTTETDG\n AlphaFold Structure: Available\n Structure Coverage: residues 1-267\n\nPROTEIN: panl-3\n UniProt ID: P34653\n Full Name: PAN2-PAN3 deadenylation complex subunit PAN3\n Organism: Caenorhabditis elegans\n Sequence Length: 632 amino acids\n Sequence: MQPGEGYHYDSGPNNAVHPHQLPAGSRLNQYLANNNRQGPSFGPGTPINVNAPVFVPKHQQPQPAQVAAPPPMVNQFAQLSIHDVPHQMIPFGQINGPPTFGPGQHMNHRASHHHQSPQMAQQPP...LNKLDCGSQEKIEMVSRSGDTQIIIDYATLKRCLDKSFRDLLGTNMMLHR\n AlphaFold Structure: Available\n Structure Coverage: residues 1-632\n Function: Regulatory subunit of the poly(A)-nuclease (PAN) deadenylation complex, one of two cytoplasmic mRNA deadenylases involved in general and miRNA-mediated mRNA turnover. PAN specifically shortens poly(A)...",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"dcr-1\" name=\"dcr-1\" uniprot=\"A0A0C9QPE9\"/>\n <p id=\"elks-1\" name=\"elks-1\" uniprot=\"A8XZ97\"/>\n <p id=\"meg-3\" name=\"meg-3\" uniprot=\"A0A5K4EK08\"/>\n <p id=\"mrt-2\" name=\"mrt-2\" uniprot=\"A8XHC3\"/>\n <p id=\"panl-3\" name=\"panl-3\" uniprot=\"P34653\" fullname=\"PAN2-PAN3 deadenylation complex subunit PAN3\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"mrt-2\" b=\"panl-3\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"dcr-1\" b=\"panl-3\" type=\"Affinity Capture-MS\"/>\n <i id=\"3\" a=\"elks-1\" b=\"panl-3\" type=\"Proximity Label-MS\"/>\n <i id=\"4\" a=\"meg-3\" b=\"panl-3\" type=\"Affinity Capture-MS\"/>\n <i id=\"5\" a=\"dcr-1\" b=\"meg-3\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Predict the protein interaction network:\n\nPROTEIN: CG10077\n UniProt ID: Q8MZI3\n Full Name: RNA helicase\n Organism: Drosophila melanogaster\n Sequence Length: 818 amino acids\n Sequence: MNMYNGQMNAFGGGGGGGAGGLAGGMVPNRMGGGAPGGGPGGAGMFQRNRSAPYPGFNGHGPANGGQRRMNGGGPSMGPGGPRNQDGFGGQNGGQRSSNHGAHLPKIVWSEVNLTPFRKNFYKPC...MATVSLNGGAAAVASSYRAPYAVPTQAAPYMMANGGDIFAYPPPPLPVQN\n AlphaFold Structure: Available\n Structure Coverage: residues 1-818\n\nPROTEIN: CG14812\n UniProt ID: O96824\n Full Name: Late endosomal/lysosomal adaptor and MAPK and MTOR activator 5\n Organism: Drosophila melanogaster\n Sequence Length: 100 amino acids\n Sequence: MEQQLEKVLAEIAARQDTVGALLANRQGLCLGTKGDIDPNVSGIGMAISEQVAKLELNATAPATICLYSGNKRCVIQKDGEITGVIFKQPTGTSATAPSN\n AlphaFold Structure: Available\n Structure Coverage: residues 1-100\n\nPROTEIN: CG40127\n UniProt ID: A0A0M4ECV7\n Organism: Drosophila busckii\n Sequence Length: 95 amino acids\n Sequence: MKICGPKCSLCGLIISVWGIVQLVLMGLFFYIHSVALIEDLPLEEEYKTLDEFYTAANTAYNQNAYNCWIAACIYVLTLLLSAQQFYMNSRITAN\n AlphaFold Structure: Available\n Structure Coverage: residues 1-95\n\nPROTEIN: DIP1\n UniProt ID: O74771\n Full Name: Protein dip1\n Organism: Schizosaccharomyces pombe (strain 972 / ATCC 24843)\n Sequence Length: 374 amino acids\n Sequence: MEFTDVFYNLENEKQFLAEIDELLTIPYEKNELEIGVSKFLSFINKYGEPYLITEFQLQRCMEKFLNSPLYQLDENAVLSIFYDCFFFLKEQQTLKFIIIVFQSEIQENEYCLRLLASTGFIPVL...TKCIVDAVNNVLISHSKSSNMEDARTTDVAIRVLEVPWLQQEMKSLGTAQ\n AlphaFold Structure: Available\n Structure Coverage: residues 1-374\n Function: May be involved in protein-linked oligosaccharide phosphorylation\n\nPROTEIN: RpL23A\n UniProt ID: A0A1W0E5D9\n Organism: Enterocytozoon hepatopenaei\n Sequence Length: 130 amino acids\n Sequence: MVRVRKTNKSLSIKDRYRGIKKDQKEDIVSKSGKYERNVLKKDHSDKMIIKYAIKNERTAKAMEKDNTLVFVVDVSATKPEIKKAVTEKYNTVVKKVNTLVKFKKHEKKAFVRFAEEGKAVEIAGQVGIL\n AlphaFold Structure: Available\n Structure Coverage: residues 1-130\n Function: Belongs to the universal ribosomal protein uL23 family\n\nPROTEIN: RpS20\n UniProt ID: A0A6M5XIG1\n Organism: Lindavia intermedia\n Sequence Length: 9 amino acids\n Sequence: KLAALSKTV\n AlphaFold Structure: Not available\n\nPROTEIN: adat\n UniProt ID: A0AAW2Z500\n Organism: Acrasis kona\n Sequence Length: 392 amino acids\n Sequence: MSSVHNQIAKCALDQYAKLSNNGKPQHKNNEWTMMASIVMENCGKLQAVTMGTGTKCIGYSHMTNDGRLINDSHAEVSSRRSLLLYFYEQLRLLNEGNIESIFEKTEEPSQKRRLRPDIFFHLYI...KVTDSEENSEITYKDAKEGAKDYVMVKKKFLETGPFVNWSKKDESLLLFK\n AlphaFold Structure: Not available\n Function: The sequence shown here is derived from an EMBL/GenBank/DDBJ whole genome shotgun (WGS) entry which is preliminary data",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg10077\" name=\"CG10077\" uniprot=\"Q8MZI3\" fullname=\"RNA helicase\"/>\n <p id=\"cg14812\" name=\"CG14812\" uniprot=\"O96824\" fullname=\"Late endosomal/lysosomal adaptor and MAPK and MTOR activator 5\"/>\n <p id=\"cg40127\" name=\"CG40127\" uniprot=\"A0A0M4ECV7\"/>\n <p id=\"dip1\" name=\"DIP1\" uniprot=\"O74771\" fullname=\"Protein dip1\"/>\n <p id=\"rpl23a\" name=\"RpL23A\" uniprot=\"A0A1W0E5D9\"/>\n <p id=\"rps20\" name=\"RpS20\" uniprot=\"A0A6M5XIG1\"/>\n <p id=\"adat\" name=\"adat\" uniprot=\"A0AAW2Z500\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg10077\" b=\"adat\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg14812\" b=\"adat\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"rps20\" b=\"adat\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg40127\" b=\"adat\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"rpl23a\" b=\"adat\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"dip1\" b=\"adat\" type=\"Affinity Capture-Western\"/>\n <i id=\"7\" a=\"rpl23a\" b=\"rps20\" type=\"Co-fractionation\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Generate a protein network in compressed BioPAX format with the following properties:\n- Proteins: SPAC644.07, SPAP27G11.14c, cbp3, coq7, cyt1, pgr1, ppr1, ppr4, ppr8, sls1\n- Network density: approximately 0.20\n- Hub proteins (highly connected): pgr1, ppr8\n- Total interactions: approximately 9",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"spac644.07\" name=\"SPAC644.07\" uniprot=\"A0A2C5WXD9\"/>\n <p id=\"spap27g11.14c\" name=\"SPAP27G11.14c\" uniprot=\"Q9P7M4\" fullname=\"Uncharacterized protein SPAP27G11.14c\"/>\n <p id=\"cbp3\" name=\"cbp3\" uniprot=\"A0A812NAM5\"/>\n <p id=\"coq7\" name=\"coq7\" uniprot=\"A0A7K4QL04\"/>\n <p id=\"cyt1\" name=\"cyt1\" uniprot=\"A0A088FS96\"/>\n <p id=\"pgr1\" name=\"pgr1\" uniprot=\"Q6NV75\" fullname=\"Probable G-protein coupled receptor 153\"/>\n <p id=\"ppr1\" name=\"ppr1\" uniprot=\"A0A8K1Z799\"/>\n <p id=\"ppr4\" name=\"ppr4\" uniprot=\"A0A812KHN4\"/>\n <p id=\"ppr8\" name=\"ppr8\" uniprot=\"A0AAE9WF34\"/>\n <p id=\"sls1\" name=\"sls1\" uniprot=\"Q9UT03\" fullname=\"Mitochondrial translation factor sls1\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"pgr1\" b=\"ppr8\" type=\"Dosage Rescue\"/>\n <i id=\"2\" a=\"spac644.07\" b=\"pgr1\" type=\"Synthetic Rescue\"/>\n <i id=\"3\" a=\"pgr1\" b=\"ppr4\" type=\"Synthetic Rescue\"/>\n <i id=\"4\" a=\"spap27g11.14c\" b=\"pgr1\" type=\"Synthetic Rescue\"/>\n <i id=\"5\" a=\"pgr1\" b=\"sls1\" type=\"Synthetic Rescue\"/>\n <i id=\"6\" a=\"pgr1\" b=\"ppr1\" type=\"Synthetic Rescue\"/>\n <i id=\"7\" a=\"cyt1\" b=\"pgr1\" type=\"Synthetic Rescue\"/>\n <i id=\"8\" a=\"coq7\" b=\"pgr1\" type=\"Synthetic Rescue\"/>\n <i id=\"9\" a=\"cbp3\" b=\"pgr1\" type=\"Synthetic Rescue\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a partial protein network in compressed BioPAX format, predict the complete network including missing interactions. Generate the complete network in compressed BioPAX format.",
"role": "system"
},
{
"content": "Complete this partial protein network in compressed BioPAX format:\n<biopax>\n <proteins>\n <p id=\"cg14073\" name=\"CG14073\" uniprot=\"A0A0M4F031\"/>\n <p id=\"cg4286\" name=\"CG4286\" uniprot=\"A0A0M5IX66\"/>\n <p id=\"cg4300\" name=\"CG4300\" uniprot=\"A0A0M4EYR0\"/>\n <p id=\"rybp\" name=\"RYBP\" uniprot=\"A0A347ZJF3\"/>\n <p id=\"rps24\" name=\"RpS24\" uniprot=\"A0A0A9H9G6\"/>\n <p id=\"grh\" name=\"grh\" uniprot=\"A0A0C9QBR8\"/>\n <p id=\"l(3)73ah\" name=\"l(3)73Ah\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg14073\" b=\"l(3)73ah\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg14073\" b=\"cg4300\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg14073\" b=\"cg4286\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg14073\" b=\"rybp\" type=\"Affinity Capture-MS\"/>\n <i id=\"5\" a=\"grh\" b=\"l(3)73ah\" type=\"Affinity Capture-MS\"/>\n <i id=\"6\" a=\"cg14073\" b=\"grh\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg14073\" name=\"CG14073\" uniprot=\"A0A0M4F031\"/>\n <p id=\"cg4286\" name=\"CG4286\" uniprot=\"A0A0M5IX66\"/>\n <p id=\"cg4300\" name=\"CG4300\" uniprot=\"A0A0M4EYR0\"/>\n <p id=\"rybp\" name=\"RYBP\" uniprot=\"A0A347ZJF3\"/>\n <p id=\"rps24\" name=\"RpS24\" uniprot=\"A0A0A9H9G6\"/>\n <p id=\"grh\" name=\"grh\" uniprot=\"A0A0C9QBR8\"/>\n <p id=\"l(3)73ah\" name=\"l(3)73Ah\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg14073\" b=\"l(3)73ah\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg14073\" b=\"cg4300\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg14073\" b=\"rps24\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg14073\" b=\"cg4286\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"rybp\" b=\"grh\" type=\"Affinity Capture-MS\"/>\n <i id=\"6\" a=\"cg14073\" b=\"rybp\" type=\"Affinity Capture-MS\"/>\n <i id=\"7\" a=\"grh\" b=\"l(3)73ah\" type=\"Affinity Capture-MS\"/>\n <i id=\"8\" a=\"cg14073\" b=\"grh\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction network generator. Given network constraints and properties, generate a biologically plausible protein network in compressed BioPAX format with <proteins> and <interactions> sections.",
"role": "system"
},
{
"content": "Generate a protein network with the following properties:\n- Proteins: CG14932, CG32581, CG4747, CG4813, CG8974\n- Network density: approximately 0.40\n- Hub proteins (highly connected): CG14932, CG4747\n- Total interactions: approximately 4",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg14932\" name=\"CG14932\" uniprot=\"E1JHF9\"/>\n <p id=\"cg32581\" name=\"CG32581\" uniprot=\"Q8IR26\" fullname=\"RING-type E3 ubiquitin transferase\"/>\n <p id=\"cg4747\" name=\"CG4747\" uniprot=\"A0A0A1XQ53\" fullname=\"Cytokine-like nuclear factor N-PAC\"/>\n <p id=\"cg4813\" name=\"CG4813\" uniprot=\"A0A0M3QXK0\"/>\n <p id=\"cg8974\" name=\"CG8974\" uniprot=\"Q9VXP1\" fullname=\"RING-type E3 ubiquitin transferase\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg14932\" b=\"cg4747\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg14932\" b=\"cg4813\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg14932\" b=\"cg32581\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg14932\" b=\"cg8974\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Predict the protein interaction network for these proteins:\n\nPROTEIN: NR3C1\n UniProt ID: A1YFI6\n Organism: Saguinus labiatus\n Sequence Length: 50 amino acids\n Sequence: VVENLLNYCFQTFLDKTMSIEFPEMLAEIITNQLPKYSNGNIRKLLFHQK\n AlphaFold Structure: Available\n Structure Coverage: residues 1-50\n\nPROTEIN: cdc42\n UniProt ID: A0A034WPG8\n Organism: Bactrocera dorsalis\n Sequence Length: 191 amino acids\n Sequence: MQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAGQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCQKTPFLLVGTQIDLRDESSTLEKLAKNKQKPITMEQGEKLAKELKAVKYVECSALTQKGLKNVFDEAILAALEPPEPSKKRKCKFL\n AlphaFold Structure: Available\n Structure Coverage: residues 1-191\n\nPROTEIN: cut11\n UniProt ID: A0AAF0ASR7\n Organism: Schizosaccharomyces osmophilus\n Sequence Length: 597 amino acids\n Sequence: MVALRTSFLNGSKIKAVRYHTILRPILQQRFLRASLALYCLCCVTSYWLASGSIFSLKLILGSFLKGMLCFLFVFPYFVMLKSRMTTTRDVHSSLAKEIMIKFSPKSFFPVYISFLVSVGILALA...FDDMDRIISCLKDGIVEITEKFQDFFLQLNIPTKVERRCWVLYRGRNSAT\n AlphaFold Structure: Not available\n\nPROTEIN: ima1\n UniProt ID: B6K4D5\n Organism: Schizosaccharomyces japonicus (strain yFS275 / FY16936)\n Sequence Length: 541 amino acids\n Sequence: MKSSGILFRFTDVMKRTSHTRVQLRCFYCNKKAKINAVLPVREWTCPLCEATNRLDENGEIVDYVPPLTSELNETDPGNDNETKTNEINSPFCWKCQRNQQLYIQAMASYLPESSHPDYAAYEAA...TSFVVPLTLQFTYSTWYRSLYLRLLFFCPLLLFVVLSLMQLLRFCIRKMT\n AlphaFold Structure: Available\n Structure Coverage: residues 1-541\n\nPROTEIN: lem2\n UniProt ID: Q8L8I5\n Organism: Hordeum vulgare subsp. vulgare\n Sequence Length: 302 amino acids\n Sequence: MAVVMKVGAWGAPDGSPQDINAESRPQRLESITIYSVESPGVCGIKGFSFKYVDQQGSSVKSAIWGSNSGNPNTIEMREGEQLKLVGGTFDNEGIGSLTLETNTTKHKTYGYPVQGGEFSLPLPQ...FGRNPSAGTKTFSVPLPDNGALDDAAAVAFFGSSGDSLVAIGAYVGVAPE\n AlphaFold Structure: Available\n Structure Coverage: residues 1-302\n\nPROTEIN: nrf1\n UniProt ID: A0A1W0E5A3\n Organism: Enterocytozoon hepatopenaei\n Sequence Length: 166 amino acids\n Sequence: MNSRPTNSEFTDSNEYINTNNGQQENISEYQREMQNSSAFPRPHCENPTRIAIPVRVEPKVFFANERTFLSWVQFAIFLGGIGTAMLGLESYRANICGIVMIFVAIVFACYALHLFFWRAERIRRREPGPYDDTRGPFLLVGMFIVALIFSVLFKFPMKGGKHLID\n AlphaFold Structure: Available\n Structure Coverage: residues 1-166\n\nPROTEIN: scd1\n UniProt ID: F4I062\n Organism: Arabidopsis thaliana\n Sequence Length: 909 amino acids\n Sequence: MGRIFEYFVVCGLGPEMRTVDGDLGFHGMQTFYLPALLDQFPPTDQSPYPAPPPQLPTCVLPAGVEFHSSGFVSSDPASFPRSYPIVLTEGDGSKIFVSCIAFRDRVCEDIIEAYRLPPNTYADK...LVGDREDAGFFISGSTDCLVGIKCLIGKMFIWLFFIHQFFNHLVDVALHL\n AlphaFold Structure: Available\n Structure Coverage: residues 1-909",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"nr3c1\" name=\"NR3C1\" uniprot=\"A1YFI6\"/>\n <p id=\"cdc42\" name=\"cdc42\" uniprot=\"A0A034WPG8\"/>\n <p id=\"cut11\" name=\"cut11\" uniprot=\"A0AAF0ASR7\"/>\n <p id=\"ima1\" name=\"ima1\" uniprot=\"B6K4D5\"/>\n <p id=\"lem2\" name=\"lem2\" uniprot=\"Q8L8I5\"/>\n <p id=\"nrf1\" name=\"nrf1\" uniprot=\"A0A1W0E5A3\"/>\n <p id=\"scd1\" name=\"scd1\" uniprot=\"F4I062\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cdc42\" b=\"scd1\" type=\"Synthetic Rescue\"/>\n <i id=\"2\" a=\"cdc42\" b=\"nrf1\" type=\"Phenotypic Suppression\"/>\n <i id=\"3\" a=\"nrf1\" b=\"scd1\" type=\"Dosage Lethality\"/>\n <i id=\"4\" a=\"cdc42\" b=\"scd1\" type=\"Phenotypic Suppression\"/>\n <i id=\"5\" a=\"cdc42\" b=\"scd1\" type=\"Affinity Capture-Western\"/>\n <i id=\"6\" a=\"cdc42\" b=\"scd1\" type=\"Dosage Rescue\"/>\n <i id=\"7\" a=\"ima1\" b=\"lem2\" type=\"Synthetic Growth Defect\"/>\n <i id=\"8\" a=\"ima1\" b=\"lem2\" type=\"Phenotypic Enhancement\"/>\n <i id=\"9\" a=\"ima1\" b=\"lem2\" type=\"Two-hybrid\"/>\n <i id=\"10\" a=\"cdc42\" b=\"scd1\" type=\"Two-hybrid\"/>\n <i id=\"11\" a=\"ima1\" b=\"lem2\" type=\"Phenotypic Suppression\"/>\n <i id=\"12\" a=\"nr3c1\" b=\"nrf1\" type=\"Affinity Capture-MS\"/>\n <i id=\"13\" a=\"cut11\" b=\"ima1\" type=\"PCA\"/>\n <i id=\"14\" a=\"cut11\" b=\"nrf1\" type=\"PCA\"/>\n <i id=\"15\" a=\"ima1\" b=\"nrf1\" type=\"PCA\"/>\n <i id=\"16\" a=\"ima1\" b=\"lem2\" type=\"PCA\"/>\n <i id=\"17\" a=\"lem2\" b=\"nrf1\" type=\"PCA\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a list of proteins with their sequence and structural information, predict all likely interactions between them in compressed BioPAX format. Use <proteins> with <p> elements and <interactions> with <i> elements.",
"role": "system"
},
{
"content": "Predict the protein interaction network for these proteins in compressed BioPAX format:\n\nPROTEIN: CG16885\n UniProt ID: A0A0M3QTW3\n Organism: Drosophila busckii\n Sequence Length: 300 amino acids\n Sequence: FNLQFVVGLVAMCVLFVSATEEAAKKVEVEAAASATVEKKQEKRGIAHSGYGYGPSAGAVLSSGHGAVLSSGHGVTYTAPVAFSAPAVSHLPTNVHTNTVVKTVQVPYQVERHVPYPVEKTVTYP...VAGVAGVSGVTGFAGHGVSGSGIAYGHGLSGSGIAYGHGLSGHGISAHGL\n AlphaFold Structure: Available\n Structure Coverage: residues 1-300\n\nPROTEIN: CG3838\n UniProt ID: A0A0M5J6L8\n Organism: Drosophila busckii\n Sequence Length: 372 amino acids\n Sequence: MQADEDFNIRFVNLVRTHRCLYDKKVPEYRNRDNQEKAWALISKETRESVIHCKERWRNLRACLSRYIKQQSGSEPQHKPYYLTEHMAFLLPFLKSTRNSLEGNNSLATLYQFSQHLQLQQQQQQ...ERYPTQEHCNVNGNGNGMLNGSVGSSNGNVSLASTGVRPHRSNSARDWRK\n AlphaFold Structure: Available\n Structure Coverage: residues 1-372\n\nPROTEIN: CG7669\n UniProt ID: A0A0M4EN87\n Organism: Drosophila busckii\n Sequence Length: 605 amino acids\n Sequence: MAEPPQNSYDDTYADEQFEEETLSEVEEESDSQSETDVEAEFLRGNPHARRQQLYATRTGGGSGFAREKLMTYPSSSEDEQQGIITKTVAEVNQLTLPFEQTDDETMSVRTLMPKSNRELEQQQE...NMQGKKQAPPAPRLTSAAVNRKKYQRQIDLDNEVLKRKLEAVGTRRPIFK\n AlphaFold Structure: Available\n Structure Coverage: residues 1-605\n Function: Belongs to the CFAP97 family\n\nPROTEIN: mbl\n UniProt ID: Q6WX77\n Organism: Bacillus mycoides\n Sequence Length: 120 amino acids\n Sequence: GGGTTDIAVLSMGDIVTSSSIKMAGDKFDMEILNYIKRKYKLLIGERTSEDIKIKVGTVFPGARSEELEIRGRDMVTGLPRTITVCSEEITEALKENAAVIVQAAKGVLERTPPELSADI\n AlphaFold Structure: Available\n Structure Coverage: residues 1-120\n\nPROTEIN: p53\n UniProt ID: Q8IMZ4\n Organism: Drosophila melanogaster\n Sequence Length: 495 amino acids\n Sequence: MSLHKSASFSLTFNQNTSIVSRSNSRTIFEAFKEFLDFWDIGNEVSAESAVRVSSNGAFNLPQSFGNESNEYAHLATPVDPAYGGNNTNNMMQFTNNLEILANNNSDGNNKINACNKFVCHKGTD...TCPNKEWLLQSIEGMIKEAAAEVLRNPNQENLRRHANKLLSLKKRAYELP\n AlphaFold Structure: Available\n Structure Coverage: residues 1-495",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg16885\" name=\"CG16885\" uniprot=\"A0A0M3QTW3\"/>\n <p id=\"cg3838\" name=\"CG3838\" uniprot=\"A0A0M5J6L8\"/>\n <p id=\"cg7669\" name=\"CG7669\" uniprot=\"A0A0M4EN87\"/>\n <p id=\"mbl\" name=\"mbl\" uniprot=\"Q6WX77\"/>\n <p id=\"p53\" name=\"p53\" uniprot=\"Q8IMZ4\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg3838\" b=\"cg7669\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg7669\" b=\"mbl\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg7669\" b=\"p53\" type=\"Affinity Capture-Western\"/>\n <i id=\"4\" a=\"cg16885\" b=\"cg7669\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction network generator. Given network constraints and properties, generate a biologically plausible protein network in compressed BioPAX format with <proteins> and <interactions> sections.",
"role": "system"
},
{
"content": "Generate a protein network with the following properties:\n- Proteins: CG14961, CG43691, Neto, dia, koi, krimp\n- Network density: approximately 0.33\n- Hub proteins (highly connected): CG14961, krimp\n- Total interactions: approximately 5",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg14961\" name=\"CG14961\" uniprot=\"A0A0M3QW11\"/>\n <p id=\"cg43691\" name=\"CG43691\" uniprot=\"A0A0B4LGD0\"/>\n <p id=\"neto\" name=\"Neto\" uniprot=\"A0A9R1U0X3\"/>\n <p id=\"dia\" name=\"dia\" uniprot=\"A0A836E1T4\"/>\n <p id=\"koi\" name=\"koi\" uniprot=\"A0A0M3QVC7\"/>\n <p id=\"krimp\" name=\"krimp\" uniprot=\"L0CPG6\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg14961\" b=\"krimp\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg14961\" b=\"dia\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg14961\" b=\"neto\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg14961\" b=\"cg43691\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"cg14961\" b=\"koi\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a known protein network in compressed BioPAX format and a new protein with sequence and structural information, predict which proteins in the network the new protein will interact with. Generate the interactions in compressed BioPAX format.",
"role": "system"
},
{
"content": "Known protein network in compressed BioPAX format:\n<biopax>\n <proteins>\n <p id=\"c49g7.3\" name=\"C49G7.3\" uniprot=\"O16226\"/>\n <p id=\"y54g2a.32\" name=\"Y54G2A.32\" uniprot=\"Q95XX6\"/>\n <p id=\"y71g12b.27\" name=\"Y71G12B.27\" uniprot=\"Q95XM4\" fullname=\"Cyclin-dependent kinases regulatory subunit\"/>\n <p id=\"zk370.8\" name=\"ZK370.8\" uniprot=\"Q02335\" fullname=\"Mitochondrial import receptor subunit tomm-70\"/>\n <p id=\"arid-1\" name=\"arid-1\" uniprot=\"A8X278\"/>\n <p id=\"hsp-1\" name=\"hsp-1\" uniprot=\"A0A0H4J4B2\"/>\n <p id=\"lin-53\" name=\"lin-53\" uniprot=\"A8VSY7\"/>\n <p id=\"meg-3\" name=\"meg-3\" uniprot=\"A0A5K4EK08\"/>\n <p id=\"rbx-1\" name=\"rbx-1\" uniprot=\"A8XVE5\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"y71g12b.27\" b=\"zk370.8\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"zk370.8\" b=\"rbx-1\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"y54g2a.32\" b=\"zk370.8\" type=\"Co-fractionation\"/>\n <i id=\"4\" a=\"hsp-1\" b=\"lin-53\" type=\"Co-fractionation\"/>\n <i id=\"5\" a=\"c49g7.3\" b=\"zk370.8\" type=\"Co-fractionation\"/>\n <i id=\"6\" a=\"zk370.8\" b=\"hsp-1\" type=\"Co-fractionation\"/>\n <i id=\"7\" a=\"zk370.8\" b=\"lin-53\" type=\"Affinity Capture-MS\"/>\n <i id=\"8\" a=\"hsp-1\" b=\"lin-53\" type=\"Affinity Capture-MS\"/>\n <i id=\"9\" a=\"zk370.8\" b=\"meg-3\" type=\"Affinity Capture-MS\"/>\n <i id=\"10\" a=\"meg-3\" b=\"rbx-1\" type=\"Affinity Capture-MS\"/>\n <i id=\"11\" a=\"hsp-1\" b=\"meg-3\" type=\"Affinity Capture-MS\"/>\n <i id=\"12\" a=\"lin-53\" b=\"meg-3\" type=\"Affinity Capture-MS\"/>\n <i id=\"13\" a=\"arid-1\" b=\"meg-3\" type=\"Affinity Capture-MS\"/>\n <i id=\"14\" a=\"zk370.8\" b=\"arid-1\" type=\"Affinity Capture-MS\"/>\n <i id=\"15\" a=\"arid-1\" b=\"lin-53\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>\n\nNew protein to integrate:\nPROTEIN: daf-21\n UniProt ID: A0A0H4IQK5\n Organism: Ancylostoma caninum\n Sequence Length: 707 amino acids\n Sequence: MSDDKGETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYQALTEPGELDTGKELYIKIIPNKEDKTLTIMDTGIGMTKADLVNNLGTIAKSGTKAFMEALQAGADISMIGQFGV...SHASRIYRMIKLGLDIGDDEDEDMPAASCAAEVPKVAGAEEDASRMEEVD\n AlphaFold Structure: Available\n Structure Coverage: residues 1-707\n Function: Belongs to the heat shock protein 90 family\n\nPredict the interactions for daf-21 in compressed BioPAX format:",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"c49g7.3\" name=\"C49G7.3\" uniprot=\"O16226\"/>\n <p id=\"y54g2a.32\" name=\"Y54G2A.32\" uniprot=\"Q95XX6\"/>\n <p id=\"y71g12b.27\" name=\"Y71G12B.27\" uniprot=\"Q95XM4\" fullname=\"Cyclin-dependent kinases regulatory subunit\"/>\n <p id=\"zk370.8\" name=\"ZK370.8\" uniprot=\"Q02335\" fullname=\"Mitochondrial import receptor subunit tomm-70\"/>\n <p id=\"arid-1\" name=\"arid-1\" uniprot=\"A8X278\"/>\n <p id=\"daf-21\" name=\"daf-21\" uniprot=\"A0A0H4IQK5\"/>\n <p id=\"hsp-1\" name=\"hsp-1\" uniprot=\"A0A0H4J4B2\"/>\n <p id=\"lin-53\" name=\"lin-53\" uniprot=\"A8VSY7\"/>\n <p id=\"meg-3\" name=\"meg-3\" uniprot=\"A0A5K4EK08\"/>\n <p id=\"rbx-1\" name=\"rbx-1\" uniprot=\"A8XVE5\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"daf-21\" b=\"hsp-1\" type=\"Co-fractionation\"/>\n <i id=\"2\" a=\"zk370.8\" b=\"daf-21\" type=\"Co-fractionation\"/>\n <i id=\"3\" a=\"daf-21\" b=\"hsp-1\" type=\"Reconstituted Complex\"/>\n <i id=\"4\" a=\"daf-21\" b=\"lin-53\" type=\"Affinity Capture-MS\"/>\n <i id=\"5\" a=\"daf-21\" b=\"meg-3\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Predict the protein interaction network:\n\nPROTEIN: CG10510\n UniProt ID: Q95U04\n Full Name: Dynein regulatory complex subunit 2\n Organism: Drosophila melanogaster\n Sequence Length: 523 amino acids\n Sequence: MAEILARLTRVSENYLQELEEEPEPQGPPKLTKAQKKAAKKEAKRLAMIEEKRLIMRDALMRELEMGKHMEEKGNEEWHEMCREIKIKELNEEMRAWGERSERNIQAKNDHIKMLLDDMAQTQDQ...VSSPTQPMPPKLFETKCQEFKSRKVVHSPTAHKEAKWEAEATLNEVILDF\n AlphaFold Structure: Available\n Structure Coverage: residues 1-523\n Function: Component of the nexin-dynein regulatory complex (N-DRC), a key regulator of ciliary/flagellar motility which maintains the alignment and integrity of the distal axoneme and regulates microtubule slid...\n\nPROTEIN: CG11539\n UniProt ID: A0A0M4EGE4\n Organism: Drosophila busckii\n Sequence Length: 204 amino acids\n Sequence: MRLNEHVKLVGNRVLLVPYEASMVPKYHEWMSDATLRDLTASEQLSLEEEYEMQLSWREDNDKLTFIILCAETYERTKDEITAMVGDTNLFIHCDEESGDCVAEAEIMIAAVEARGKGYGREAMLLMLKYAQTQLPLKKFEAKIDIDNAKSIRLFESFQFVEVRRVEVFHEVTFDRAITAAWLAWLDEQVQLKCEHYGAIDKSS\n AlphaFold Structure: Available\n Structure Coverage: residues 1-204\n Function: Belongs to the acetyltransferase family. GNAT subfamily\n\nPROTEIN: CG13627\n UniProt ID: A0A3Q7YNK5\n Organism: Drosophila simulans\n Sequence Length: 178 amino acids\n Sequence: QTAAQTAPEIYPIQYAQPAVQSQSFIAAIPAAHIPIYNPTYLVTQSNQLYSAHKQQLFKPSSEPVVETGYVNADLTQEVASNGQILQAAKDPHHNIHPVLDSGPQYAALIAAPALGDPNEGAYETASFHLPNVASAVTASVPEGGFVVSNFYGHAHDSSQLLQAYAEEEARRQQLETE\n AlphaFold Structure: Available\n Structure Coverage: residues 1-178\n\nPROTEIN: CG13671\n UniProt ID: A0A0M4EDQ3\n Organism: Drosophila busckii\n Sequence Length: 692 amino acids\n Sequence: MILFIYIWLNFAFGLLPYTQGNIIECPGRSVRQVRAEVDTSAEISLVFYYVSWSSEARQARLVYDGVAHYFKDYASFGAIDCWHLQCNCSHTHPQIPGIAANGGYPDLWPTLMVKYGQKVHLRLQ...CLDFARGLVMQHIGQYLKYWETYVSERDSILKHLKQFNELHTAIESSFRS\n AlphaFold Structure: Available\n Structure Coverage: residues 1-692\n\nPROTEIN: CG13843\n UniProt ID: A0A0M4F3D1\n Organism: Drosophila busckii\n Sequence Length: 363 amino acids\n Sequence: QLKQLKKLYEDVYAYPPKQPAPKTKYIACGKHPFYDDEKQSYQPCWKVPAGMTKAAQFGPCWDYAPASYKRYPLPAPCRGSVIPAHLLRPEFEHCETLYTRYDFQLEQCVHQQILHVERLFSKAE...VSLQLDNYICHKKIDAKLKSSDSGFIEEQSDTSLLMQEMEQAKLLEDDYD\n AlphaFold Structure: Available\n Structure Coverage: residues 1-363\n\nPROTEIN: CG9121\n UniProt ID: A0A0M4EP14\n Organism: Drosophila busckii\n Sequence Length: 597 amino acids\n Sequence: MLSYDLNERLMTAVHSGDFADALNCIIEGAQATYVSSTCGRTAVGTAALLGDAEILQLLIQSCEEPQLNRFHQGAHTDSMETDSTPDGMEKLEWVDEFEGAECDEHSDEHSAEDDGGLYHYYAKT...EQSSALARIVDAQLCVPNTLKIYLSKFSDLPQMRGTQHNGQMINAPESWD\n AlphaFold Structure: Available\n Structure Coverage: residues 1-597\n\nPROTEIN: Cp15\n UniProt ID: T2BQ67\n Organism: Nicotiana tabacum\n Sequence Length: 474 amino acids\n Sequence: MAIHTSTLSISILVMLMFSVVSSSAAEDMSIISYNEKHHTNGESTVWRTDDEVMSLYESWLVEHKKVYNALGEKDKRFQIFKDNLRYIDEQNSAPEKSYKLGLTQFADLTNEEYKSIYLGTKPDG...CCPHDYPVCNVKAGTCSISKNNPLGVKAMQHILAKPIGTFGNEGKKSPSS\n AlphaFold Structure: Available\n Structure Coverage: residues 1-474\n Function: Belongs to the peptidase C1 family\n\nPROTEIN: Sgf11\n UniProt ID: A0A812ANH5\n Organism: Sepia pharaonis\n Sequence Length: 376 amino acids\n Sequence: MMTTTTIGLTQKKRALFQFPRQLGKNLKKKKAAATMAQRVRTKPTRQKTVRNEVCKTITNSFLFFLFPFPFFSLPSLSFFSLPSLSFFSLPSLSFFSLPSLSFFSLSLLSLFSLSPFSLFFLSLP...RKRGGPSKPLKASVTKKKKVVKQTTPTSTPTASSNHPSNNPVGASLYDFV\n AlphaFold Structure: Available\n Structure Coverage: residues 1-376\n Function: The sequence shown here is derived from an EMBL/GenBank/DDBJ whole genome shotgun (WGS) entry which is preliminary data\n\nPROTEIN: cpb\n UniProt ID: E3UN16\n Organism: Clostridium perfringens C\n Sequence Length: 66 amino acids\n Sequence: LTAPNGTEESIIKVKMERERNCYYLNWNGANWVGQVYSRLAFDTPNVDSHIFTFKINWLTHKVTAI\n AlphaFold Structure: Available\n Structure Coverage: residues 1-66\n\nPROTEIN: scb\n UniProt ID: A0A0C9RZZ6\n Organism: Fopius arisanus\n Sequence Length: 136 amino acids\n Sequence: ALFSGENITLLLNYEMNWKKAEKLLPSNSQYLAHVAMVNLKTDIPINGNLSIKQHFKGAIFKKDAKRNLFWIYLGAIIGGILLLIGMILLLRKLGFFKRLTKEEMEKNLIEKREKARMKEDLDVCVAEIEDDLDSS\n AlphaFold Structure: Available\n Structure Coverage: residues 1-136",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg10510\" name=\"CG10510\" uniprot=\"Q95U04\" fullname=\"Dynein regulatory complex subunit 2\"/>\n <p id=\"cg11539\" name=\"CG11539\" uniprot=\"A0A0M4EGE4\"/>\n <p id=\"cg13627\" name=\"CG13627\" uniprot=\"A0A3Q7YNK5\"/>\n <p id=\"cg13671\" name=\"CG13671\" uniprot=\"A0A0M4EDQ3\"/>\n <p id=\"cg13843\" name=\"CG13843\" uniprot=\"A0A0M4F3D1\"/>\n <p id=\"cg9121\" name=\"CG9121\" uniprot=\"A0A0M4EP14\"/>\n <p id=\"cp15\" name=\"Cp15\" uniprot=\"T2BQ67\"/>\n <p id=\"sgf11\" name=\"Sgf11\" uniprot=\"A0A812ANH5\"/>\n <p id=\"cpb\" name=\"cpb\" uniprot=\"E3UN16\"/>\n <p id=\"scb\" name=\"scb\" uniprot=\"A0A0C9RZZ6\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg10510\" b=\"cp15\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg11539\" b=\"cp15\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cp15\" b=\"sgf11\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg13627\" b=\"cp15\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"cg13671\" b=\"cp15\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"cg13843\" b=\"cp15\" type=\"Two-hybrid\"/>\n <i id=\"7\" a=\"cp15\" b=\"cpb\" type=\"Two-hybrid\"/>\n <i id=\"8\" a=\"cp15\" b=\"scb\" type=\"Two-hybrid\"/>\n <i id=\"9\" a=\"cg9121\" b=\"cp15\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Known protein network in compressed BioPAX format:\n<biopax>\n <proteins>\n <p id=\"cg11321\" name=\"CG11321\" uniprot=\"A0A0M4ENX1\"/>\n <p id=\"cg12362\" name=\"CG12362\" uniprot=\"Q9VT94\" fullname=\"RBR-type E3 ubiquitin transferase\"/>\n <p id=\"ubcd10\" name=\"UbcD10\" uniprot=\"A0A0M5IXZ9\"/>\n <p id=\"ari-2\" name=\"ari-2\" uniprot=\"A0A812QY75\"/>\n <p id=\"egg\" name=\"egg\" uniprot=\"A0A0C9RD60\"/>\n <p id=\"rap\" name=\"rap\" uniprot=\"A0A812NGQ4\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg12362\" b=\"ubcd10\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"ubcd10\" b=\"ari-2\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg11321\" b=\"ubcd10\" type=\"Biochemical Activity\"/>\n <i id=\"4\" a=\"ubcd10\" b=\"egg\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"ubcd10\" b=\"rap\" type=\"Phenotypic Suppression\"/>\n </interactions>\n</biopax>\n\nNew protein to integrate:\nPROTEIN: ari-1\n UniProt ID: A0A0M4F8T5\n Organism: Drosophila busckii\n Sequence Length: 68 amino acids\n Sequence: MIFEDNQKDLESATETLSEYLERDITSENLADIKQKVQDKYRYCEKRCSVLLNHVHEGYEKDWWDYTE\n AlphaFold Structure: Available\n Structure Coverage: residues 1-68\n\nPredict the interactions for ari-1 in compressed BioPAX format:",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg11321\" name=\"CG11321\" uniprot=\"A0A0M4ENX1\"/>\n <p id=\"cg12362\" name=\"CG12362\" uniprot=\"Q9VT94\" fullname=\"RBR-type E3 ubiquitin transferase\"/>\n <p id=\"ubcd10\" name=\"UbcD10\" uniprot=\"A0A0M5IXZ9\"/>\n <p id=\"ari-1\" name=\"ari-1\" uniprot=\"A0A0M4F8T5\"/>\n <p id=\"ari-2\" name=\"ari-2\" uniprot=\"A0A812QY75\"/>\n <p id=\"egg\" name=\"egg\" uniprot=\"A0A0C9RD60\"/>\n <p id=\"rap\" name=\"rap\" uniprot=\"A0A812NGQ4\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"ubcd10\" b=\"ari-1\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"ari-1\" b=\"ari-2\" type=\"Affinity Capture-Western\"/>\n <i id=\"3\" a=\"ubcd10\" b=\"ari-1\" type=\"Affinity Capture-Western\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Predict the protein interaction network for these proteins in compressed BioPAX format:\n\nPROTEIN: CG13871\n UniProt ID: Q4V5P0\n Organism: Drosophila melanogaster\n Sequence Length: 479 amino acids\n Sequence: PRRPFGSERRDLAPSEQRYFSDPELLFQRLDDMEQKLGIPEKMAAAGKVKSEHYLVGPTNVAAQMLKDNLYKFPIDDGAIGQGMHDDCLGKEDVDDPFESLARMNFNEHLNERKSDRELKRVLGG...KDSLSSSPRAQMNAVQLEGTSDDELHPGNTFELRPRKKKKKKKKKKKKKK\n AlphaFold Structure: Available\n Structure Coverage: residues 1-479\n\nPROTEIN: CG15651\n UniProt ID: A0A0M4EG19\n Organism: Drosophila busckii\n Sequence Length: 575 amino acids\n Sequence: MKVYRLRLVKLLLLGFILANMLFFYYTWNSLFWRRISNALTGGAAEAKAKSVSAKLTPKDKTRNANKHIRKSITIVFYGHYNFEQDLRASIDSILNIVPNMPILVLQEAGADYAYPPISLERNLT...KASTFSADYLHPMSTVLFLGKSIMCPNNVLEYLEAKHIKVKSEDIAIEDE\n AlphaFold Structure: Available\n Structure Coverage: residues 1-575\n\nPROTEIN: CG17122\n UniProt ID: Q8T4A0\n Full Name: Cilia- and flagella-associated protein 157\n Organism: Drosophila melanogaster\n Sequence Length: 598 amino acids\n Sequence: MPPKVKKEKKDVNKVTQVDRTFYELTITDLNQKLARLRSHVTTVDESNITLTEKLKEVEADGVDVAAHLERTLAERNNSITELEERLVEITKVRDVENRVAQEKIGDLESKYKAMHDQLTSEIKL...VSASSKDIKGAPSIGALDTLTATSKMTGVTNEDEGEEEGEEEDFDVQFVY\n AlphaFold Structure: Available\n Structure Coverage: residues 1-598\n\nPROTEIN: CG18766\n UniProt ID: A0A0M4EWP8\n Organism: Drosophila busckii\n Sequence Length: 310 amino acids\n Sequence: MQYEKFNKKRRQWEDSGVLELIKLWKVCAYELRTIKRNGHLYVAMAKQLTGLGVPVTALEVHFKVNNLTQRYRQEQKTFETTGIISTWKFYSQVDDVFKSLAAHTGYKDKRMTSSSNASSLPSTS...IKSYMKRWPERLQDEAINHITNYVIVKNMEHSMGGGGGGLHNPEGVNNRQ\n AlphaFold Structure: Available\n Structure Coverage: residues 1-310\n\nPROTEIN: CG2199\n UniProt ID: A0A0K8U6F5\n Organism: Bactrocera latifrons\n Sequence Length: 513 amino acids\n Sequence: MKTCKLCKSKSESVFEPKEYILGTKISDVIKFIFSDQSLEFPPKFFICSACAAALVQTEIVLKRLSEALPHSRNFGKLNLSNHKNNDNNEEPQTEQNDINEISKASASETFLKDWIFRCTHCEYT...VSHSVDLTGIESDSSQDNVAKKQKLNGTANSLEKHTLENSSQEQMPSKKT\n AlphaFold Structure: Available\n Structure Coverage: residues 1-513\n\nPROTEIN: CG44009\n UniProt ID: B7Z0M0\n Organism: Drosophila melanogaster\n Sequence Length: 122 amino acids\n Sequence: MSYAGYSQLPSGSDQERRQAQLAASTYDVLQRTTDSIQRSNQIAIETENMGAEVLGELGEQRESLLRTTRRLEDADQDLSKSRVIIRKLSREVLYNKIILILIIILEVGILVGLLVLKFAHL\n AlphaFold Structure: Available\n Structure Coverage: residues 1-122\n\nPROTEIN: CG7115\n UniProt ID: A0A0M3QTI3\n Organism: Drosophila busckii\n Sequence Length: 525 amino acids\n Sequence: MDDELEDKIFYQTYVSHMKILSKFAVGFSSINSPLAYLWKLCRLYVLRPEVILCGIILFVLLIYLQAVDVWSRSILGRIQATLGRQHAATRVMEMSGAAGDHQSWEEVRQQSAAYAVLGRRPHME...VLVIVFRNDIYRIGSSGGGGSLSGKLVDTPPLAKSASGVAVARSNSIKTK\n AlphaFold Structure: Available\n Structure Coverage: residues 1-525\n Function: Belongs to the PP2C family\n\nPROTEIN: CalpB\n UniProt ID: A0A812MPZ8\n Organism: Symbiodinium sp. CCMP2592\n Sequence Length: 411 amino acids\n Sequence: MAEDLALPLARQTPDWATEPCHDQYRSCELDPGQAGDREQDHESPMFAVDMDSMPIRACYPLRAAVVQAKQQWYSERAEQNYSFPPSGMVLHLSDADCGKLQRENGDIYWAHLMSAIIDGTEQVR...RAAAGAGDEGACGTSSTGTQFFSFAENEKAQIHARERAAAGKVDEGASGT\n AlphaFold Structure: Available\n Structure Coverage: residues 1-411\n Function: Belongs to the peptidase C2 family\n\nPROTEIN: Git\n UniProt ID: A2NVX4\n Organism: Lambdavirus lambda\n Sequence Length: 62 amino acids\n Sequence: DPLVILGRVFSNEPLERTMYMIVIWVGLLLLSPDNWPEYVNERIGIPHVWHVFVFALAFSLA\n AlphaFold Structure: Not available\n\nPROTEIN: bip2\n UniProt ID: Q9XZU7\n Organism: Drosophila melanogaster\n Sequence Length: 1408 amino acids\n Sequence: MMADRYASDLALVVVAQITQTIGYSCTLSAPLELLQDILQKFVQEFARNMHRHMEHANRIEPNLKDARLSIKNLSINVQELLDYIGNVAPVGFIRDVPQFPIGKSVNMNFLKPGSAETLTRPVYI...GCDGCDAWYHWICVGITFAPKDNDDWFCRVCVTKKRIHGSEKKKRRNKKK\n AlphaFold Structure: Not available",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg13871\" name=\"CG13871\" uniprot=\"Q4V5P0\"/>\n <p id=\"cg15651\" name=\"CG15651\" uniprot=\"A0A0M4EG19\"/>\n <p id=\"cg17122\" name=\"CG17122\" uniprot=\"Q8T4A0\" fullname=\"Cilia- and flagella-associated protein 157\"/>\n <p id=\"cg18766\" name=\"CG18766\" uniprot=\"A0A0M4EWP8\"/>\n <p id=\"cg2199\" name=\"CG2199\" uniprot=\"A0A0K8U6F5\"/>\n <p id=\"cg44009\" name=\"CG44009\" uniprot=\"B7Z0M0\"/>\n <p id=\"cg7115\" name=\"CG7115\" uniprot=\"A0A0M3QTI3\"/>\n <p id=\"calpb\" name=\"CalpB\" uniprot=\"A0A812MPZ8\"/>\n <p id=\"git\" name=\"Git\" uniprot=\"A2NVX4\"/>\n <p id=\"bip2\" name=\"bip2\" uniprot=\"Q9XZU7\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg13871\" b=\"cg18766\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg15651\" b=\"cg18766\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg17122\" b=\"cg18766\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg18766\" b=\"cg7115\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"cg13871\" b=\"bip2\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"cg18766\" b=\"git\" type=\"Two-hybrid\"/>\n <i id=\"7\" a=\"cg18766\" b=\"bip2\" type=\"Two-hybrid\"/>\n <i id=\"8\" a=\"cg18766\" b=\"cg2199\" type=\"Two-hybrid\"/>\n <i id=\"9\" a=\"cg18766\" b=\"cg44009\" type=\"Two-hybrid\"/>\n <i id=\"10\" a=\"cg18766\" b=\"calpb\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Generate a protein network with the following properties:\n- Proteins: CG12672, CG17739, CG6656, Cyp28d1, Cyp28d2\n- Network density: approximately 0.50\n- Hub proteins (highly connected): Cyp28d2, Cyp28d1\n- Total interactions: approximately 5",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg12672\" name=\"CG12672\" uniprot=\"Q9VWZ8\"/>\n <p id=\"cg17739\" name=\"CG17739\" uniprot=\"Q7K3Y9\" fullname=\"Spondin-1\"/>\n <p id=\"cg6656\" name=\"CG6656\" uniprot=\"A0A0M5J2Q6\"/>\n <p id=\"cyp28d1\" name=\"Cyp28d1\" uniprot=\"A0A0M4ER59\"/>\n <p id=\"cyp28d2\" name=\"Cyp28d2\" uniprot=\"Q9VMT6\" fullname=\"Probable cytochrome P450 28d2\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg12672\" b=\"cyp28d2\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg17739\" b=\"cyp28d2\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cyp28d1\" b=\"cyp28d2\" type=\"Affinity Capture-MS\"/>\n <i id=\"4\" a=\"cg6656\" b=\"cyp28d2\" type=\"Affinity Capture-MS\"/>\n <i id=\"5\" a=\"cg6656\" b=\"cyp28d1\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Known protein network in compressed BioPAX format:\n<biopax>\n <proteins>\n <p id=\"cg10859\" name=\"CG10859\" uniprot=\"A0A0M3QZ12\"/>\n <p id=\"cg3713\" name=\"CG3713\" uniprot=\"Q9V3D7\"/>\n <p id=\"cg8219\" name=\"CG8219\" uniprot=\"Q9VRV9\" fullname=\"Importin N-terminal domain-containing protein\"/>\n <p id=\"mfe2\" name=\"Mfe2\" uniprot=\"A0A812JW80\"/>\n <p id=\"dbo\" name=\"dbo\" uniprot=\"A0A812MZ42\"/>\n <p id=\"mam\" name=\"mam\" uniprot=\"A0A836F8X3\"/>\n <p id=\"oc\" name=\"oc\" uniprot=\"A0A0C9RPE4\"/>\n <p id=\"per\" name=\"per\" uniprot=\"Q2QKP3\"/>\n <p id=\"zuc\" name=\"zuc\" uniprot=\"L0CRJ9\" fullname=\"Mitochondrial cardiolipin hydrolase\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg3713\" b=\"mfe2\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg8219\" b=\"mfe2\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"mfe2\" b=\"mam\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"mfe2\" b=\"per\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"cg10859\" b=\"mfe2\" type=\"Affinity Capture-MS\"/>\n <i id=\"6\" a=\"mfe2\" b=\"oc\" type=\"Two-hybrid\"/>\n <i id=\"7\" a=\"mfe2\" b=\"dbo\" type=\"Two-hybrid\"/>\n <i id=\"8\" a=\"mfe2\" b=\"zuc\" type=\"Proximity Label-MS\"/>\n </interactions>\n</biopax>\n\nNew protein to integrate:\nPROTEIN: brat\n UniProt ID: A0A7L9A3K8\n Organism: Neptis ananta\n Sequence Length: 420 amino acids\n Sequence: QYHKAQNEINDTFQFYRSMLDERKQELLKELESVFSTKQIALTVVGQKAQETVDKIYQTCDFVDRLTKCANIAEILMFRKLLDTKLQTLMSTNPEQSVQTACELEFVSNYQAIQVGVRNTFGYVR...RSPTHQIQIYNQYGQFVRKFGANILQHPRGVTVDNKGRIVVVECKVMRVI\n AlphaFold Structure: Available\n Structure Coverage: residues 1-420\n\nPredict the interactions for brat in compressed BioPAX format:",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg10859\" name=\"CG10859\" uniprot=\"A0A0M3QZ12\"/>\n <p id=\"cg3713\" name=\"CG3713\" uniprot=\"Q9V3D7\"/>\n <p id=\"cg8219\" name=\"CG8219\" uniprot=\"Q9VRV9\" fullname=\"Importin N-terminal domain-containing protein\"/>\n <p id=\"mfe2\" name=\"Mfe2\" uniprot=\"A0A812JW80\"/>\n <p id=\"brat\" name=\"brat\" uniprot=\"A0A7L9A3K8\"/>\n <p id=\"dbo\" name=\"dbo\" uniprot=\"A0A812MZ42\"/>\n <p id=\"mam\" name=\"mam\" uniprot=\"A0A836F8X3\"/>\n <p id=\"oc\" name=\"oc\" uniprot=\"A0A0C9RPE4\"/>\n <p id=\"per\" name=\"per\" uniprot=\"Q2QKP3\"/>\n <p id=\"zuc\" name=\"zuc\" uniprot=\"L0CRJ9\" fullname=\"Mitochondrial cardiolipin hydrolase\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"mfe2\" b=\"brat\" type=\"Phenotypic Enhancement\"/>\n <i id=\"2\" a=\"mfe2\" b=\"brat\" type=\"Phenotypic Suppression\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a list of proteins with their sequence and structural information, predict all likely interactions between them in compressed BioPAX format. Use <proteins> with <p> elements and <interactions> with <i> elements.",
"role": "system"
},
{
"content": "Predict the protein interaction network for these proteins in compressed BioPAX format:\n\nPROTEIN: cpar-1\n UniProt ID: A0A812RX96\n Organism: Symbiodinium sp. CCMP2456\n Sequence Length: 177 amino acids\n Sequence: MRTPTRAIFFCACSYTNCRPACLCLVPSNRICRPCVETTAEEKRQLLLPAAEPAPNEVRAREVAFALRATPEVNVEEEPDSPEDAGGPQSLTELANQLFGVAELEEASQRTESTEIPSPLAAGASTALSEHSEALEAPAPSSGLRLLQQRRRERAEAAPRAAGSAEAATDGDTSAGN\n AlphaFold Structure: Available\n Structure Coverage: residues 1-177\n Function: The sequence shown here is derived from an EMBL/GenBank/DDBJ whole genome shotgun (WGS) entry which is preliminary data\n\nPROTEIN: ify-1\n UniProt ID: A8WU94\n Organism: Caenorhabditis briggsae\n Sequence Length: 281 amino acids\n Sequence: MEDLHFEETGNLPMPTSMQQHMRKFPFFYVNVSFFPSEMKKLGKPMDVQKTPLRSGLGMIVNESKTPGARSLQNLASARKITSSAVKQTIPAIGFEIFEDGVDDEVVEKKMEPEQEEVRETLFHF...EATDYPELYNDVETDTMSREEFQKMVESLLNKYEDYNIDDLLAEEASIQI\n AlphaFold Structure: Available\n Structure Coverage: residues 1-281\n\nPROTEIN: plk-1\n UniProt ID: P34331\n Full Name: Serine/threonine-protein kinase plk-1\n Organism: Caenorhabditis elegans\n Sequence Length: 649 amino acids\n Sequence: MNRLPNIAKPPQKSNQRKEKAPPEVPALIADKDRGTYYEKGRFLGKGGFAHCYELTNRATREVVAGKVVPKSMLVKQYQRDKVDNERILIHRELGHINIVKLFNFFEDNLNVYITLELCARRSLM...NVVSQNPARQPDMPRSMAAARSASAGSRGPNQAASHLPQSASGSNIHPRR\n AlphaFold Structure: Available\n Structure Coverage: residues 1-649\n Function: Required for oocyte nuclear envelope breakdown before entry of oocyte into spermatheca (PubMed:10660671). In meiotic cells, required for spindle dynamics and probably for spindle attachment to the chr...\n\nPROTEIN: sep-1\n UniProt ID: G5ED39\n Full Name: Separin homolog sep-1\n Organism: Caenorhabditis elegans\n Sequence Length: 1262 amino acids\n Sequence: MKITNKSVDKQHIEKLDELRKNVSCTVIGFAEQTAELQQEISELFIAEFGVNGPIDMNSLSKLARITSYYASSEYFQGLAKYQRTACKMFITWQTLRKEAMECRSKDREIFASIPAKLCFFYFYN...VKTFQEEDDEAPKRSTTRQLKPLVAPPIPATPTTRTTRSSARTPSRSRNL\n AlphaFold Structure: Available\n Structure Coverage: residues 1-1262\n Function: Cysteine protease, which plays a central role in homologous chromosome separation during meiosis I and in sister chromatid separation during embryonic mitosis (PubMed:11728305, PubMed:12498686, PubMed...\n\nPROTEIN: sma-4\n UniProt ID: C6KIH3\n Organism: Caenorhabditis brenneri\n Sequence Length: 210 amino acids\n Sequence: QIGETFKVSALDHGKVVVDGGMDPHGENEGRFCLGALSNVHRTEASEKARIHIGGGVELTCHADGNVSITSNCKIFVRSGYLDYSQGSEYSSKAHRFTPNETNFTVFDIRWAYMQMLRRSESSNEAVRAQAAAVAGYAPMSVMPVVMPDSGVDRMRRDFCTIAISFVKAWGDVYQRKTIKETPCWIEVTLHRPLQLLDQLLKNSSQFGSS\n AlphaFold Structure: Available\n Structure Coverage: residues 1-210\n\nPROTEIN: vps-39\n UniProt ID: A0A2A6CGA7\n Organism: Pristionchus pacificus\n Sequence Length: 943 amino acids\n Sequence: RSSQAYHCAMYEAYVSSEVAFKLPVEINAITFHTSAKRIFALSKCDLHFYTPAKSGRRGYELENVAKRISRKPVQQLKVVDDADFLLTLSDQVLSLHSLTFPFPVKAIVRVKGVTAFTAHVDKKN...VLITSNTQCVHCEKKIGTRLTIDAFVRYAQTGELEHLYCHEKSDRNKIQV\n AlphaFold Structure: Available\n Structure Coverage: residues 1-943",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cpar-1\" name=\"cpar-1\" uniprot=\"A0A812RX96\"/>\n <p id=\"ify-1\" name=\"ify-1\" uniprot=\"A8WU94\"/>\n <p id=\"plk-1\" name=\"plk-1\" uniprot=\"P34331\" fullname=\"Serine/threonine-protein kinase plk-1\"/>\n <p id=\"sep-1\" name=\"sep-1\" uniprot=\"G5ED39\" fullname=\"Separin homolog sep-1\"/>\n <p id=\"sma-4\" name=\"sma-4\" uniprot=\"C6KIH3\"/>\n <p id=\"vps-39\" name=\"vps-39\" uniprot=\"A0A2A6CGA7\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"sep-1\" b=\"sma-4\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"sep-1\" b=\"vps-39\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"ify-1\" b=\"sep-1\" type=\"Affinity Capture-Western\"/>\n <i id=\"4\" a=\"ify-1\" b=\"sep-1\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"ify-1\" b=\"sep-1\" type=\"Reconstituted Complex\"/>\n <i id=\"6\" a=\"ify-1\" b=\"sep-1\" type=\"Co-purification\"/>\n <i id=\"7\" a=\"cpar-1\" b=\"sep-1\" type=\"Biochemical Activity\"/>\n <i id=\"8\" a=\"plk-1\" b=\"sep-1\" type=\"Proximity Label-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction network generator. Given network constraints and properties, generate a biologically plausible protein network in compressed BioPAX format with <proteins> and <interactions> sections.",
"role": "system"
},
{
"content": "Generate a protein network in compressed BioPAX format with the following properties:\n- Proteins: CG31955, CG9727, Dr, Oli, Rtnl1, brk, drm, polo\n- Network density: approximately 0.32\n- Hub proteins (highly connected): CG9727, Oli\n- Total interactions: approximately 9",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg31955\" name=\"CG31955\" uniprot=\"Q8IQ04\"/>\n <p id=\"cg9727\" name=\"CG9727\" uniprot=\"A0A0M4EK49\"/>\n <p id=\"dr\" name=\"Dr\" uniprot=\"A0A0C9Q017\"/>\n <p id=\"oli\" name=\"Oli\" uniprot=\"A0A4Q8KEV4\"/>\n <p id=\"rtnl1\" name=\"Rtnl1\" uniprot=\"Q9VMW4\" fullname=\"Reticulon-like protein\"/>\n <p id=\"brk\" name=\"brk\" uniprot=\"Q9XTN4\"/>\n <p id=\"drm\" name=\"drm\" uniprot=\"A0A0U2UL64\"/>\n <p id=\"polo\" name=\"polo\" uniprot=\"B6UXN9\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg9727\" b=\"oli\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg9727\" b=\"brk\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg9727\" b=\"polo\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg9727\" b=\"rtnl1\" type=\"Affinity Capture-MS\"/>\n <i id=\"5\" a=\"cg31955\" b=\"brk\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"cg9727\" b=\"dr\" type=\"Two-hybrid\"/>\n <i id=\"7\" a=\"cg9727\" b=\"drm\" type=\"Two-hybrid\"/>\n <i id=\"8\" a=\"cg31955\" b=\"cg9727\" type=\"Two-hybrid\"/>\n <i id=\"9\" a=\"dr\" b=\"oli\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a known protein network in compressed BioPAX format and a new protein with sequence and structural information, predict which proteins in the network the new protein will interact with. Generate the interactions in compressed BioPAX format.",
"role": "system"
},
{
"content": "Known protein network in compressed BioPAX format:\n<biopax>\n <proteins>\n <p id=\"cg15482\" name=\"CG15482\" uniprot=\"A0A0M3QT71\"/>\n <p id=\"cg9014\" name=\"CG9014\" uniprot=\"Q9VJW5\" fullname=\"E3 ubiquitin-protein ligase NRDP1\"/>\n <p id=\"prosalpha6\" name=\"Prosalpha6\" uniprot=\"T0L633\"/>\n <p id=\"prosalpha6t\" name=\"Prosalpha6T\" uniprot=\"Q9VK14\" fullname=\"Proteasome subunit alpha type\"/>\n <p id=\"prosbeta2\" name=\"Prosbeta2\" uniprot=\"Q9VUJ1\" fullname=\"Proteasome subunit beta\"/>\n <p id=\"ubqn\" name=\"Ubqn\" uniprot=\"A0A0M3QZL1\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg15482\" b=\"prosalpha6t\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg9014\" b=\"prosalpha6t\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"prosalpha6\" b=\"prosbeta2\" type=\"Affinity Capture-MS\"/>\n <i id=\"4\" a=\"prosalpha6t\" b=\"prosbeta2\" type=\"Affinity Capture-MS\"/>\n <i id=\"5\" a=\"prosalpha6t\" b=\"ubqn\" type=\"Reconstituted Complex\"/>\n <i id=\"6\" a=\"prosbeta2\" b=\"ubqn\" type=\"Reconstituted Complex\"/>\n <i id=\"7\" a=\"prosalpha6\" b=\"prosalpha6t\" type=\"Phenotypic Suppression\"/>\n </interactions>\n</biopax>\n\nNew protein to integrate:\nPROTEIN: Rpn12\n UniProt ID: A0A4U6XV99\n Organism: Colletotrichum tanaceti\n Sequence Length: 281 amino acids\n Sequence: MAERNLQQVLTQLRGKGSSLPYAESSALLSKAKLHLLQLNALTPSSGPAQQQTSPQLLALARETYEHGALTSIRAKNPDAFTRYVQQLQPFYELPSNLLPPNLADRNKVTGLYLLLLLTQGRYAE...QRGWILKDGQIFFPDTAEGVAAEDGTTDKEMSQMVIENTLGYARELETIV\n AlphaFold Structure: Available\n Structure Coverage: residues 1-281\n Function: Belongs to the proteasome subunit S14 family\n\nPredict the interactions for Rpn12 in compressed BioPAX format:",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg15482\" name=\"CG15482\" uniprot=\"A0A0M3QT71\"/>\n <p id=\"cg9014\" name=\"CG9014\" uniprot=\"Q9VJW5\" fullname=\"E3 ubiquitin-protein ligase NRDP1\"/>\n <p id=\"prosalpha6\" name=\"Prosalpha6\" uniprot=\"T0L633\"/>\n <p id=\"prosalpha6t\" name=\"Prosalpha6T\" uniprot=\"Q9VK14\" fullname=\"Proteasome subunit alpha type\"/>\n <p id=\"prosbeta2\" name=\"Prosbeta2\" uniprot=\"Q9VUJ1\" fullname=\"Proteasome subunit beta\"/>\n <p id=\"rpn12\" name=\"Rpn12\" uniprot=\"A0A4U6XV99\"/>\n <p id=\"ubqn\" name=\"Ubqn\" uniprot=\"A0A0M3QZL1\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"prosalpha6t\" b=\"rpn12\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"rpn12\" b=\"ubqn\" type=\"Reconstituted Complex\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a partial protein network in compressed BioPAX format, predict the complete network including missing interactions. Generate the complete network in compressed BioPAX format.",
"role": "system"
},
{
"content": "Complete this network:\n<biopax>\n <proteins>\n <p id=\"pnuts\" name=\"PNUTS\" uniprot=\"O55000\" fullname=\"Serine/threonine-protein phosphatase 1 regulatory subunit 10\"/>\n <p id=\"pp1-13c\" name=\"Pp1-13C\" uniprot=\"A0A0A9VX68\" fullname=\"protein-serine/threonine phosphatase\"/>\n <p id=\"pp1-87b\" name=\"Pp1-87B\" uniprot=\"A0A812X3N9\"/>\n <p id=\"pp1alpha-96a\" name=\"Pp1alpha-96A\" uniprot=\"A0A0B4KHS9\" fullname=\"Serine/threonine-protein phosphatase\"/>\n <p id=\"rpii215\" name=\"RpII215\" uniprot=\"A0A0C9PIM9\"/>\n <p id=\"rpl27a\" name=\"RpL27A\" uniprot=\"A0A1W0E6K7\"/>\n <p id=\"spx\" name=\"Spx\" uniprot=\"A0A2U8JFZ4\"/>\n <p id=\"wdr82\" name=\"Wdr82\" uniprot=\"A0A1Y1S5V9\"/>\n <p id=\"ewg\" name=\"ewg\" uniprot=\"A0A0C9RZD4\"/>\n <p id=\"flw\" name=\"flw\" uniprot=\"A0A4D6K293\" fullname=\"Serine/threonine-protein phosphatase\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"pnuts\" b=\"pp1-13c\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"pnuts\" b=\"ewg\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"pnuts\" b=\"spx\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"pp1-87b\" b=\"flw\" type=\"Affinity Capture-MS\"/>\n <i id=\"5\" a=\"pp1-87b\" b=\"pp1alpha-96a\" type=\"Phenotypic Suppression\"/>\n <i id=\"6\" a=\"pnuts\" b=\"rpii215\" type=\"Affinity Capture-Western\"/>\n <i id=\"7\" a=\"pnuts\" b=\"wdr82\" type=\"Affinity Capture-Western\"/>\n <i id=\"8\" a=\"pnuts\" b=\"pp1alpha-96a\" type=\"Two-hybrid\"/>\n <i id=\"9\" a=\"pnuts\" b=\"pp1-87b\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"pnuts\" name=\"PNUTS\" uniprot=\"O55000\" fullname=\"Serine/threonine-protein phosphatase 1 regulatory subunit 10\"/>\n <p id=\"pp1-13c\" name=\"Pp1-13C\" uniprot=\"A0A0A9VX68\" fullname=\"protein-serine/threonine phosphatase\"/>\n <p id=\"pp1-87b\" name=\"Pp1-87B\" uniprot=\"A0A812X3N9\"/>\n <p id=\"pp1alpha-96a\" name=\"Pp1alpha-96A\" uniprot=\"A0A0B4KHS9\" fullname=\"Serine/threonine-protein phosphatase\"/>\n <p id=\"rpii215\" name=\"RpII215\" uniprot=\"A0A0C9PIM9\"/>\n <p id=\"rpl27a\" name=\"RpL27A\" uniprot=\"A0A1W0E6K7\"/>\n <p id=\"spx\" name=\"Spx\" uniprot=\"A0A2U8JFZ4\"/>\n <p id=\"wdr82\" name=\"Wdr82\" uniprot=\"A0A1Y1S5V9\"/>\n <p id=\"ewg\" name=\"ewg\" uniprot=\"A0A0C9RZD4\"/>\n <p id=\"flw\" name=\"flw\" uniprot=\"A0A4D6K293\" fullname=\"Serine/threonine-protein phosphatase\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"pnuts\" b=\"pp1-13c\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"pnuts\" b=\"ewg\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"pnuts\" b=\"spx\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"pp1-87b\" b=\"flw\" type=\"Affinity Capture-MS\"/>\n <i id=\"5\" a=\"pnuts\" b=\"rpl27a\" type=\"Phenotypic Suppression\"/>\n <i id=\"6\" a=\"pp1-87b\" b=\"pp1alpha-96a\" type=\"Phenotypic Suppression\"/>\n <i id=\"7\" a=\"pp1-87b\" b=\"flw\" type=\"Phenotypic Suppression\"/>\n <i id=\"8\" a=\"pnuts\" b=\"rpii215\" type=\"Affinity Capture-Western\"/>\n <i id=\"9\" a=\"pnuts\" b=\"wdr82\" type=\"Affinity Capture-Western\"/>\n <i id=\"10\" a=\"pnuts\" b=\"pp1-87b\" type=\"Affinity Capture-Western\"/>\n <i id=\"11\" a=\"pnuts\" b=\"pp1alpha-96a\" type=\"Two-hybrid\"/>\n <i id=\"12\" a=\"pnuts\" b=\"flw\" type=\"Two-hybrid\"/>\n <i id=\"13\" a=\"pnuts\" b=\"pp1-87b\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a known protein network in compressed BioPAX format and a new protein with sequence and structural information, predict which proteins in the network the new protein will interact with. Generate the interactions in compressed BioPAX format.",
"role": "system"
},
{
"content": "Known protein network in compressed BioPAX format:\n<biopax>\n <proteins>\n <p id=\"c06g1.5\" name=\"C06G1.5\"/>\n <p id=\"c45g9.7\" name=\"C45G9.7\" uniprot=\"A0A0C9PVZ9\"/>\n <p id=\"abu-15\" name=\"abu-15\" uniprot=\"O16500\"/>\n </proteins>\n <interactions/>\n</biopax>\n\nNew protein to integrate:\nPROTEIN: T20F5.4\n UniProt ID: P91479\n Organism: Caenorhabditis elegans\n Sequence Length: 333 amino acids\n Sequence: MTMNHDDRLRNRYEACRSGMQELDMLRAKHTLLIQNLRSRLPIIPGSLDDVQTREKKTRDVFLDRFSLQSVDSGISSQNTISSTRSSTPEDFKTSNRHSNIYENSSTTMNYSTFRKMSLESTHSS...KPTQHFAQPCKIRSPKLNTKTVFAAKPIAVRPSISPKVAQRSTWLQSQPL\n AlphaFold Structure: Available\n Structure Coverage: residues 1-333\n\nPredict the interactions for T20F5.4 in compressed BioPAX format:",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"c06g1.5\" name=\"C06G1.5\"/>\n <p id=\"c45g9.7\" name=\"C45G9.7\" uniprot=\"A0A0C9PVZ9\"/>\n <p id=\"t20f5.4\" name=\"T20F5.4\" uniprot=\"P91479\"/>\n <p id=\"abu-15\" name=\"abu-15\" uniprot=\"O16500\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"t20f5.4\" b=\"abu-15\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"c45g9.7\" b=\"t20f5.4\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"c06g1.5\" b=\"t20f5.4\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Predict the protein interaction network for these proteins:\n\nPROTEIN: CG8177\n UniProt ID: Q1PQ27\n Organism: Drosophila miranda\n Sequence Length: 355 amino acids\n Sequence: RRMPMYKSDILDGLNTETLAATIFMYFACLSTAITFGGLVSDKTKSWIGISETLISCSFVGIVFHCLSCQPLVIIGTTGPLLLFDEALMVFCTQNDFDFLSLRVYVGIWLIIIALCVSAFEGSVY...CVVPALLVYILIFMESQISELIVDKPERGLKKGSGLHWDIVLLCLLNTFC\n AlphaFold Structure: Available\n Structure Coverage: residues 1-355\n\nPROTEIN: FANCI\n UniProt ID: A0A7K9ASG5\n Organism: Dromaius novaehollandiae\n Sequence Length: 1340 amino acids\n Sequence: MAQHILALAAEEAPERLQAALQSLGEGELGDMVTKQALKGRETAALLRGIFKGSPCSQESGVLRRLMVYKHCVPLVESGDLHLAKASEIIGLLMLEARQLPGRALAELATLFVDVIKGGSLSNGK...DFRINASMLESALQEHNTEDAENEPDNDQSSTAEQPDENQEPKKKRQRKK\n AlphaFold Structure: Not available\n\nPROTEIN: Nhe2\n UniProt ID: Q9NGU8\n Organism: Drosophila melanogaster\n Sequence Length: 71 amino acids\n Sequence: YMLPPIILDAGYFMPNRLFFDNLGTILLMAVVGTIFNIATIGGSLYACGKMGIYGESETPGLMDVFLFASL\n AlphaFold Structure: Available\n Structure Coverage: residues 1-71\n\nPROTEIN: fz\n UniProt ID: M9PFL6\n Organism: Drosophila melanogaster\n Sequence Length: 612 amino acids\n Sequence: MWRQILFILPTLIQGVQRYDQSPLDASPYYRSGGGLMASSGTELDGLPHHNRCEPITISICKNIPYNMTIMPNLIGHTKQEEAGLEVHQFAPLVKIGCSDDLQLFLCSLYVPVCTILERPIPPCR...NFVERLQGKEPRTRAQAYVXYETGPAGGAKSTPLTPDPEAANESYLEFST\n AlphaFold Structure: Not available\n\nPROTEIN: phl\n UniProt ID: A0A812TZP1\n Organism: Symbiodinium natans\n Sequence Length: 78 amino acids\n Sequence: MLELKGLLCSSPFKLGVEEGGNVVKGQRPALEEVPVSEDFGAEHREHLCAIMQACWTEDADERESAAGAASRIEALLA\n AlphaFold Structure: Available\n Structure Coverage: residues 1-78\n Function: The sequence shown here is derived from an EMBL/GenBank/DDBJ whole genome shotgun (WGS) entry which is preliminary data\n\nPROTEIN: ptc\n UniProt ID: A0A346A6L3\n Organism: Drosophila subpulchrella\n Sequence Length: 1047 amino acids\n Sequence: GKARGSRTAIYLRSVFQSHLETLGSSVQKHAGKVLFVAILVLSTFCVGLKSAQIHSKVHQLWIQEGGRLEAEMAYTQKTIGEDEAATHQLLIQTTHDPNASVLHPQALLAHLEVLVKATAVKVHL...MMLCSNVLISLGFMTSVGNRQRRVQLGMQMALGPLVHGMLTSGVAVFMLS\n AlphaFold Structure: Not available",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg8177\" name=\"CG8177\" uniprot=\"Q1PQ27\"/>\n <p id=\"fanci\" name=\"FANCI\" uniprot=\"A0A7K9ASG5\"/>\n <p id=\"nhe2\" name=\"Nhe2\" uniprot=\"Q9NGU8\"/>\n <p id=\"fz\" name=\"fz\" uniprot=\"M9PFL6\"/>\n <p id=\"phl\" name=\"phl\" uniprot=\"A0A812TZP1\"/>\n <p id=\"ptc\" name=\"ptc\" uniprot=\"A0A346A6L3\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"fanci\" b=\"nhe2\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"nhe2\" b=\"phl\" type=\"Phenotypic Enhancement\"/>\n <i id=\"3\" a=\"nhe2\" b=\"fz\" type=\"Phenotypic Suppression\"/>\n <i id=\"4\" a=\"nhe2\" b=\"fz\" type=\"Affinity Capture-Western\"/>\n <i id=\"5\" a=\"nhe2\" b=\"ptc\" type=\"Phenotypic Suppression\"/>\n <i id=\"6\" a=\"cg8177\" b=\"nhe2\" type=\"Phenotypic Suppression\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a known protein network in compressed BioPAX format and a new protein with sequence and structural information, predict which proteins in the network the new protein will interact with. Generate the interactions in compressed BioPAX format.",
"role": "system"
},
{
"content": "Known protein network in compressed BioPAX format:\n<biopax>\n <proteins>\n <p id=\"cam-1\" name=\"cam-1\" uniprot=\"G5EGK5\" fullname=\"Tyrosine-protein kinase receptor cam-1\"/>\n <p id=\"lin-18\" name=\"lin-18\" uniprot=\"A8XJR3\"/>\n <p id=\"mrt-2\" name=\"mrt-2\" uniprot=\"A8XHC3\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cam-1\" b=\"lin-18\" type=\"Phenotypic Enhancement\"/>\n </interactions>\n</biopax>\n\nNew protein to integrate:\nPROTEIN: cwn-1\n UniProt ID: A8X402\n Organism: Caenorhabditis briggsae\n Sequence Length: 372 amino acids\n Sequence: MLKPTKILLFLTVSVSIVESLSWLSLGLASSRFDRDKPGTSCKSLKGLTRRQMRFCKKNIDLMESVRTGALAAHAECQFQFHKRRWNCTLIDPMTHEVIPDVFLHENTRESAFVHAISSAAVAYK...AIDDCSLLCCGRGYEKKVQIVEEKCNCKFIYCCEVKCQPCQKRIEKYFCL\n AlphaFold Structure: Available\n Structure Coverage: residues 1-372\n\nPredict the interactions for cwn-1 in compressed BioPAX format:",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cam-1\" name=\"cam-1\" uniprot=\"G5EGK5\" fullname=\"Tyrosine-protein kinase receptor cam-1\"/>\n <p id=\"cwn-1\" name=\"cwn-1\" uniprot=\"A8X402\"/>\n <p id=\"lin-18\" name=\"lin-18\" uniprot=\"A8XJR3\"/>\n <p id=\"mrt-2\" name=\"mrt-2\" uniprot=\"A8XHC3\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cwn-1\" b=\"mrt-2\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cwn-1\" b=\"lin-18\" type=\"Phenotypic Suppression\"/>\n <i id=\"3\" a=\"cam-1\" b=\"cwn-1\" type=\"Phenotypic Suppression\"/>\n <i id=\"4\" a=\"cam-1\" b=\"cwn-1\" type=\"Affinity Capture-Western\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Generate a protein network with the following properties:\n- Proteins: Dg, Mad, Pdp, Su(var)3-9\n- Network density: approximately 0.67\n- Hub proteins (highly connected): Pdp, Mad\n- Total interactions: approximately 4",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"dg\" name=\"Dg\" uniprot=\"Q8WR08\" fullname=\"Dystroglycan 1\"/>\n <p id=\"mad\" name=\"Mad\" uniprot=\"M9PBX0\" fullname=\"Mothers against decapentaplegic homolog\"/>\n <p id=\"pdp\" name=\"Pdp\" uniprot=\"A0A1W1H760\"/>\n <p id=\"su(var)3-9\" name=\"Su(var)3-9\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"pdp\" b=\"su(var)3-9\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"dg\" b=\"pdp\" type=\"Phenotypic Suppression\"/>\n <i id=\"3\" a=\"mad\" b=\"pdp\" type=\"Affinity Capture-Western\"/>\n <i id=\"4\" a=\"mad\" b=\"pdp\" type=\"Biochemical Activity\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Complete this network:\n<biopax>\n <proteins>\n <p id=\"arnt\" name=\"ARNT\" uniprot=\"Q80T29\"/>\n <p id=\"arnt2\" name=\"ARNT2\" uniprot=\"A0A7K4JWC9\"/>\n <p id=\"arntl\" name=\"ARNTL\" uniprot=\"A0A8K0EMB6\"/>\n <p id=\"maged1\" name=\"MAGED1\" uniprot=\"A0AAU9YY36\"/>\n <p id=\"npas4\" name=\"NPAS4\" uniprot=\"A0A7K4P7V6\"/>\n <p id=\"tcp1\" name=\"TCP1\" uniprot=\"A0M9Q9\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"arnt\" b=\"npas4\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"arntl\" b=\"npas4\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"arnt2\" b=\"npas4\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"arnt2\" b=\"maged1\" type=\"Affinity Capture-Western\"/>\n <i id=\"5\" a=\"arnt2\" b=\"maged1\" type=\"FRET\"/>\n <i id=\"6\" a=\"arnt\" b=\"npas4\" type=\"Reconstituted Complex\"/>\n <i id=\"7\" a=\"npas4\" b=\"tcp1\" type=\"Proximity Label-MS\"/>\n </interactions>\n</biopax>",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"arnt\" name=\"ARNT\" uniprot=\"Q80T29\"/>\n <p id=\"arnt2\" name=\"ARNT2\" uniprot=\"A0A7K4JWC9\"/>\n <p id=\"arntl\" name=\"ARNTL\" uniprot=\"A0A8K0EMB6\"/>\n <p id=\"maged1\" name=\"MAGED1\" uniprot=\"A0AAU9YY36\"/>\n <p id=\"npas4\" name=\"NPAS4\" uniprot=\"A0A7K4P7V6\"/>\n <p id=\"tcp1\" name=\"TCP1\" uniprot=\"A0M9Q9\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"arnt\" b=\"npas4\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"arntl\" b=\"npas4\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"arnt2\" b=\"npas4\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"arnt2\" b=\"maged1\" type=\"Affinity Capture-Western\"/>\n <i id=\"5\" a=\"maged1\" b=\"npas4\" type=\"FRET\"/>\n <i id=\"6\" a=\"arnt2\" b=\"maged1\" type=\"FRET\"/>\n <i id=\"7\" a=\"maged1\" b=\"npas4\" type=\"Affinity Capture-Western\"/>\n <i id=\"8\" a=\"arnt\" b=\"npas4\" type=\"Reconstituted Complex\"/>\n <i id=\"9\" a=\"arnt2\" b=\"npas4\" type=\"Affinity Capture-Western\"/>\n <i id=\"10\" a=\"npas4\" b=\"tcp1\" type=\"Proximity Label-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Generate a protein network with the following properties:\n- Proteins: Akh, AkhR, CCAP, CG11635, CG2865, Crz, Gl\n- Network density: approximately 0.29\n- Hub proteins (highly connected): AkhR, CG11635\n- Total interactions: approximately 6",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"akh\" name=\"Akh\" uniprot=\"P61856\" fullname=\"Adipokinetic hormone\"/>\n <p id=\"akhr\" name=\"AkhR\" uniprot=\"Q9VM96\"/>\n <p id=\"ccap\" name=\"CCAP\" uniprot=\"A0A1E1G7R6\"/>\n <p id=\"cg11635\" name=\"CG11635\" uniprot=\"Q5BI51\"/>\n <p id=\"cg2865\" name=\"CG2865\" uniprot=\"A0A0M4FA30\"/>\n <p id=\"crz\" name=\"Crz\" uniprot=\"Q26377\" fullname=\"Pro-corazonin\"/>\n <p id=\"gl\" name=\"Gl\" uniprot=\"T2FLA1\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"akhr\" b=\"cg11635\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"akhr\" b=\"cg2865\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"akhr\" b=\"gl\" type=\"Phenotypic Suppression\"/>\n <i id=\"4\" a=\"akh\" b=\"akhr\" type=\"Biochemical Activity\"/>\n <i id=\"5\" a=\"akhr\" b=\"ccap\" type=\"Biochemical Activity\"/>\n <i id=\"6\" a=\"akhr\" b=\"crz\" type=\"Biochemical Activity\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Complete this network:\n<biopax>\n <proteins>\n <p id=\"cg1598\" name=\"CG1598\" uniprot=\"Q6XIF0\"/>\n <p id=\"cg17327\" name=\"CG17327\" uniprot=\"Q6XHQ9\"/>\n <p id=\"cg3097\" name=\"CG3097\" uniprot=\"A0A0M4F8W7\"/>\n <p id=\"cg4820\" name=\"CG4820\" uniprot=\"A0A0M5JC24\"/>\n <p id=\"cg8206\" name=\"CG8206\" uniprot=\"A0A0M4EYJ7\"/>\n <p id=\"rpl15\" name=\"RpL15\" uniprot=\"A0A812HUA2\"/>\n <p id=\"shroom\" name=\"Shroom\" uniprot=\"A1Z9P3\" fullname=\"Protein Shroom\"/>\n <p id=\"dup\" name=\"dup\" uniprot=\"D2DN34\"/>\n <p id=\"eif-4a\" name=\"eIF-4a\" uniprot=\"C9QP42\" fullname=\"RNA helicase\"/>\n <p id=\"zip\" name=\"zip\" uniprot=\"A0A7L9AW43\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg1598\" b=\"shroom\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg3097\" b=\"shroom\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg8206\" b=\"shroom\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"shroom\" b=\"eif-4a\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"cg4820\" b=\"shroom\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"shroom\" b=\"zip\" type=\"Phenotypic Suppression\"/>\n </interactions>\n</biopax>",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg1598\" name=\"CG1598\" uniprot=\"Q6XIF0\"/>\n <p id=\"cg17327\" name=\"CG17327\" uniprot=\"Q6XHQ9\"/>\n <p id=\"cg3097\" name=\"CG3097\" uniprot=\"A0A0M4F8W7\"/>\n <p id=\"cg4820\" name=\"CG4820\" uniprot=\"A0A0M5JC24\"/>\n <p id=\"cg8206\" name=\"CG8206\" uniprot=\"A0A0M4EYJ7\"/>\n <p id=\"rpl15\" name=\"RpL15\" uniprot=\"A0A812HUA2\"/>\n <p id=\"shroom\" name=\"Shroom\" uniprot=\"A1Z9P3\" fullname=\"Protein Shroom\"/>\n <p id=\"dup\" name=\"dup\" uniprot=\"D2DN34\"/>\n <p id=\"eif-4a\" name=\"eIF-4a\" uniprot=\"C9QP42\" fullname=\"RNA helicase\"/>\n <p id=\"zip\" name=\"zip\" uniprot=\"A0A7L9AW43\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg1598\" b=\"shroom\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg3097\" b=\"shroom\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"rpl15\" b=\"shroom\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"shroom\" b=\"dup\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"cg8206\" b=\"shroom\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"shroom\" b=\"eif-4a\" type=\"Two-hybrid\"/>\n <i id=\"7\" a=\"cg4820\" b=\"shroom\" type=\"Two-hybrid\"/>\n <i id=\"8\" a=\"cg17327\" b=\"shroom\" type=\"Two-hybrid\"/>\n <i id=\"9\" a=\"shroom\" b=\"zip\" type=\"Phenotypic Suppression\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a known protein network in compressed BioPAX format and a new protein with sequence and structural information, predict which proteins in the network the new protein will interact with. Generate the interactions in compressed BioPAX format.",
"role": "system"
},
{
"content": "Network:\n<biopax>\n <proteins>\n <p id=\"dlx2\" name=\"Dlx2\" uniprot=\"D2KA82\"/>\n <p id=\"dlx4\" name=\"Dlx4\" uniprot=\"A1YEZ9\"/>\n <p id=\"dlx5\" name=\"Dlx5\" uniprot=\"Q5MLG1\"/>\n <p id=\"mp1\" name=\"MP1\" uniprot=\"Q0H9Y1\"/>\n <p id=\"nr2f6\" name=\"Nr2f6\" uniprot=\"A0A7K6WTJ5\"/>\n <p id=\"sp7\" name=\"Sp7\" uniprot=\"A0A2J8SX65\"/>\n <p id=\"spn27a\" name=\"Spn27A\" uniprot=\"A0A0M5J8W1\"/>\n <p id=\"spn77ba\" name=\"Spn77Ba\" uniprot=\"A0A0M3QWH6\"/>\n <p id=\"rols\" name=\"rols\" uniprot=\"A0A7L9AQN1\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"sp7\" b=\"rols\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"dlx2\" b=\"sp7\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"dlx4\" b=\"sp7\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"dlx5\" b=\"sp7\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"nr2f6\" b=\"sp7\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"mp1\" b=\"spn77ba\" type=\"Phenotypic Enhancement\"/>\n <i id=\"7\" a=\"mp1\" b=\"spn77ba\" type=\"Phenotypic Suppression\"/>\n <i id=\"8\" a=\"sp7\" b=\"spn77ba\" type=\"Phenotypic Suppression\"/>\n <i id=\"9\" a=\"spn27a\" b=\"spn77ba\" type=\"Phenotypic Suppression\"/>\n <i id=\"10\" a=\"mp1\" b=\"sp7\" type=\"Phenotypic Suppression\"/>\n <i id=\"11\" a=\"sp7\" b=\"spn27a\" type=\"Biochemical Activity\"/>\n <i id=\"12\" a=\"sp7\" b=\"spn27a\" type=\"Co-fractionation\"/>\n </interactions>\n</biopax>\n\nNew to integrate:\nPROTEIN: Stub1\n UniProt ID: Q9XYW6\n Full Name: E3 ubiquitin-protein ligase CHIP\n Organism: Drosophila melanogaster\n Sequence Length: 289 amino acids\n Sequence: MTTKHIYSTTNLSDLQLKEQGNCLFAARKYDDAINCYSKAIIKNPTNATYFTNRALCNLKLKRWELCCQDSRRALDIDGNLLKGHFFLGQGLMEIDNFDEAIKHLQRAYDLSKEQKQNFGDDITL...RKDIEEHLQRVGHFDPVTRVKLTQDQLIPNFSMKEVVDSFIAENEWSLDY\n AlphaFold Structure: Available\n Structure Coverage: residues 1-289\n\nPredict for Stub1:",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"dlx2\" name=\"Dlx2\" uniprot=\"D2KA82\"/>\n <p id=\"dlx4\" name=\"Dlx4\" uniprot=\"A1YEZ9\"/>\n <p id=\"dlx5\" name=\"Dlx5\" uniprot=\"Q5MLG1\"/>\n <p id=\"mp1\" name=\"MP1\" uniprot=\"Q0H9Y1\"/>\n <p id=\"nr2f6\" name=\"Nr2f6\" uniprot=\"A0A7K6WTJ5\"/>\n <p id=\"sp7\" name=\"Sp7\" uniprot=\"A0A2J8SX65\"/>\n <p id=\"spn27a\" name=\"Spn27A\" uniprot=\"A0A0M5J8W1\"/>\n <p id=\"spn77ba\" name=\"Spn77Ba\" uniprot=\"A0A0M3QWH6\"/>\n <p id=\"stub1\" name=\"Stub1\" uniprot=\"Q9XYW6\" fullname=\"E3 ubiquitin-protein ligase CHIP\"/>\n <p id=\"rols\" name=\"rols\" uniprot=\"A0A7L9AQN1\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"sp7\" b=\"stub1\" type=\"Affinity Capture-Western\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a known protein network in compressed BioPAX format and a new protein with sequence and structural information, predict which proteins in the network the new protein will interact with. Generate the interactions in compressed BioPAX format.",
"role": "system"
},
{
"content": "Known protein network in compressed BioPAX format:\n<biopax>\n <proteins>\n <p id=\"bsg\" name=\"Bsg\" uniprot=\"A0AB39ZC04\"/>\n <p id=\"cg7173\" name=\"CG7173\" uniprot=\"A0A0M4EAU5\"/>\n <p id=\"hlh106\" name=\"HLH106\" uniprot=\"Q24146\"/>\n <p id=\"marf\" name=\"Marf\" uniprot=\"W8Q7Y0\"/>\n <p id=\"nd42\" name=\"ND42\" uniprot=\"A0A0C9R0R1\"/>\n <p id=\"bsk\" name=\"bsk\" uniprot=\"A0A0C9RV20\"/>\n <p id=\"out\" name=\"out\" uniprot=\"A0AB39ZKC3\"/>\n <p id=\"p53\" name=\"p53\" uniprot=\"Q8IMZ4\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg7173\" b=\"out\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"out\" b=\"p53\" type=\"Phenotypic Suppression\"/>\n <i id=\"3\" a=\"bsg\" b=\"marf\" type=\"Phenotypic Suppression\"/>\n <i id=\"4\" a=\"nd42\" b=\"out\" type=\"Phenotypic Suppression\"/>\n <i id=\"5\" a=\"bsk\" b=\"out\" type=\"Phenotypic Suppression\"/>\n <i id=\"6\" a=\"bsg\" b=\"nd42\" type=\"Phenotypic Suppression\"/>\n <i id=\"7\" a=\"marf\" b=\"out\" type=\"Phenotypic Suppression\"/>\n <i id=\"8\" a=\"hlh106\" b=\"out\" type=\"Phenotypic Suppression\"/>\n <i id=\"9\" a=\"bsg\" b=\"out\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>\n\nNew protein to integrate:\nPROTEIN: sicily\n UniProt ID: A0A9R1SZU6\n Full Name: 15-cis-phytoene synthase\n Organism: Fopius arisanus\n Sequence Length: 303 amino acids\n Sequence: MNGVKWVFRYRGDEFKRCFSAVQRHNPSHYCLDLVRRNDFENYLCTLLLPSALRGPAFAIRAFNVEIALIQDQTSETAISGMRYNFWNDTLKKIYNNNPPQAPVPLELHRVLKTFKLSKHYFQRL...LASIFLPVVNVEKYLTKLQQLDFNIYSFHLHRKENMLPLQILKAKLFSSW\n AlphaFold Structure: Not available\n\nPredict the interactions for sicily in compressed BioPAX format:",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"bsg\" name=\"Bsg\" uniprot=\"A0AB39ZC04\"/>\n <p id=\"cg7173\" name=\"CG7173\" uniprot=\"A0A0M4EAU5\"/>\n <p id=\"hlh106\" name=\"HLH106\" uniprot=\"Q24146\"/>\n <p id=\"marf\" name=\"Marf\" uniprot=\"W8Q7Y0\"/>\n <p id=\"nd42\" name=\"ND42\" uniprot=\"A0A0C9R0R1\"/>\n <p id=\"bsk\" name=\"bsk\" uniprot=\"A0A0C9RV20\"/>\n <p id=\"out\" name=\"out\" uniprot=\"A0AB39ZKC3\"/>\n <p id=\"p53\" name=\"p53\" uniprot=\"Q8IMZ4\"/>\n <p id=\"sicily\" name=\"sicily\" uniprot=\"A0A9R1SZU6\" fullname=\"15-cis-phytoene synthase\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"nd42\" b=\"sicily\" type=\"Affinity Capture-Western\"/>\n <i id=\"2\" a=\"nd42\" b=\"sicily\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"out\" b=\"sicily\" type=\"Phenotypic Suppression\"/>\n <i id=\"4\" a=\"bsg\" b=\"sicily\" type=\"Phenotypic Suppression\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a known protein network in compressed BioPAX format and a new protein with sequence and structural information, predict which proteins in the network the new protein will interact with. Generate the interactions in compressed BioPAX format.",
"role": "system"
},
{
"content": "Known protein network in compressed BioPAX format:\n<biopax>\n <proteins>\n <p id=\"cg15631\" name=\"CG15631\" uniprot=\"A0A0M4E847\"/>\n <p id=\"cg5204\" name=\"CG5204\" uniprot=\"A0A0M4E1Y0\"/>\n <p id=\"cg7484\" name=\"CG7484\" uniprot=\"C0MK70\" fullname=\"Selenoprotein F\"/>\n <p id=\"ubp64e\" name=\"Ubp64E\" uniprot=\"Q24574\" fullname=\"Ubiquitin carboxyl-terminal hydrolase 47\"/>\n <p id=\"ugt\" name=\"Ugt\" uniprot=\"F0XX36\"/>\n <p id=\"mwh\" name=\"mwh\" uniprot=\"A0AB39ZEG9\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg15631\" b=\"cg7484\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg7484\" b=\"ubp64e\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg5204\" b=\"cg7484\" type=\"Affinity Capture-MS\"/>\n <i id=\"4\" a=\"cg7484\" b=\"ugt\" type=\"Affinity Capture-MS\"/>\n <i id=\"5\" a=\"cg7484\" b=\"mwh\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>\n\nNew protein to integrate:\nPROTEIN: CG10209\n UniProt ID: Q7K3Q3\n Full Name: Regulatory protein zeste\n Organism: Drosophila melanogaster\n Sequence Length: 501 amino acids\n Sequence: MDRVTKPQKKMLITLLRETKYMEGKKEKEWYWEKIQAALNTIGPKKTIIQWKKCWRDMRLTTRKKLAELKRCQLSGGSPPPGIELNQEDNDIIDIVGTEYFYEEMNGELKAENFLTGLDYAPEHL...AQQHQHGHNPHQQQQQHPHQQQQQGQQHHPPTIFGSTASERPPMSYENVG\n AlphaFold Structure: Available\n Structure Coverage: residues 1-501\n Function: Involved in transvection phenomena (= synapsis-dependent gene expression), where the synaptic pairing of chromosomes carrying genes with which zeste interacts influences the expression of these genes....\n\nPredict the interactions for CG10209 in compressed BioPAX format:",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg10209\" name=\"CG10209\" uniprot=\"Q7K3Q3\" fullname=\"Regulatory protein zeste\"/>\n <p id=\"cg15631\" name=\"CG15631\" uniprot=\"A0A0M4E847\"/>\n <p id=\"cg5204\" name=\"CG5204\" uniprot=\"A0A0M4E1Y0\"/>\n <p id=\"cg7484\" name=\"CG7484\" uniprot=\"C0MK70\" fullname=\"Selenoprotein F\"/>\n <p id=\"ubp64e\" name=\"Ubp64E\" uniprot=\"Q24574\" fullname=\"Ubiquitin carboxyl-terminal hydrolase 47\"/>\n <p id=\"ugt\" name=\"Ugt\" uniprot=\"F0XX36\"/>\n <p id=\"mwh\" name=\"mwh\" uniprot=\"A0AB39ZEG9\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg10209\" b=\"mwh\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg10209\" b=\"cg7484\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Generate a protein network in compressed BioPAX format with the following properties:\n- Proteins: CG2224, Mer, Nrx-1, Spn, Tmem173, rictor\n- Network density: approximately 0.53\n- Hub proteins (highly connected): Spn, Nrx-1\n- Total interactions: approximately 8",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg2224\" name=\"CG2224\" uniprot=\"A0A0M3QYH5\"/>\n <p id=\"mer\" name=\"Mer\" uniprot=\"W8E6B9\"/>\n <p id=\"nrx-1\" name=\"Nrx-1\" uniprot=\"A8X8F2\"/>\n <p id=\"spn\" name=\"Spn\" uniprot=\"H2RA91\" fullname=\"SPN\"/>\n <p id=\"tmem173\" name=\"Tmem173\" uniprot=\"A0A6A4WTS3\"/>\n <p id=\"rictor\" name=\"rictor\" uniprot=\"A0A8J9YYW7\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg2224\" b=\"spn\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"mer\" b=\"spn\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"spn\" b=\"rictor\" type=\"Affinity Capture-MS\"/>\n <i id=\"4\" a=\"nrx-1\" b=\"spn\" type=\"Affinity Capture-Western\"/>\n <i id=\"5\" a=\"nrx-1\" b=\"spn\" type=\"Reconstituted Complex\"/>\n <i id=\"6\" a=\"nrx-1\" b=\"spn\" type=\"Two-hybrid\"/>\n <i id=\"7\" a=\"nrx-1\" b=\"spn\" type=\"Co-crystal Structure\"/>\n <i id=\"8\" a=\"spn\" b=\"tmem173\" type=\"Proximity Label-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a known protein network in compressed BioPAX format and a new protein with sequence and structural information, predict which proteins in the network the new protein will interact with. Generate the interactions in compressed BioPAX format.",
"role": "system"
},
{
"content": "Network:\n<biopax>\n <proteins>\n <p id=\"t27a3.1\" name=\"T27A3.1\" uniprot=\"Q86NB7\"/>\n <p id=\"fut-3\" name=\"fut-3\" uniprot=\"G5EFP5\" fullname=\"Alpha-(1,3)-fucosyltransferase fut-3\"/>\n <p id=\"immt-1\" name=\"immt-1\" uniprot=\"A8WRX1\" fullname=\"MICOS complex subunit MIC60\"/>\n <p id=\"mtx-2\" name=\"mtx-2\" uniprot=\"A8WM64\"/>\n <p id=\"nhr-79\" name=\"nhr-79\" uniprot=\"A8XY15\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"fut-3\" b=\"mtx-2\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"t27a3.1\" b=\"mtx-2\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"immt-1\" b=\"mtx-2\" type=\"Co-fractionation\"/>\n <i id=\"4\" a=\"mtx-2\" b=\"nhr-79\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>\n\nNew to integrate:\nPROTEIN: unc-62\n UniProt ID: A8WL06\n Full Name: Homeobox protein unc-62\n Organism: Caenorhabditis briggsae\n Sequence Length: 725 amino acids\n Sequence: MSADSKVWAHASADTWTTAQGISTYDLDTSSIKREKIDCHEQFNDGYGPPPGTASTDAVSYAADPTAYFNLYTNMGAAPTTTPMMHHEMGEAMKRDKEAIYAHPLYPLLVVLFEKCELATSTPRE...LYMQRTMNYGGFQPFPNPAMQFMNPMMGFPVAPAVDAISQQWIDLSAPHE\n AlphaFold Structure: Available\n Structure Coverage: residues 1-725\n Function: Acts redundantly with ceh-20 and ceh-40 to perform overlapping roles during embryogenesis. Required for postembryonic development of the ectoderm, including the Q, V and P cell lineages, playing a cru...\n\nPredict for unc-62:",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"t27a3.1\" name=\"T27A3.1\" uniprot=\"Q86NB7\"/>\n <p id=\"fut-3\" name=\"fut-3\" uniprot=\"G5EFP5\" fullname=\"Alpha-(1,3)-fucosyltransferase fut-3\"/>\n <p id=\"immt-1\" name=\"immt-1\" uniprot=\"A8WRX1\" fullname=\"MICOS complex subunit MIC60\"/>\n <p id=\"mtx-2\" name=\"mtx-2\" uniprot=\"A8WM64\"/>\n <p id=\"nhr-79\" name=\"nhr-79\" uniprot=\"A8XY15\"/>\n <p id=\"unc-62\" name=\"unc-62\" uniprot=\"A8WL06\" fullname=\"Homeobox protein unc-62\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"mtx-2\" b=\"unc-62\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a list of proteins with their sequence and structural information, predict all likely interactions between them in compressed BioPAX format. Use <proteins> with <p> elements and <interactions> with <i> elements.",
"role": "system"
},
{
"content": "Predict the protein interaction network for these proteins:\n\nPROTEIN: Atxn7\n UniProt ID: B2RQB7\n Organism: Mus musculus\n Sequence Length: 870 amino acids\n Sequence: MSERAADDVRGEPRRAAGGAAAARQQQQQQQPQPLQPQRQHPPLRRPRAEDGGTGDTTTSAAAMATVGERRPLPSPEAMLGQSWNLWVEASKLPGKDGTELDESFKEFGKNREVMGLCREDMPIF...SSTVGNSGSKPTKVAKLPAMNNVHMKHTGNISGAQGLTNNSLLHQPKARP\n AlphaFold Structure: Available\n Structure Coverage: residues 1-870\n\nPROTEIN: CG12054\n UniProt ID: A0A0M4EHF6\n Organism: Drosophila busckii\n Sequence Length: 662 amino acids\n Sequence: MAVFLINICKFNGCSKTFQSLSDLISHIEDTHIDYDPKVVEQKELAQPSCLPLSYVLRFISEDARKEAPTFLSNSSNSNTNSITNNGNNGNTGNAELKRKLAIKHHSYSISSSNRSNTPTGSEMD...LITTDCLTTTANATVDGKEMPSSIAAAVTSGTITVAAIEVVGAGVVNTET\n AlphaFold Structure: Available\n Structure Coverage: residues 1-662\n\nPROTEIN: E(Pc)\n UniProt ID: A8JNZ4\n Full Name: Envelope small membrane protein\n Organism: Rhinolophus bat coronavirus HKU2\n Sequence Length: 75 amino acids\n Sequence: MFLKIVEDDGLFINTVLWLLVLILVLLVAITVIKLIQLCFSCHRLMSNTIYIPVYNAYLVYKSYMEVEPCPIINV\n AlphaFold Structure: Not available\n Function: Plays a central role in virus morphogenesis and assembly. Acts as a viroporin and self-assembles in host membranes forming pentameric protein-lipid pores that allow ion transport. Also plays a role in...\n\nPROTEIN: Hr78\n UniProt ID: A0A0V1A749\n Organism: Trichinella patagoniensis\n Sequence Length: 803 amino acids\n Sequence: MVELVSVGLLEKRLLRLCCVNGGRKSFVELELYVASDWNLCCACDPAPVGLLQPQPPSQLQLQHQLTTSQSSSSTTSTTNNTTSTTTAIAATNTNTAISAAAAAAAAAAVDDDDDDDATTAADHI...FSKQIIVELFFSGLIGNLQIENVLPFILKMDVLQIFGEVTSGGDMAETQS\n AlphaFold Structure: Available\n Structure Coverage: residues 1-803\n\nPROTEIN: L\n UniProt ID: J7H8Q3\n Full Name: RNA-directed RNA polymerase L\n Organism: Alethinophid 1 reptarenavirus (isolate AlRrV1/Boa/USA/BC/2009)\n Sequence Length: 2066 amino acids\n Sequence: MSSICPEDSELERLKGLVLEVLSYERDLYRPGWISNTAGEMAMNAIKLRSTIHELNCCRDTGLKHNNDLKEMNELFDEAIGSHETVKTIVPDGYLIDKNNNVLTVLEVSTRTEPSDQTKKVQLDR...FTTKGPTLVFHRLKGLLVSYPAGPLLYKGHRLMLYKDWASGTPEPETLED\n AlphaFold Structure: Not available\n Function: RNA-dependent RNA polymerase, which is responsible for the replication and transcription of the viral RNA genome. During transcription, synthesizes subgenomic RNAs and assures their capping by a cap-s...\n\nPROTEIN: MrgBP\n UniProt ID: A0A7L4NBP2\n Organism: Ceyx cyanopectus\n Sequence Length: 209 amino acids\n Sequence: AAAVAAAAAAVAAAAAAAASAPEPGVPAEEAVVVWSPEVEVCLFHAMLGHKPVGVNRHFHMICIRDKFSQNIGRQISSKVIWDHLSTMYDMQALHESEILPFPNMEKNFALPDEMIQEVREGKVMIEEEVKEEIKEEMETHAGPEEVFAPSGSLGKPTEKPSSKEKEKTSSDPGSKEGSDKRKRNRVTEKVLNANSNPSSPSAAKRRRT\n AlphaFold Structure: Available\n Structure Coverage: residues 1-209\n\nPROTEIN: Nipped-A\n UniProt ID: A0A0M4EGI2\n Organism: Drosophila busckii\n Sequence Length: 3665 amino acids\n Sequence: MIMQSASYPSFLENALKIFMRILQEGEPQFIQENTMQHIRKLILEMIHRLPITENLRQHVKSIISMMLKLLKTDNEENVLISLRIIIELHKHFRPSFNPEIQLFLGFVKEIYTNLPNHLTSIFET...VNSAVDIILLRLNKISYFDNIDKKKVSMLIQSATNIDNLCRMDPAWHPWL\n AlphaFold Structure: Not available\n Function: Belongs to the PI3/PI4-kinase family. TRA1 subfamily\n\nPROTEIN: dom\n UniProt ID: A0A812RR59\n Organism: Symbiodinium natans\n Sequence Length: 1890 amino acids\n Sequence: MQPRAAVAASKDVDALPAQAVPVRRAAQAVLRLEAKRRAVAKKAAKQVQSLVRQHRRNEAQRLEEEHRCARAGAARIAKEIAKFWSDCCRAAEYFAVQQRHAAKTQQHLENMQALVSRSEAFSSE...LEETEQPGTHFIRFLDGQGRRHLSAVMLGDDAEARFQIMLGRWTSRVDLR\n AlphaFold Structure: Not available\n\nPROTEIN: drm\n UniProt ID: A0A0U2UL64\n Organism: Bombyx mori\n Sequence Length: 80 amino acids\n Sequence: MFAVMQIDEEHTRDFRRKLRPKCEFVCKYCQRRFTKSYNLMIHERTHKSPELSFSCEVCGKSFKRQDNLRQHRCSQCLWR\n AlphaFold Structure: Available\n Structure Coverage: residues 1-80\n\nPROTEIN: wda\n UniProt ID: Q9VCN9\n Organism: Drosophila melanogaster\n Sequence Length: 743 amino acids\n Sequence: MSLPSASNHAHAASPVYSNSNNNKSSASSKKTSSKNDLLRCAVGLLLKQKNYVSNERFRRSDFLLLQNKQQFAVNKMLDTDLHGGNSFTFSNVQVITNNQHTVDQQFGRFSQFVEAQAEPLRLEM...IKKLSPMSDNSSAGSSSSATTNRVLTVNSSCQRLVDVFYGTSKTLYCIGT\n AlphaFold Structure: Available\n Structure Coverage: residues 1-743\n Function: Belongs to the WD repeat TAF5 family",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"atxn7\" name=\"Atxn7\" uniprot=\"B2RQB7\"/>\n <p id=\"cg12054\" name=\"CG12054\" uniprot=\"A0A0M4EHF6\"/>\n <p id=\"e(pc)\" name=\"E(Pc)\" uniprot=\"A8JNZ4\" fullname=\"Envelope small membrane protein\"/>\n <p id=\"hr78\" name=\"Hr78\" uniprot=\"A0A0V1A749\"/>\n <p id=\"l\" name=\"L\" uniprot=\"J7H8Q3\" fullname=\"RNA-directed RNA polymerase L\"/>\n <p id=\"mrgbp\" name=\"MrgBP\" uniprot=\"A0A7L4NBP2\"/>\n <p id=\"nipped-a\" name=\"Nipped-A\" uniprot=\"A0A0M4EGI2\"/>\n <p id=\"dom\" name=\"dom\" uniprot=\"A0A812RR59\"/>\n <p id=\"drm\" name=\"drm\" uniprot=\"A0A0U2UL64\"/>\n <p id=\"wda\" name=\"wda\" uniprot=\"Q9VCN9\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"mrgbp\" b=\"dom\" type=\"Affinity Capture-MS\"/>\n <i id=\"2\" a=\"atxn7\" b=\"nipped-a\" type=\"Affinity Capture-MS\"/>\n <i id=\"3\" a=\"atxn7\" b=\"wda\" type=\"Affinity Capture-MS\"/>\n <i id=\"4\" a=\"cg12054\" b=\"l\" type=\"Phenotypic Suppression\"/>\n <i id=\"5\" a=\"nipped-a\" b=\"dom\" type=\"Phenotypic Enhancement\"/>\n <i id=\"6\" a=\"e(pc)\" b=\"dom\" type=\"Phenotypic Enhancement\"/>\n <i id=\"7\" a=\"nipped-a\" b=\"wda\" type=\"Affinity Capture-MS\"/>\n <i id=\"8\" a=\"cg12054\" b=\"hr78\" type=\"Two-hybrid\"/>\n <i id=\"9\" a=\"cg12054\" b=\"drm\" type=\"Two-hybrid\"/>\n <i id=\"10\" a=\"hr78\" b=\"drm\" type=\"Two-hybrid\"/>\n <i id=\"11\" a=\"cg12054\" b=\"dom\" type=\"Affinity Capture-MS\"/>\n <i id=\"12\" a=\"cg12054\" b=\"nipped-a\" type=\"Affinity Capture-MS\"/>\n <i id=\"13\" a=\"cg12054\" b=\"e(pc)\" type=\"Affinity Capture-MS\"/>\n <i id=\"14\" a=\"cg12054\" b=\"mrgbp\" type=\"Affinity Capture-MS\"/>\n <i id=\"15\" a=\"cg12054\" b=\"wda\" type=\"Affinity Capture-MS\"/>\n <i id=\"16\" a=\"atxn7\" b=\"cg12054\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a list of proteins with their sequence and structural information, predict all likely interactions between them in compressed BioPAX format. Use <proteins> with <p> elements and <interactions> with <i> elements.",
"role": "system"
},
{
"content": "Predict the protein interaction network for these proteins in compressed BioPAX format:\n\nPROTEIN: DMA1\n UniProt ID: B6K1Q7\n Organism: Schizosaccharomyces japonicus (strain yFS275 / FY16936)\n Sequence Length: 279 amino acids\n Sequence: MQETPQVATALADQTVLPDSSEKAASCLDNPPEETISIRFTNFVSANGHSFNFEPVVRTWSKKNKNLPIHIGRYTDKYNGGNVSAVVFRSKVVSRRHAQVFYEGGEWYVQDLGSSSGTFLNHIRL...WCIHPTLQKNHPYFNCFICRKYHDLSTPVEEGELELRELMKHATVVDKSP\n AlphaFold Structure: Available\n Structure Coverage: residues 1-279\n\nPROTEIN: PHO2\n UniProt ID: A0A0C9R021\n Organism: Fopius arisanus\n Sequence Length: 151 amino acids\n Sequence: KEATWHPLEVGSGRNTSTPYSSVPQECAVSPPLSKDGDHADNNNTNADDLTYLRHLELEPIDPTTGLPLHPGFTAKGGRTPCTITRRLVRQSGPHQVLHSSLMRMRLQCDSGGGTKFQRALKLAYSSLFRRGLLVRTCPTAAASSSSQNGT\n AlphaFold Structure: Available\n Structure Coverage: residues 1-151\n\nPROTEIN: PUB1\n UniProt ID: A0A0H5BYG0\n Organism: Cyberlindnera jadinii (strain ATCC 18201 / CBS 1600 / BCRC 20928 / JCM 3617 / NBRC 0987 / NRRL Y-1542)\n Sequence Length: 492 amino acids\n Sequence: MSVEDKGATVVDAETTDQTTTLKVVVPPAEDGSVVEPTESEQTEESGSDNAEAIANNGTDVNEESPKVTPALASQGGREVSHKILYVGGLNAKVTDETIQQVFGANGELAKVNILADKNSPGGSF...RSSHHHQYQNNSANGGANANGNANGSLNDQAAPPDGYNSQSYGHAVVYGQ\n AlphaFold Structure: Available\n Structure Coverage: residues 1-492\n\nPROTEIN: RPN11\n UniProt ID: A0A1W0E794\n Organism: Enterocytozoon hepatopenaei\n Sequence Length: 290 amino acids\n Sequence: MENFMSFGANSNGPVYDTSETIHISSLALLKMMKHGRAGIPLEVMGLMLGEFVDEYNVKVIDVFSMPQSGTSVTIEAVDPVFQTKMLDVLRATGRTETVVGWYHSHPGFGCWLSSTDVSTQSAFE...SFKKTKEEVEMSKIGKINYKKRILENYADVVENQVINSLIKAIHRNIFGV\n AlphaFold Structure: Available\n Structure Coverage: residues 1-290\n Function: The sequence shown here is derived from an EMBL/GenBank/DDBJ whole genome shotgun (WGS) entry which is preliminary data\n\nPROTEIN: YLR256W-A\n UniProt ID: P0C2I8\n Full Name: Transposon Ty1-LR4 Gag polyprotein\n Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)\n Sequence Length: 440 amino acids\n Sequence: MESQQLSQHPHISHGSACASVTSKEVHTNQDPLDVSASKTEECEKASTKANSQQTTTPASSAVPENPHHASPQPASVPPPQNGPYPQQCMMTQNQANPSGWSFYGHPSMIPYTPYQMSPMYFPPG...NNSKSKTARAHNVSTSNNSPSTDNDSISKSTTEPIQLNNKHDLHLRPGTY\n AlphaFold Structure: Available\n Structure Coverage: residues 1-440\n Function: Capsid protein (CA) is the structural component of the virus-like particle (VLP), forming the shell that encapsulates the retrotransposons dimeric RNA genome. The particles are assembled from trimer-c...",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"dma1\" name=\"DMA1\" uniprot=\"B6K1Q7\"/>\n <p id=\"pho2\" name=\"PHO2\" uniprot=\"A0A0C9R021\"/>\n <p id=\"pub1\" name=\"PUB1\" uniprot=\"A0A0H5BYG0\"/>\n <p id=\"rpn11\" name=\"RPN11\" uniprot=\"A0A1W0E794\"/>\n <p id=\"ylr256w-a\" name=\"YLR256W-A\" uniprot=\"P0C2I8\" fullname=\"Transposon Ty1-LR4 Gag polyprotein\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"pho2\" b=\"ylr256w-a\" type=\"Affinity Capture-MS\"/>\n <i id=\"2\" a=\"dma1\" b=\"ylr256w-a\" type=\"Affinity Capture-MS\"/>\n <i id=\"3\" a=\"rpn11\" b=\"ylr256w-a\" type=\"Affinity Capture-MS\"/>\n <i id=\"4\" a=\"pub1\" b=\"ylr256w-a\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Complete this network:\n<biopax>\n <proteins>\n <p id=\"btbd9\" name=\"Btbd9\" uniprot=\"A0A7K4YNQ0\"/>\n <p id=\"cacna1h\" name=\"Cacna1h\" uniprot=\"A0A812NI47\"/>\n <p id=\"dst\" name=\"Dst\" uniprot=\"A0A8J9W0F9\"/>\n <p id=\"faf1\" name=\"Faf1\" uniprot=\"A0A7K8NE75\"/>\n <p id=\"kbtbd4\" name=\"Kbtbd4\" uniprot=\"A0AAU9Z984\"/>\n <p id=\"klhl1\" name=\"Klhl1\" uniprot=\"A0A6G1ASW8\"/>\n <p id=\"klhl24\" name=\"Klhl24\" uniprot=\"A0A813C5D4\"/>\n <p id=\"mical2\" name=\"Mical2\" uniprot=\"A0A812WAB6\"/>\n <p id=\"tgfbr1\" name=\"TGFBR1\" uniprot=\"A0A2J8JWH7\"/>\n <p id=\"tmtc3\" name=\"Tmtc3\" uniprot=\"A0A7K4Y3J2\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"klhl1\" b=\"tgfbr1\" type=\"Affinity Capture-Luminescence\"/>\n <i id=\"2\" a=\"dst\" b=\"mical2\" type=\"Co-fractionation\"/>\n <i id=\"3\" a=\"btbd9\" b=\"klhl1\" type=\"Co-fractionation\"/>\n <i id=\"4\" a=\"dst\" b=\"klhl1\" type=\"Co-fractionation\"/>\n <i id=\"5\" a=\"faf1\" b=\"klhl1\" type=\"Co-fractionation\"/>\n <i id=\"6\" a=\"klhl1\" b=\"klhl24\" type=\"Co-fractionation\"/>\n <i id=\"7\" a=\"klhl1\" b=\"mical2\" type=\"Co-fractionation\"/>\n <i id=\"8\" a=\"faf1\" b=\"klhl24\" type=\"Co-fractionation\"/>\n </interactions>\n</biopax>",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"btbd9\" name=\"Btbd9\" uniprot=\"A0A7K4YNQ0\"/>\n <p id=\"cacna1h\" name=\"Cacna1h\" uniprot=\"A0A812NI47\"/>\n <p id=\"dst\" name=\"Dst\" uniprot=\"A0A8J9W0F9\"/>\n <p id=\"faf1\" name=\"Faf1\" uniprot=\"A0A7K8NE75\"/>\n <p id=\"kbtbd4\" name=\"Kbtbd4\" uniprot=\"A0AAU9Z984\"/>\n <p id=\"klhl1\" name=\"Klhl1\" uniprot=\"A0A6G1ASW8\"/>\n <p id=\"klhl24\" name=\"Klhl24\" uniprot=\"A0A813C5D4\"/>\n <p id=\"mical2\" name=\"Mical2\" uniprot=\"A0A812WAB6\"/>\n <p id=\"tgfbr1\" name=\"TGFBR1\" uniprot=\"A0A2J8JWH7\"/>\n <p id=\"tmtc3\" name=\"Tmtc3\" uniprot=\"A0A7K4Y3J2\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"klhl1\" b=\"tgfbr1\" type=\"Affinity Capture-Luminescence\"/>\n <i id=\"2\" a=\"cacna1h\" b=\"klhl1\" type=\"Affinity Capture-Western\"/>\n <i id=\"3\" a=\"dst\" b=\"mical2\" type=\"Co-fractionation\"/>\n <i id=\"4\" a=\"kbtbd4\" b=\"klhl24\" type=\"Co-fractionation\"/>\n <i id=\"5\" a=\"btbd9\" b=\"klhl1\" type=\"Co-fractionation\"/>\n <i id=\"6\" a=\"dst\" b=\"klhl1\" type=\"Co-fractionation\"/>\n <i id=\"7\" a=\"faf1\" b=\"klhl1\" type=\"Co-fractionation\"/>\n <i id=\"8\" a=\"kbtbd4\" b=\"klhl1\" type=\"Co-fractionation\"/>\n <i id=\"9\" a=\"klhl1\" b=\"klhl24\" type=\"Co-fractionation\"/>\n <i id=\"10\" a=\"klhl1\" b=\"mical2\" type=\"Co-fractionation\"/>\n <i id=\"11\" a=\"klhl1\" b=\"tmtc3\" type=\"Co-fractionation\"/>\n <i id=\"12\" a=\"faf1\" b=\"klhl24\" type=\"Co-fractionation\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a partial protein network in compressed BioPAX format, predict the complete network including missing interactions. Generate the complete network in compressed BioPAX format.",
"role": "system"
},
{
"content": "Complete this network:\n<biopax>\n <proteins>\n <p id=\"cg15282\" name=\"CG15282\" uniprot=\"Q9VJS1\"/>\n <p id=\"cg1648\" name=\"CG1648\" uniprot=\"A0A0M4EI88\"/>\n <p id=\"cg17147\" name=\"CG17147\" uniprot=\"A0A0M4EQ64\"/>\n <p id=\"cg31775\" name=\"CG31775\" uniprot=\"Q7KT85\"/>\n <p id=\"cg8668\" name=\"CG8668\" uniprot=\"A0A0M4EBD2\"/>\n <p id=\"ctpsyn\" name=\"CTPsyn\" uniprot=\"A0AB39ZFS9\"/>\n <p id=\"drsl4\" name=\"Drsl4\" uniprot=\"Q8IRD6\"/>\n <p id=\"peritrophin-15a\" name=\"Peritrophin-15a\" uniprot=\"Q9VLL8\"/>\n <p id=\"ric-3\" name=\"RIC-3\" uniprot=\"A0A0C9QLA2\"/>\n <p id=\"sll\" name=\"sll\" uniprot=\"A0A812JN41\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg8668\" b=\"ric-3\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg15282\" b=\"cg1648\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg1648\" b=\"ric-3\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg1648\" b=\"cg17147\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"cg17147\" b=\"ric-3\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"cg1648\" b=\"drsl4\" type=\"Two-hybrid\"/>\n <i id=\"7\" a=\"cg1648\" b=\"cg31775\" type=\"Two-hybrid\"/>\n <i id=\"8\" a=\"cg1648\" b=\"ctpsyn\" type=\"Proximity Label-MS\"/>\n </interactions>\n</biopax>",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg15282\" name=\"CG15282\" uniprot=\"Q9VJS1\"/>\n <p id=\"cg1648\" name=\"CG1648\" uniprot=\"A0A0M4EI88\"/>\n <p id=\"cg17147\" name=\"CG17147\" uniprot=\"A0A0M4EQ64\"/>\n <p id=\"cg31775\" name=\"CG31775\" uniprot=\"Q7KT85\"/>\n <p id=\"cg8668\" name=\"CG8668\" uniprot=\"A0A0M4EBD2\"/>\n <p id=\"ctpsyn\" name=\"CTPsyn\" uniprot=\"A0AB39ZFS9\"/>\n <p id=\"drsl4\" name=\"Drsl4\" uniprot=\"Q8IRD6\"/>\n <p id=\"peritrophin-15a\" name=\"Peritrophin-15a\" uniprot=\"Q9VLL8\"/>\n <p id=\"ric-3\" name=\"RIC-3\" uniprot=\"A0A0C9QLA2\"/>\n <p id=\"sll\" name=\"sll\" uniprot=\"A0A812JN41\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg1648\" b=\"cg8668\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg8668\" b=\"ric-3\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg15282\" b=\"cg1648\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg1648\" b=\"ric-3\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"cg1648\" b=\"cg17147\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"cg17147\" b=\"ric-3\" type=\"Two-hybrid\"/>\n <i id=\"7\" a=\"cg1648\" b=\"sll\" type=\"Two-hybrid\"/>\n <i id=\"8\" a=\"cg1648\" b=\"peritrophin-15a\" type=\"Two-hybrid\"/>\n <i id=\"9\" a=\"cg1648\" b=\"drsl4\" type=\"Two-hybrid\"/>\n <i id=\"10\" a=\"cg1648\" b=\"cg31775\" type=\"Two-hybrid\"/>\n <i id=\"11\" a=\"cg1648\" b=\"ctpsyn\" type=\"Proximity Label-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a partial protein network in compressed BioPAX format, predict the complete network including missing interactions. Generate the complete network in compressed BioPAX format.",
"role": "system"
},
{
"content": "Complete this partial protein network in compressed BioPAX format:\n<biopax>\n <proteins>\n <p id=\"y39b6a.1\" name=\"Y39B6A.1\" uniprot=\"Q9NES7\"/>\n <p id=\"y77e11a.2\" name=\"Y77E11A.2\" uniprot=\"U6M7U0\"/>\n <p id=\"zk1307.8\" name=\"ZK1307.8\" uniprot=\"G5EC87\" fullname=\"Glucosidase 2 subunit beta\"/>\n <p id=\"gly-8\" name=\"gly-8\" uniprot=\"A8XHE5\"/>\n <p id=\"hacd-1\" name=\"hacd-1\" uniprot=\"O44608\" fullname=\"3-hydroxyacyl-CoA dehydrogenase\"/>\n <p id=\"nfyb-1\" name=\"nfyb-1\" uniprot=\"A8X3S4\"/>\n <p id=\"rps-7\" name=\"rps-7\" uniprot=\"A0A0B4N5Q4\" fullname=\"40S ribosomal protein S7\"/>\n <p id=\"ttm-1\" name=\"ttm-1\" uniprot=\"A0A812KQH0\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"zk1307.8\" b=\"hacd-1\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"zk1307.8\" b=\"gly-8\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"y77e11a.2\" b=\"zk1307.8\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"zk1307.8\" b=\"rps-7\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"zk1307.8\" b=\"ttm-1\" type=\"Co-fractionation\"/>\n </interactions>\n</biopax>",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"y39b6a.1\" name=\"Y39B6A.1\" uniprot=\"Q9NES7\"/>\n <p id=\"y77e11a.2\" name=\"Y77E11A.2\" uniprot=\"U6M7U0\"/>\n <p id=\"zk1307.8\" name=\"ZK1307.8\" uniprot=\"G5EC87\" fullname=\"Glucosidase 2 subunit beta\"/>\n <p id=\"gly-8\" name=\"gly-8\" uniprot=\"A8XHE5\"/>\n <p id=\"hacd-1\" name=\"hacd-1\" uniprot=\"O44608\" fullname=\"3-hydroxyacyl-CoA dehydrogenase\"/>\n <p id=\"nfyb-1\" name=\"nfyb-1\" uniprot=\"A8X3S4\"/>\n <p id=\"rps-7\" name=\"rps-7\" uniprot=\"A0A0B4N5Q4\" fullname=\"40S ribosomal protein S7\"/>\n <p id=\"ttm-1\" name=\"ttm-1\" uniprot=\"A0A812KQH0\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"zk1307.8\" b=\"hacd-1\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"y39b6a.1\" b=\"zk1307.8\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"zk1307.8\" b=\"gly-8\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"y77e11a.2\" b=\"zk1307.8\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"zk1307.8\" b=\"rps-7\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"zk1307.8\" b=\"nfyb-1\" type=\"Co-fractionation\"/>\n <i id=\"7\" a=\"zk1307.8\" b=\"ttm-1\" type=\"Co-fractionation\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a partial protein network in compressed BioPAX format, predict the complete network including missing interactions. Generate the complete network in compressed BioPAX format.",
"role": "system"
},
{
"content": "Complete this network:\n<biopax>\n <proteins>\n <p id=\"gnbp3\" name=\"GNBP3\" uniprot=\"A0A1V1FYD5\"/>\n <p id=\"myo10a\" name=\"Myo10A\" uniprot=\"A0AB40AE36\"/>\n <p id=\"ppo1\" name=\"PPO1\" uniprot=\"Q00024\" fullname=\"Polyphenol oxidase 1\"/>\n <p id=\"nec\" name=\"nec\" uniprot=\"Q7JWX3\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"gnbp3\" b=\"myo10a\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"gnbp3\" b=\"ppo1\" type=\"Affinity Capture-Western\"/>\n <i id=\"3\" a=\"gnbp3\" b=\"ppo1\" type=\"Reconstituted Complex\"/>\n </interactions>\n</biopax>",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"gnbp3\" name=\"GNBP3\" uniprot=\"A0A1V1FYD5\"/>\n <p id=\"myo10a\" name=\"Myo10A\" uniprot=\"A0AB40AE36\"/>\n <p id=\"ppo1\" name=\"PPO1\" uniprot=\"Q00024\" fullname=\"Polyphenol oxidase 1\"/>\n <p id=\"nec\" name=\"nec\" uniprot=\"Q7JWX3\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"gnbp3\" b=\"myo10a\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"gnbp3\" b=\"ppo1\" type=\"Affinity Capture-Western\"/>\n <i id=\"3\" a=\"gnbp3\" b=\"nec\" type=\"Affinity Capture-Western\"/>\n <i id=\"4\" a=\"gnbp3\" b=\"ppo1\" type=\"Reconstituted Complex\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a known protein network in compressed BioPAX format and a new protein with sequence and structural information, predict which proteins in the network the new protein will interact with. Generate the interactions in compressed BioPAX format.",
"role": "system"
},
{
"content": "Network:\n<biopax>\n <proteins>\n <p id=\"arp5\" name=\"Arp5\" uniprot=\"A0A1W0E5X5\"/>\n <p id=\"cg12659\" name=\"CG12659\" uniprot=\"A0A0M4F7Z8\"/>\n <p id=\"cg33017\" name=\"CG33017\" uniprot=\"A0A0B4LGM7\"/>\n <p id=\"csn4\" name=\"CSN4\" uniprot=\"A0A812MBI1\"/>\n <p id=\"rap2l\" name=\"Rap2l\" uniprot=\"A0A0M4EBK5\"/>\n <p id=\"pho\" name=\"pho\" uniprot=\"A0A224L134\"/>\n <p id=\"spz\" name=\"spz\" uniprot=\"Q6V6V9\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"arp5\" b=\"spz\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"arp5\" b=\"cg33017\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"arp5\" b=\"csn4\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"arp5\" b=\"rap2l\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"arp5\" b=\"pho\" type=\"Affinity Capture-MS\"/>\n <i id=\"6\" a=\"arp5\" b=\"cg12659\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>\n\nNew to integrate:\nPROTEIN: rasp\n UniProt ID: A0A174HTR4\n Organism: Collinsella aerofaciens\n Sequence Length: 453 amino acids\n Sequence: MDTVLSVLSSVFWGLLMLSVLVFLHEGGHFLAARACCVRVTEFFLGLPCRFDIHYTSRRIGTKFGVTPLLLGGYAAICGMDPTDVSCADRVLAAIYRHGRVTVADLAVELELSEEDVLEACALLL...GGKLVIEIIQKIAGRELPLKVQTIVSYVGIALFVLLFVYMLRSDILRFIL\n AlphaFold Structure: Available\n Structure Coverage: residues 1-453\n\nPredict for rasp:",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"arp5\" name=\"Arp5\" uniprot=\"A0A1W0E5X5\"/>\n <p id=\"cg12659\" name=\"CG12659\" uniprot=\"A0A0M4F7Z8\"/>\n <p id=\"cg33017\" name=\"CG33017\" uniprot=\"A0A0B4LGM7\"/>\n <p id=\"csn4\" name=\"CSN4\" uniprot=\"A0A812MBI1\"/>\n <p id=\"rap2l\" name=\"Rap2l\" uniprot=\"A0A0M4EBK5\"/>\n <p id=\"pho\" name=\"pho\" uniprot=\"A0A224L134\"/>\n <p id=\"rasp\" name=\"rasp\" uniprot=\"A0A174HTR4\"/>\n <p id=\"spz\" name=\"spz\" uniprot=\"Q6V6V9\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"arp5\" b=\"rasp\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Predict the protein interaction network for these proteins:\n\nPROTEIN: ATbp\n UniProt ID: A0A0M4ES44\n Organism: Drosophila busckii\n Sequence Length: 401 amino acids\n Sequence: MGFPRILSKNNKIYTKLGEFCLSGESFWIVCHTCQEELQTQDAFWKHIQDEHNFLHGVAKQDHSRTSSYCLTDVETATATTGATTAQATGGVTAVSVPLALYHCAAKYSEEEQREVAAAVELHEA...VVHSKERRFNCDMCSASFKQSCNLSTHRKKKHSMRGIKSDLLPQRFLAGP\n AlphaFold Structure: Available\n Structure Coverage: residues 1-401\n\nPROTEIN: CG14071\n UniProt ID: A0A0M4E4D2\n Organism: Drosophila busckii\n Sequence Length: 144 amino acids\n Sequence: MASMPKVFVRQINAGVVLSRELSMKIFSYDAMSQEFSQLDNEICKIRKQQDDMENSLAEALAEDEYERCLNSSSQQLPQQYVPSEEEFYEIFKQHLSRIIEKLTAKYERKIYLELDMRKLKLCIEKGIVAANEETAAAEAAANN\n AlphaFold Structure: Available\n Structure Coverage: residues 1-144\n\nPROTEIN: CG14220\n UniProt ID: A0A0M4EJY1\n Organism: Drosophila busckii\n Sequence Length: 330 amino acids\n Sequence: MNAYPFIPTWGESIYDDESIGDERSEEDTDDASETEYRSPHRYGGTNGTSSNNSITNNNTGGNTNNNSELKEQMYQHKLVNLQKQLDELNQLMHPEYMKRVRKLDSQLRERRRLNEIYKDYMREC...IYVEGKDMNKFPATITAIGNDVIWVKRSNETKFKINMSHLAKGKISIKRR\n AlphaFold Structure: Available\n Structure Coverage: residues 1-330\n\nPROTEIN: CG14546\n UniProt ID: A0A0M4EUI0\n Organism: Drosophila busckii\n Sequence Length: 366 amino acids\n Sequence: MFPNYCFKKSAEDLGYEVLFLPKLRYDSESHCNSRCRLRSKSHTRNCAKMHCNDLISLQALREHTERVRQSQLTESNHSPEPNSVPRNIEFRLPPNDQQQEQSAREAAGQEPSSETLAAGKSSEQ...ASMPELHRRISLMSTTVHKLKQSQCTRSPTPSFWTPTQCSSAGPPQRHVD\n AlphaFold Structure: Available\n Structure Coverage: residues 1-366\n\nPROTEIN: CG31224\n UniProt ID: A0A0M5JCB7\n Organism: Drosophila busckii\n Sequence Length: 1816 amino acids\n Sequence: MSSVDCVQCPVCTLYLHAGMNLSDHLETHPKEKVIKALVQMTISGNSHGNALAAAMLGNDGSSNAAAIEAAPSSSCSNNNNNNNSSSCSATATAAVAAEIKSPSSSSSSNNNSLKQSNNPPIKVE...RHYYLIEHRRIHTGERPFHCTICGKSSTTKTNHNKHLKIHHSRDPFTVEV\n AlphaFold Structure: Not available\n\nPROTEIN: CG31999\n UniProt ID: A0A0M4EWT3\n Organism: Drosophila busckii\n Sequence Length: 569 amino acids\n Sequence: MQSSIHHQFSKVYAIILLLTIGHVRAEVGLAVKASQQNCRDPLFSFLTNIESYRICCSDKEFSESDEEVLHNPAIEFPEDAKVSDVENNEGIKNSQENSDGTIVLKDDDDICGKVPNLCQQICEN...DIDECAGSTGMTPSNHVCTGRNDVCTNIRGNYKCTTINCPHGYIKDPDVD\n AlphaFold Structure: Available\n Structure Coverage: residues 1-569\n Function: Lacks conserved residue(s) required for the propagation of feature annotation\n\nPROTEIN: CG8301\n UniProt ID: A0A0M4EHL6\n Organism: Drosophila busckii\n Sequence Length: 330 amino acids\n Sequence: METCRCCAKCDFDGNNNYWLDLFHPSRCQKEIAEIRLELVNWKLQIFPNDGLPQKICSDCFMKFFSLHTFRLACQDAQIKLSNIFDKIDANTLYDRTDSADDNEKSVNSHQINTAGNIEHNTTQA...RQLRCRHDGCDRIFINRRHLKCHEVTHTTDPRKSEYCCFCGKGIYGTQRT\n AlphaFold Structure: Available\n Structure Coverage: residues 1-330\n\nPROTEIN: DOR\n UniProt ID: A0A438HZX3\n Organism: Vitis vinifera\n Sequence Length: 380 amino acids\n Sequence: MKMNPVSVPNDLVFGILTHLPVKSLLRFRCVCKSWRSMISDPLFVEAHQSRSASALLISFPDMRDPDRKRTLFCINEGEAHRIPGFSHWNISQSVNGLICIYGQYSPKQSHRVRVCNPSTREHVT...HCNLEEESPRRAVLSGLPQNDWNVPYPSIYCSEVSEYAESLVSLKEICRH\n AlphaFold Structure: Available\n Structure Coverage: residues 1-380\n Function: The sequence shown here is derived from an EMBL/GenBank/DDBJ whole genome shotgun (WGS) entry which is preliminary data\n\nPROTEIN: Mer\n UniProt ID: W8E6B9\n Organism: Schmidtea mediterranea\n Sequence Length: 388 amino acids\n Sequence: MEECAKDTNQNHIEIKPKKSGFFRRFKRRFTSIFQRKPNRKRNKSEPCLPGTNENNLKEGSEKRLSLNNDDKSKEKPDENGENQISSASFRPVSKAPFFVNDFTAELKKSLLQRSKMVEEGQTSE...EIKTEINADNNCQSCLVTESQGSQSCLTEASAAHGNLLNETDSVQLTNDT\n AlphaFold Structure: Available\n Structure Coverage: residues 1-388\n\nPROTEIN: prc\n UniProt ID: C8CAF1\n Organism: Rhizobium leguminosarum bv. trifolii\n Sequence Length: 130 amino acids\n Sequence: LFGIGAVLQERDDYPTIRELVPGGPAQLSGKLAVGDRITGVGQGKDGAIKEVVGTRLDEVVQMIRGKKGSVVRLDILPADAGADGTHRVISLVRDKISLDKQAARKTVLSVKAGDATRKIGIITLPVFYE\n AlphaFold Structure: Available\n Structure Coverage: residues 1-130",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"atbp\" name=\"ATbp\" uniprot=\"A0A0M4ES44\"/>\n <p id=\"cg14071\" name=\"CG14071\" uniprot=\"A0A0M4E4D2\"/>\n <p id=\"cg14220\" name=\"CG14220\" uniprot=\"A0A0M4EJY1\"/>\n <p id=\"cg14546\" name=\"CG14546\" uniprot=\"A0A0M4EUI0\"/>\n <p id=\"cg31224\" name=\"CG31224\" uniprot=\"A0A0M5JCB7\"/>\n <p id=\"cg31999\" name=\"CG31999\" uniprot=\"A0A0M4EWT3\"/>\n <p id=\"cg8301\" name=\"CG8301\" uniprot=\"A0A0M4EHL6\"/>\n <p id=\"dor\" name=\"DOR\" uniprot=\"A0A438HZX3\"/>\n <p id=\"mer\" name=\"Mer\" uniprot=\"W8E6B9\"/>\n <p id=\"prc\" name=\"prc\" uniprot=\"C8CAF1\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg14220\" b=\"cg31224\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg31224\" b=\"dor\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg14071\" b=\"cg31224\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg14546\" b=\"cg31224\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"cg31224\" b=\"cg31999\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"cg31224\" b=\"prc\" type=\"Two-hybrid\"/>\n <i id=\"7\" a=\"cg31224\" b=\"cg8301\" type=\"Two-hybrid\"/>\n <i id=\"8\" a=\"cg31224\" b=\"mer\" type=\"Two-hybrid\"/>\n <i id=\"9\" a=\"atbp\" b=\"cg31224\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction network generator. Given network constraints and properties, generate a biologically plausible protein network in compressed BioPAX format with <proteins> and <interactions> sections.",
"role": "system"
},
{
"content": "Generate a protein network with the following properties:\n- Proteins: DMA1, HEK2, PHO2, RPN11, SSB2, YML040W\n- Network density: approximately 0.80\n- Hub proteins (highly connected): SSB2, YML040W\n- Total interactions: approximately 12",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"dma1\" name=\"DMA1\" uniprot=\"B6K1Q7\"/>\n <p id=\"hek2\" name=\"HEK2\" uniprot=\"A0AAD5BFY7\"/>\n <p id=\"pho2\" name=\"PHO2\" uniprot=\"A0A0C9R021\"/>\n <p id=\"rpn11\" name=\"RPN11\" uniprot=\"A0A1W0E794\"/>\n <p id=\"ssb2\" name=\"SSB2\" uniprot=\"A5N269\"/>\n <p id=\"yml040w\" name=\"YML040W\" uniprot=\"P0CX76\" fullname=\"Transposon Ty1-ML2 Gag polyprotein\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"pho2\" b=\"yml040w\" type=\"Affinity Capture-MS\"/>\n <i id=\"2\" a=\"dma1\" b=\"yml040w\" type=\"Affinity Capture-MS\"/>\n <i id=\"3\" a=\"dma1\" b=\"hek2\" type=\"Affinity Capture-RNA\"/>\n <i id=\"4\" a=\"hek2\" b=\"pho2\" type=\"Affinity Capture-RNA\"/>\n <i id=\"5\" a=\"hek2\" b=\"yml040w\" type=\"Affinity Capture-RNA\"/>\n <i id=\"6\" a=\"rpn11\" b=\"ssb2\" type=\"Affinity Capture-MS\"/>\n <i id=\"7\" a=\"rpn11\" b=\"yml040w\" type=\"Affinity Capture-MS\"/>\n <i id=\"8\" a=\"hek2\" b=\"ssb2\" type=\"Co-purification\"/>\n <i id=\"9\" a=\"dma1\" b=\"ssb2\" type=\"Co-purification\"/>\n <i id=\"10\" a=\"ssb2\" b=\"yml040w\" type=\"Co-purification\"/>\n <i id=\"11\" a=\"pho2\" b=\"ssb2\" type=\"Co-purification\"/>\n <i id=\"12\" a=\"rpn11\" b=\"ssb2\" type=\"Co-purification\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction network generator. Given network constraints and properties, generate a biologically plausible protein network in compressed BioPAX format with <proteins> and <interactions> sections.",
"role": "system"
},
{
"content": "Generate a protein network with the following properties:\n- Proteins: R02F11.1, Y66D12A.10, alg-1, asp-5, elks-1, lin-53, pqn-54\n- Network density: approximately 0.33\n- Hub proteins (highly connected): asp-5, lin-53\n- Total interactions: approximately 7",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"r02f11.1\" name=\"R02F11.1\" uniprot=\"O16364\"/>\n <p id=\"y66d12a.10\" name=\"Y66D12A.10\" uniprot=\"Q95Q05\"/>\n <p id=\"alg-1\" name=\"alg-1\" uniprot=\"I3WQY9\"/>\n <p id=\"asp-5\" name=\"asp-5\" uniprot=\"A8XDC0\"/>\n <p id=\"elks-1\" name=\"elks-1\" uniprot=\"A8XZ97\"/>\n <p id=\"lin-53\" name=\"lin-53\" uniprot=\"A8VSY7\"/>\n <p id=\"pqn-54\" name=\"pqn-54\" uniprot=\"G0M993\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"r02f11.1\" b=\"asp-5\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"asp-5\" b=\"pqn-54\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"y66d12a.10\" b=\"asp-5\" type=\"Co-fractionation\"/>\n <i id=\"4\" a=\"alg-1\" b=\"lin-53\" type=\"Affinity Capture-MS\"/>\n <i id=\"5\" a=\"asp-5\" b=\"lin-53\" type=\"Affinity Capture-MS\"/>\n <i id=\"6\" a=\"alg-1\" b=\"asp-5\" type=\"Affinity Capture-MS\"/>\n <i id=\"7\" a=\"asp-5\" b=\"elks-1\" type=\"Proximity Label-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a known protein network in compressed BioPAX format and a new protein with sequence and structural information, predict which proteins in the network the new protein will interact with. Generate the interactions in compressed BioPAX format.",
"role": "system"
},
{
"content": "Known protein network in compressed BioPAX format:\n<biopax>\n <proteins>\n <p id=\"cg13871\" name=\"CG13871\" uniprot=\"Q4V5P0\"/>\n <p id=\"cg17122\" name=\"CG17122\" uniprot=\"Q8T4A0\" fullname=\"Cilia- and flagella-associated protein 157\"/>\n <p id=\"cg18766\" name=\"CG18766\" uniprot=\"A0A0M4EWP8\"/>\n <p id=\"cg2199\" name=\"CG2199\" uniprot=\"A0A0K8U6F5\"/>\n <p id=\"cg44009\" name=\"CG44009\" uniprot=\"B7Z0M0\"/>\n <p id=\"cg7115\" name=\"CG7115\" uniprot=\"A0A0M3QTI3\"/>\n <p id=\"calpb\" name=\"CalpB\" uniprot=\"A0A812MPZ8\"/>\n <p id=\"git\" name=\"Git\" uniprot=\"A2NVX4\"/>\n <p id=\"bip2\" name=\"bip2\" uniprot=\"Q9XZU7\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg13871\" b=\"cg18766\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg17122\" b=\"cg18766\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg18766\" b=\"cg7115\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg13871\" b=\"bip2\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"cg18766\" b=\"git\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"cg18766\" b=\"bip2\" type=\"Two-hybrid\"/>\n <i id=\"7\" a=\"cg18766\" b=\"cg2199\" type=\"Two-hybrid\"/>\n <i id=\"8\" a=\"cg18766\" b=\"cg44009\" type=\"Two-hybrid\"/>\n <i id=\"9\" a=\"cg18766\" b=\"calpb\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>\n\nNew protein to integrate:\nPROTEIN: CG15651\n UniProt ID: A0A0M4EG19\n Organism: Drosophila busckii\n Sequence Length: 575 amino acids\n Sequence: MKVYRLRLVKLLLLGFILANMLFFYYTWNSLFWRRISNALTGGAAEAKAKSVSAKLTPKDKTRNANKHIRKSITIVFYGHYNFEQDLRASIDSILNIVPNMPILVLQEAGADYAYPPISLERNLT...KASTFSADYLHPMSTVLFLGKSIMCPNNVLEYLEAKHIKVKSEDIAIEDE\n AlphaFold Structure: Available\n Structure Coverage: residues 1-575\n\nPredict the interactions for CG15651 in compressed BioPAX format:",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg13871\" name=\"CG13871\" uniprot=\"Q4V5P0\"/>\n <p id=\"cg15651\" name=\"CG15651\" uniprot=\"A0A0M4EG19\"/>\n <p id=\"cg17122\" name=\"CG17122\" uniprot=\"Q8T4A0\" fullname=\"Cilia- and flagella-associated protein 157\"/>\n <p id=\"cg18766\" name=\"CG18766\" uniprot=\"A0A0M4EWP8\"/>\n <p id=\"cg2199\" name=\"CG2199\" uniprot=\"A0A0K8U6F5\"/>\n <p id=\"cg44009\" name=\"CG44009\" uniprot=\"B7Z0M0\"/>\n <p id=\"cg7115\" name=\"CG7115\" uniprot=\"A0A0M3QTI3\"/>\n <p id=\"calpb\" name=\"CalpB\" uniprot=\"A0A812MPZ8\"/>\n <p id=\"git\" name=\"Git\" uniprot=\"A2NVX4\"/>\n <p id=\"bip2\" name=\"bip2\" uniprot=\"Q9XZU7\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg15651\" b=\"cg18766\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Predict the protein interaction network:\n\nPROTEIN: Y62E10A.17\n UniProt ID: G2HK15\n Full Name: Transcription factor aptf-2\n Organism: Caenorhabditis elegans\n Sequence Length: 367 amino acids\n Sequence: MDIQMFTTLNSTVPTEPVVGPVEPTVPTVPATKETGPSSSAECSTQPAVAEQEDNSLLAQLLKGKITSDDAKLQPPRGPFEYAPMLSEEAQFAIKLAGLLNPNPVTEQDPSTFKPPPKMSNNVRK...ETFSSASHGLGIVSQRVWLPQLTAIGNGVASELRRLTETPTESKPEELKA\n AlphaFold Structure: Available\n Structure Coverage: residues 1-367\n Function: Sequence-specific DNA-binding protein that interacts with enhancer elements to regulate transcription of selected genes (By similarity). Required for neuroblast and epidermal morphogenesis, perhaps ac...\n\nPROTEIN: alp-1\n UniProt ID: A8WKA2\n Organism: Caenorhabditis briggsae\n Sequence Length: 2170 amino acids\n Sequence: MDPNIFVLVSAENFSSKPIICSSKSSPTAAQPVHVQQESPRAAYHPQINQYARPVSVSPVPSAGGKTITTHYHTPKTQGILSPAQRGVPNAAFGADLSKTVTYGGGVGPGGTHYDPNRLSPAPSQ...RYPIEAGDRWVEALGNAFHSNCFTCARCNINLEGESFFAKNGQPFCRNHA\n AlphaFold Structure: Not available\n\nPROTEIN: aptf-3\n UniProt ID: Q19862\n Organism: Caenorhabditis elegans\n Sequence Length: 535 amino acids\n Sequence: MSYSDYPSDIADYSSFDNMMADICNPSSSSSSNRKRQADPAPDNFAKIPAGMATQPLYFPIHYPVNSGWQSFDVNQVYNNHNMNQPGFGWVALPPPMPHNLQIPDQNSYKPRSGLPVPPPMAEFQ...QRGEHQQIHQHQLYQQHHTNTHPPMPLMPPSQMNLCPPITPIPPQNVYYY\n AlphaFold Structure: Available\n Structure Coverage: residues 1-535\n\nPROTEIN: hlh-3\n UniProt ID: A8WSF8\n Organism: Caenorhabditis briggsae\n Sequence Length: 168 amino acids\n Sequence: MPASTASTSSSKTSTSTKVRSPNKPISKQTKNKRNARERKRVDQVNQGFQRLQESVPRPANNKSKLSKVETLRQAAQYIRQLQGQLGIMPTGTPVDFPTPEHSPIFPSVMYPMMAQTPSPTYLSPYYPQPTPITFEMNPYYLAESCSSVSPAASGSGDNSFYSHADIN\n AlphaFold Structure: Available\n Structure Coverage: residues 1-168\n\nPROTEIN: mdt-29\n UniProt ID: A0A4E9FLN2\n Organism: Brugia malayi\n Sequence Length: 398 amino acids\n Sequence: MYGHQSIPRSVSAGQLNAMMSHPGMVITSQQMINTPQGVMVSQAGYPQGMINTAQPPQMMPSQTHISQQMINTHMGVVQGLNQQGHMNVQHQQMQQMQQVQMAPQQAYIQQQGMSHPNFVNGQAR...NYSQYAQGYVESTARVRNAITRTLKNLNATMERMNAAKIVQKDIEEKMAM\n AlphaFold Structure: Available\n Structure Coverage: residues 1-398\n\nPROTEIN: nhr-22\n UniProt ID: A8WTT1\n Organism: Caenorhabditis briggsae\n Sequence Length: 577 amino acids\n Sequence: MSTDLLLNEYFYPQNDYFNSTFEDVPSPESVSLNAEPTFEDSSSPHDDFFEPTFDINFCLWKDNSTSPKPQPVLEAVFSPKPINVMPSPQSSSPCCHVCASPTANTLHFGGRSCKACAAFFRRSV...EDPATRVGQLLLSMSYITELVQAMTNSYLVMTFFDVVSCDSIMYDLLSFK\n AlphaFold Structure: Available\n Structure Coverage: residues 1-577\n\nPROTEIN: unc-62\n UniProt ID: A8WL06\n Full Name: Homeobox protein unc-62\n Organism: Caenorhabditis briggsae\n Sequence Length: 725 amino acids\n Sequence: MSADSKVWAHASADTWTTAQGISTYDLDTSSIKREKIDCHEQFNDGYGPPPGTASTDAVSYAADPTAYFNLYTNMGAAPTTTPMMHHEMGEAMKRDKEAIYAHPLYPLLVVLFEKCELATSTPRE...LYMQRTMNYGGFQPFPNPAMQFMNPMMGFPVAPAVDAISQQWIDLSAPHE\n AlphaFold Structure: Available\n Structure Coverage: residues 1-725\n Function: Acts redundantly with ceh-20 and ceh-40 to perform overlapping roles during embryogenesis. Required for postembryonic development of the ectoderm, including the Q, V and P cell lineages, playing a cru...\n\nPROTEIN: unc-98\n UniProt ID: Q612G6\n Full Name: Zinc finger protein unc-98\n Organism: Caenorhabditis briggsae\n Sequence Length: 308 amino acids\n Sequence: MGDDLFKEARKERDDFEELMNACDLAKMSVKNNEMVHGLETFGVNHGESSSENKPTEIMKVVAPTVEAYVGSSSSTTVTKPSGGAVDGIDQKEVRQDGTSVQKDDNGFIFYKCRFCGLTFNFMNT...LAYHMYSHRGEKQFNPRASRYMMGREGVGYTDSRSYYLFPRTSGYVSPRF\n AlphaFold Structure: Available\n Structure Coverage: residues 1-308\n Function: Probable transcription factor. Required for muscle structure. Its dual subcellular localization suggests that it may function both as a muscle adhesion complex protein and as a transcription factor, o...\n\nPROTEIN: zip-7\n UniProt ID: A8XIF4\n Organism: Caenorhabditis briggsae\n Sequence Length: 124 amino acids\n Sequence: MSDELQQQLANSSLYDAESLKAFNQMYTSANNPYAVGGAGVVHGFDKSYYERRARNNKAAQKSREARKKIDAENSHRVNQLEMENNHLKAYIYKLYQENMMMKNQLVQHYPGVVDPAAASMPGF\n AlphaFold Structure: Available\n Structure Coverage: residues 1-124\n\nPROTEIN: ztf-2\n UniProt ID: A8Y199\n Organism: Caenorhabditis briggsae\n Sequence Length: 355 amino acids\n Sequence: MDCESLLTALDVSTLLSSLASPDKEHRRKRRRGEVANPSNTLDALVARKADDQPFEKRYLSEQEAIEGPDDEIEMKKMELDPDVSTRTCSTCGYQGKWVSEMIRHKRVHTSERPFKCRYCSRTSK...LNLQPNPLMSLYLASLLQSSLLNSPTIQLPQLVPTTVIQPQSEEMVDVEM\n AlphaFold Structure: Available\n Structure Coverage: residues 1-355",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"y62e10a.17\" name=\"Y62E10A.17\" uniprot=\"G2HK15\" fullname=\"Transcription factor aptf-2\"/>\n <p id=\"alp-1\" name=\"alp-1\" uniprot=\"A8WKA2\"/>\n <p id=\"aptf-3\" name=\"aptf-3\" uniprot=\"Q19862\"/>\n <p id=\"hlh-3\" name=\"hlh-3\" uniprot=\"A8WSF8\"/>\n <p id=\"mdt-29\" name=\"mdt-29\" uniprot=\"A0A4E9FLN2\"/>\n <p id=\"nhr-22\" name=\"nhr-22\" uniprot=\"A8WTT1\"/>\n <p id=\"unc-62\" name=\"unc-62\" uniprot=\"A8WL06\" fullname=\"Homeobox protein unc-62\"/>\n <p id=\"unc-98\" name=\"unc-98\" uniprot=\"Q612G6\" fullname=\"Zinc finger protein unc-98\"/>\n <p id=\"zip-7\" name=\"zip-7\" uniprot=\"A8XIF4\"/>\n <p id=\"ztf-2\" name=\"ztf-2\" uniprot=\"A8Y199\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"alp-1\" b=\"aptf-3\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"y62e10a.17\" b=\"aptf-3\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"y62e10a.17\" b=\"ztf-2\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"aptf-3\" b=\"mdt-29\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"aptf-3\" b=\"hlh-3\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"aptf-3\" b=\"nhr-22\" type=\"Two-hybrid\"/>\n <i id=\"7\" a=\"aptf-3\" b=\"ztf-2\" type=\"Two-hybrid\"/>\n <i id=\"8\" a=\"zip-7\" b=\"ztf-2\" type=\"Two-hybrid\"/>\n <i id=\"9\" a=\"hlh-3\" b=\"ztf-2\" type=\"Two-hybrid\"/>\n <i id=\"10\" a=\"aptf-3\" b=\"unc-98\" type=\"Two-hybrid\"/>\n <i id=\"11\" a=\"unc-98\" b=\"ztf-2\" type=\"Two-hybrid\"/>\n <i id=\"12\" a=\"unc-98\" b=\"zip-7\" type=\"Two-hybrid\"/>\n <i id=\"13\" a=\"aptf-3\" b=\"unc-62\" type=\"Two-hybrid\"/>\n <i id=\"14\" a=\"unc-62\" b=\"ztf-2\" type=\"Two-hybrid\"/>\n <i id=\"15\" a=\"mdt-29\" b=\"unc-62\" type=\"Two-hybrid\"/>\n <i id=\"16\" a=\"hlh-3\" b=\"unc-62\" type=\"Two-hybrid\"/>\n <i id=\"17\" a=\"aptf-3\" b=\"zip-7\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Predict the protein interaction network:\n\nPROTEIN: CG13373\n UniProt ID: A0A0M4EUE9\n Organism: Drosophila busckii\n Sequence Length: 175 amino acids\n Sequence: MESSSNSLKRMRSEDDESNNNVTQTKVWVNEKINNSRDPDKMKAVHEKTTKMLFKAAANMDNRSESEDSAVPVPAAPTLNLCDQYQLIGDGNIILRDLNPDVANPTLERRISACCQRPTLIRGNCVNCTFDLCEECGYSCVECSQFICRTCVTLFGNRPEEAEHPLCELCQMFVA\n AlphaFold Structure: Available\n Structure Coverage: residues 1-175\n\nPROTEIN: CG18094\n UniProt ID: Q7K1T6\n Organism: Drosophila melanogaster\n Sequence Length: 282 amino acids\n Sequence: MCRHNQDSPRPEFLSGGDHISRDIALRLTALRETFEEVGILICTEQDDIQKWDSKSGHPRTVLLESSEHFEWQHRVHNDASQFLELFRHYKVIPNIWSLQEWSIWRTAATANRKYDTVYYITMLD...GSVDDLHRKSKQYNRYIVYDFHKVVLASNIPPCDGHLPLQPLVNNKLAKL\n AlphaFold Structure: Available\n Structure Coverage: residues 1-282\n\nPROTEIN: Epac\n UniProt ID: A8YPR5\n Organism: Calliphora vicina\n Sequence Length: 581 amino acids\n Sequence: TVATLKSGDDFGKLALINDAPRAATIVLKENNCHLLRVDKEHFNRILRDVEANTLRLQEHGKDVLVLERVAKQRGQHSAFKYTVMSGTPSKMLEHLLETRLGTQVSGVDPFLDDFLLTHIVFMPV...DGLVNFEKMHMMAQTMRTLRFCRSRSLGLEPPSPKSEGEVRSFISCLRVI\n AlphaFold Structure: Available\n Structure Coverage: residues 1-581\n Function: Belongs to the RAPGEF2 family\n\nPROTEIN: Hsp70Aa\n UniProt ID: A0A0M3QY45\n Organism: Drosophila busckii\n Sequence Length: 642 amino acids\n Sequence: MVAIGIDLGTTYSCVGVYQHGKVEIIANDQGNRTTPSYVAFTDSERLIGDAAKNQVAMNPRNTVFDAKRLIGRKYDDPKIAEDIKHWPFKVVSEGGKPKIGIEFKGEQKRFAPEEVSSMVLVKMK...LKELTQLCSPIMTKMHQQGQGQGNPNANCGQQAGGFGGAAYQGPTVEEVD\n AlphaFold Structure: Available\n Structure Coverage: residues 1-642\n Function: Belongs to the heat shock protein 70 family\n\nPROTEIN: Hsp70Ba\n UniProt ID: B4QS96\n Organism: Drosophila simulans\n Sequence Length: 643 amino acids\n Sequence: MPAIGIDLGTTYSCVGVYQHGKVEIIANDQGNRTTPSYVAFTDSERLIGDPAKNQVAMNPRNTVFDAKRLIGRKYDDPKIAEDMKHWPFKVVSDCGKPKIGVEYKGESKRFAPEEISSMVLAKMK...EELTRHCSPIMTKMHQQGAGAGAAGGPGANCGQQAGGFGGYSGPTVEEVD\n AlphaFold Structure: Available\n Structure Coverage: residues 1-643\n Function: Belongs to the heat shock protein 70 family\n\nPROTEIN: Hsp70Bb\n UniProt ID: Q9GSN4\n Organism: Drosophila mauritiana\n Sequence Length: 643 amino acids\n Sequence: MPAIGIDLGTTYSCVGVYQHGKVEIIANDQGNRTTPSYVAFTDSERLIGDPAKNQVAMNPRNTVFDAKRLIGRKYDDPKIAEDMKHWPFKVVSDCGKPKIGVEYKGESKQFAPEEISSMVLAKMK...EELTRHCSPIMTKMHQQGAGAGAAGGPGANCGQQAGGFGGYSGPTVEEVD\n AlphaFold Structure: Available\n Structure Coverage: residues 1-643\n Function: Belongs to the heat shock protein 70 family\n\nPROTEIN: Hsp70Bc\n UniProt ID: A0A2S2PCM4\n Organism: Schizaphis graminum\n Sequence Length: 166 amino acids\n Sequence: EEISSMVLTKMKETAEAYLGREVTDAVITVPAYFNDSQRQATKDAGVIAGLNVMRIINEPTAAALAYGLDKNLKGERNVLIFDLGGGTFDVSVLQIDEGSIFEVKSTAGDTHLGGEDFDNRLVCHLAEEFKRKCKKDVHSNPRALRRLRTAAERAKRTLSSSSEAT\n AlphaFold Structure: Available\n Structure Coverage: residues 1-166\n Function: Belongs to the heat shock protein 70 family\n\nPROTEIN: Pex5\n UniProt ID: A0A812QF93\n Organism: Symbiodinium necroappetens\n Sequence Length: 478 amino acids\n Sequence: VFGFVVGLLLTLRLFAAAPSRNCWEVAGLLVDNFDLPAADHGFFVEWLQYYPFRRDIFLQELIVEESDNVAFVKQLLVDISNAKLCDFCTPDDHLAETLAALDEVMPPKQQQQYNVPIAGDLRPE...YALEATEAIEQRDLKAATQIIEGVLDPAKLPKPLDHPTRPPDEILQSIGL\n AlphaFold Structure: Available\n Structure Coverage: residues 1-478\n\nPROTEIN: RecQ4\n UniProt ID: M4SZC2\n Organism: Brachionus calyciflorus\n Sequence Length: 366 amino acids\n Sequence: ELSDPKPLFSVDEQGNVPERLPDFAYKVLEKDFGHKNFKKNQEEAIIRILCGQSALAILSTGYGKSLIYQFAALMYARKYPGSIVLVVSPLISLMQDQLHNLTKSLKAASCDSTMTEKEFEFLVQ...DFNCDSGVSSLSREQEMKRLVADIRKFIFTYQSDIKLNGTIIARIFHGIG\n AlphaFold Structure: Available\n Structure Coverage: residues 1-366\n Function: Belongs to the helicase family. RecQ subfamily\n\nPROTEIN: sick\n UniProt ID: A0A0M4E746\n Organism: Drosophila busckii\n Sequence Length: 2493 amino acids\n Sequence: MVNRQIAPAYTKVNGGTAIPLPATVMVQRRNMDKVRPLPPTPNHTPSIPGLGKSGSDFNASRPNSPPSSNHTIQSLKSNNNSLRPPSIKSSHQSGIPSPSSLNATPTATAPQKHSMLDKLKLFNK...ALSNGEQQDPLLNMLMRLQEAANYSETQEQESDCASLDSNITPDSSAGAE\n AlphaFold Structure: Not available\n Function: Belongs to the Nav/unc-53 family",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg13373\" name=\"CG13373\" uniprot=\"A0A0M4EUE9\"/>\n <p id=\"cg18094\" name=\"CG18094\" uniprot=\"Q7K1T6\"/>\n <p id=\"epac\" name=\"Epac\" uniprot=\"A8YPR5\"/>\n <p id=\"hsp70aa\" name=\"Hsp70Aa\" uniprot=\"A0A0M3QY45\"/>\n <p id=\"hsp70ba\" name=\"Hsp70Ba\" uniprot=\"B4QS96\"/>\n <p id=\"hsp70bb\" name=\"Hsp70Bb\" uniprot=\"Q9GSN4\"/>\n <p id=\"hsp70bc\" name=\"Hsp70Bc\" uniprot=\"A0A2S2PCM4\"/>\n <p id=\"pex5\" name=\"Pex5\" uniprot=\"A0A812QF93\"/>\n <p id=\"recq4\" name=\"RecQ4\" uniprot=\"M4SZC2\"/>\n <p id=\"sick\" name=\"sick\" uniprot=\"A0A0M4E746\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg18094\" b=\"sick\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg18094\" b=\"pex5\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg18094\" b=\"epac\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg18094\" b=\"hsp70bb\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"cg18094\" b=\"hsp70ba\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"cg18094\" b=\"hsp70bc\" type=\"Two-hybrid\"/>\n <i id=\"7\" a=\"cg13373\" b=\"cg18094\" type=\"Two-hybrid\"/>\n <i id=\"8\" a=\"cg18094\" b=\"recq4\" type=\"Two-hybrid\"/>\n <i id=\"9\" a=\"cg18094\" b=\"hsp70aa\" type=\"Two-hybrid\"/>\n <i id=\"10\" a=\"hsp70aa\" b=\"hsp70ba\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Predict the protein interaction network for these proteins:\n\nPROTEIN: CG32364\n UniProt ID: A0A0M4EYT7\n Organism: Drosophila busckii\n Sequence Length: 230 amino acids\n Sequence: MPSMNFDKKYCTSQINGTVYMTTMKNLSEEQLTKLNAGAGEIYLSNIPKKCSAKRIMQVAVKLGEVYMLRNKIDFLRDSRGFAYLQYINETHMKNTMHALQQLFWNAKLGIRVRKSRNQRRLLLNNVDRLSPVQVYHELSKYSQYIKLCVHEVQPYYYIYVIEYRNNDKAAIAHHMLRSKMGHFGANAYIEWLDKYQENNTSQTLPSCCLQLQQPVTEQQLPAIHEKSEH\n AlphaFold Structure: Available\n Structure Coverage: residues 1-230\n\nPROTEIN: Cdk8\n UniProt ID: A0A851AMY5\n Organism: Sula dactylatra\n Sequence Length: 312 amino acids\n Sequence: KPANILVMGEGPERGRVKIADMGFARLFNSPLKPLADLDPVVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHS...GLIMTSDYQRSNPHAAYPNPGPSTSQPQSSMGYSTTSQQPPQYSHQTHRY\n AlphaFold Structure: Available\n Structure Coverage: residues 1-312\n\nPROTEIN: CycC\n UniProt ID: A0A0S2RRY1\n Organism: Streptomyces sp. NCIB 11649\n Sequence Length: 3713 amino acids\n Sequence: MRPALAGGVTGDGTDRGSVEFTGSAARPPDGDVQGVRRWRRRRHRLGGGRRFLVLERLSDAVRDGHRCPRLVRGSAVNQDGASNGLTAPNGPSQERVITAALANARLTTGDVDAVEAHGTGTTLG...LDHWSRSQDSEAYGTQEASEAEDALESALESASSSDLFDFIDNELGRAAG\n AlphaFold Structure: Not available\n Function: Antibiotic biosynthesis\n\nPROTEIN: IntS1\n UniProt ID: A0A8K0AE46\n Organism: Branchiostoma lanceolatum\n Sequence Length: 2495 amino acids\n Sequence: MPWLAELVESSEGSMEVLPVQCLCEFLLHDIGEEAAQQEDEELLEMEKSKMEMERLKQKSRKQDQLRRRLQTLLYGPDSQPNQTHEVLQYFLRRLGAQQRAGRNLAAKALSMLLAPRTPPRQRSS...RNLADYIVLCQEHSNVLVRKAFAVGVQMKIDTSNIIADAINMLRLEGYND\n AlphaFold Structure: Not available\n\nPROTEIN: IntS12\n UniProt ID: A0A212CLG1\n Organism: Cervus elaphus hippelaphus\n Sequence Length: 206 amino acids\n Sequence: KLEKNTSVDAGITRDDGKGQRKKMNPVQICPLATANMRVFGMAAAVNLELDPIFLKALGFLHSKSKDSAEKLKTLLDESLARGIDSSYRPSQKDVEPPKISSTKTVSVKQEPKTSSSLPSGNNNGKVLTTEKVKKEGEKRPADKMKSDVTEGVDVPKKPRLEKPETRSSPITVQTSKDLAMADLSSFEETSADDFAMEMGLACVVC\n AlphaFold Structure: Available\n Structure Coverage: residues 1-206\n Function: The sequence shown here is derived from an EMBL/GenBank/DDBJ whole genome shotgun (WGS) entry which is preliminary data\n\nPROTEIN: IntS14\n UniProt ID: A0A2J8T844\n Organism: Pongo abelii\n Sequence Length: 54 amino acids\n Sequence: DCGRRWARGEWGGRGPGAAFRCLLGLQVKGLGVKNNPGPALGLPATVAAAPRRL\n AlphaFold Structure: Available\n Structure Coverage: residues 1-54\n Function: The sequence shown here is derived from an EMBL/GenBank/DDBJ whole genome shotgun (WGS) entry which is preliminary data\n\nPROTEIN: IntS9\n UniProt ID: A0A212C594\n Organism: Cervus elaphus hippelaphus\n Sequence Length: 152 amino acids\n Sequence: LLQHFIESLVWGWNFFGTVFIDHLFLEFFFFHVFQELKECSGHVFVDSVPEFCLPEPHRTELCAEHRHVSLPPLFSQTELIDLSTVDVILISNYHCMMALPYITEHTGFTGTVYATEPTVQIGRLLMEELVNFIERVPKAQSASLWKNKDIQ\n AlphaFold Structure: Available\n Structure Coverage: residues 1-152\n\nPROTEIN: asun\n UniProt ID: A0A0S7EQY6\n Organism: Poeciliopsis prolifica\n Sequence Length: 289 amino acids\n Sequence: MKMFSVAHKTVFVVDHCPYMAESSRQQVECDVLTKSRAQGVIPLAPVSKSLWTCAVECSMEYCRILFDVYPKDKLVNYIVSDSEFHILNTWRREDQSTHELMSALAAVGPPNPREDPECCSILHG...GRHLASKLNILVQQHFDLASTTITNIPMKVRDLLLIPFVCAFLHQHKTLT\n AlphaFold Structure: Available\n Structure Coverage: residues 1-289\n\nPROTEIN: ey\n UniProt ID: Q9U8F7\n Organism: Drosophila melanogaster\n Sequence Length: 18 amino acids\n Sequence: HSGVNQLGGVFVGGIPAA\n AlphaFold Structure: Available\n Structure Coverage: residues 1-18\n\nPROTEIN: omd\n UniProt ID: A0A7K9B9Z0\n Organism: Dromaius novaehollandiae\n Sequence Length: 420 amino acids\n Sequence: MGILSQLAIIHLLLWAAMVVCQHEDYDFGDEYDEEPDHEHPYYFNFHPSTQHEVPHFPIPAQCARECFCPPTFPLSMYCDHRKLTTIPNIPIHIQQLYLQNNDIEAVLAGPFTNATILREINLSY...NKSTQLRTPVFRRFLTPEEYDETEDDHETSDHETEEDHETEDNYFHANFQ\n AlphaFold Structure: Available\n Structure Coverage: residues 1-420",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg32364\" name=\"CG32364\" uniprot=\"A0A0M4EYT7\"/>\n <p id=\"cdk8\" name=\"Cdk8\" uniprot=\"A0A851AMY5\"/>\n <p id=\"cycc\" name=\"CycC\" uniprot=\"A0A0S2RRY1\"/>\n <p id=\"ints1\" name=\"IntS1\" uniprot=\"A0A8K0AE46\"/>\n <p id=\"ints12\" name=\"IntS12\" uniprot=\"A0A212CLG1\"/>\n <p id=\"ints14\" name=\"IntS14\" uniprot=\"A0A2J8T844\"/>\n <p id=\"ints9\" name=\"IntS9\" uniprot=\"A0A212C594\"/>\n <p id=\"asun\" name=\"asun\" uniprot=\"A0A0S7EQY6\"/>\n <p id=\"ey\" name=\"ey\" uniprot=\"Q9U8F7\"/>\n <p id=\"omd\" name=\"omd\" uniprot=\"A0A7K9B9Z0\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"ints9\" b=\"ey\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cdk8\" b=\"cycc\" type=\"Co-fractionation\"/>\n <i id=\"3\" a=\"cdk8\" b=\"cycc\" type=\"Affinity Capture-Western\"/>\n <i id=\"4\" a=\"cdk8\" b=\"cycc\" type=\"Reconstituted Complex\"/>\n <i id=\"5\" a=\"ints1\" b=\"ints14\" type=\"Affinity Capture-Western\"/>\n <i id=\"6\" a=\"ints14\" b=\"ints9\" type=\"Affinity Capture-Western\"/>\n <i id=\"7\" a=\"ints12\" b=\"ints14\" type=\"Affinity Capture-Western\"/>\n <i id=\"8\" a=\"ints1\" b=\"ints12\" type=\"Two-hybrid\"/>\n <i id=\"9\" a=\"cdk8\" b=\"ints1\" type=\"Affinity Capture-Western\"/>\n <i id=\"10\" a=\"cdk8\" b=\"ints9\" type=\"Affinity Capture-Western\"/>\n <i id=\"11\" a=\"cycc\" b=\"ints1\" type=\"Affinity Capture-Western\"/>\n <i id=\"12\" a=\"cycc\" b=\"ints9\" type=\"Affinity Capture-Western\"/>\n <i id=\"13\" a=\"ints1\" b=\"asun\" type=\"Affinity Capture-Western\"/>\n <i id=\"14\" a=\"ints9\" b=\"asun\" type=\"Affinity Capture-Western\"/>\n <i id=\"15\" a=\"ints12\" b=\"asun\" type=\"Affinity Capture-Western\"/>\n <i id=\"16\" a=\"ints1\" b=\"ints12\" type=\"Affinity Capture-Western\"/>\n <i id=\"17\" a=\"cdk8\" b=\"ints12\" type=\"Affinity Capture-Western\"/>\n <i id=\"18\" a=\"ints12\" b=\"ints9\" type=\"Affinity Capture-Western\"/>\n <i id=\"19\" a=\"cg32364\" b=\"ints9\" type=\"Phenotypic Enhancement\"/>\n <i id=\"20\" a=\"cg32364\" b=\"ints9\" type=\"Protein-RNA\"/>\n <i id=\"21\" a=\"ints1\" b=\"ints9\" type=\"Affinity Capture-Western\"/>\n <i id=\"22\" a=\"ints1\" b=\"omd\" type=\"Affinity Capture-Western\"/>\n <i id=\"23\" a=\"ints9\" b=\"omd\" type=\"Affinity Capture-Western\"/>\n <i id=\"24\" a=\"cdk8\" b=\"cycc\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Predict the protein interaction network:\n\nPROTEIN: CG15308\n UniProt ID: Q9W2X3\n Organism: Drosophila melanogaster\n Sequence Length: 95 amino acids\n Sequence: MKFFIAAFLIAACMALAQCSVIYSPVSSVPVVRSVPVIRSVPVVRSVPVVRRVPVVRRVNVVESVPVVPSVVRVGQAPIYDAPLVQSYGGWLKQK\n AlphaFold Structure: Available\n Structure Coverage: residues 1-95\n\nPROTEIN: CG17107\n UniProt ID: Q9VKS2\n Organism: Drosophila melanogaster\n Sequence Length: 96 amino acids\n Sequence: MKFLAICIFLIFALVAVQAHPGGFGGFGGGGGGGGRGGGGGGGGVGGVGGSNAVANANAAATADSRGGGPASASASATATANASSGGGGGGHGRHG\n AlphaFold Structure: Available\n Structure Coverage: residues 1-96\n\nPROTEIN: CG5656\n UniProt ID: M9PD70\n Full Name: alkaline phosphatase\n Organism: Drosophila melanogaster\n Sequence Length: 530 amino acids\n Sequence: MRALRFFAALALQLTACSSQYKYGPEQSWDLDSISELKSKEFWFHDAQRTLYNKLSTPPNQYRAKNVIFFLGDGMSVPTVTAGRIFDGQLRGVVGERNRLEFEKFNYVGLSKTYCVNKQVADSAC...VVEYLLQGPWSHLFTGVYEQSTLPHLMGFASCLGPGITYCDLQPKARYSP\n AlphaFold Structure: Available\n Structure Coverage: residues 1-530\n\nPROTEIN: fra\n UniProt ID: A0A024B3G5\n Full Name: Major strawberry allergen Fra a 1.06\n Organism: Fragaria ananassa\n Sequence Length: 160 amino acids\n Sequence: MGVFTYETEFTSVIPPPRLFKAFILDADNLIPKIAPQAVKCAEIVEGDGGVGTIKKITFGEGSQFGSVTHKIDGIDKENFVYSYSLVEGDALSDKIEKISYETKLVASSDGGSVIKSTSNYHTKGDVEIKEEHVKAGKEKASHLFKLVEDYLLANPNEYC\n AlphaFold Structure: Available\n Structure Coverage: residues 1-160\n Function: Possesses ribonuclease activity in vitro",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg15308\" name=\"CG15308\" uniprot=\"Q9W2X3\"/>\n <p id=\"cg17107\" name=\"CG17107\" uniprot=\"Q9VKS2\"/>\n <p id=\"cg5656\" name=\"CG5656\" uniprot=\"M9PD70\" fullname=\"alkaline phosphatase\"/>\n <p id=\"fra\" name=\"fra\" uniprot=\"A0A024B3G5\" fullname=\"Major strawberry allergen Fra a 1.06\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg15308\" b=\"cg5656\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg17107\" b=\"cg5656\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg5656\" b=\"fra\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a list of proteins with their sequence and structural information, predict all likely interactions between them in compressed BioPAX format. Use <proteins> with <p> elements and <interactions> with <i> elements.",
"role": "system"
},
{
"content": "Predict the protein interaction network:\n\nPROTEIN: CG12992\n UniProt ID: Q5BHV2\n Organism: Drosophila melanogaster\n Sequence Length: 429 amino acids\n Sequence: MPHKKFPRMSQAQLKRLIKSQNQNIAKAACILEPPKIIQQPSMRQSIIPPNPAYSKKQGKNAARPNSERAGKVPMQGLNHVVPEDTVKQHNQSKQMQRNRRNPSSKMQQNGNEASKQEKPNQHED...PLISETYQAEAQQHPCWPVYIPEYVSHFMFGEPQDANASCSRNSNHGNKM\n AlphaFold Structure: Available\n Structure Coverage: residues 1-429\n\nPROTEIN: Sxl\n UniProt ID: A0A140B9G0\n Organism: Drosophila melanogaster\n Sequence Length: 288 amino acids\n Sequence: YAFSPQDTEFSFPSSSSRRGYNDFPGCGGSGGNGGSANNLGGGNMCHLPPMASNNSLNNLCGLSLGSGGSDDLMNDPRASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSFGY...QPLSVRLAEEHGKAKAAHFMSQMGVVPANVPPPPPQPPAHMAAAFNMMHR\n AlphaFold Structure: Available\n Structure Coverage: residues 1-288\n\nPROTEIN: ci\n UniProt ID: D4GNN4\n Organism: Pantoea ananatis (strain LMG 20103)\n Sequence Length: 198 amino acids\n Sequence: MSIKMSVYTNFKFPNSSAEALDRVVDAYGFTMKMQLADHLGIAASSLSARYKRDVFPSDIVLQCVMETGADLQWLITGKGSKFSESKPDTPTLVRKKLISGKIEEAGYVMLDKALYAPLKQEPRSAFLLLAETTQYIIDTDFEDMHDGVWLVEIEGTASVRTLTRIPVRKVHVSGIGVAFDCGIDDIRLIGRVVLTIQ\n AlphaFold Structure: Available\n Structure Coverage: residues 1-198\n\nPROTEIN: grim\n UniProt ID: A0A7S6VG14\n Organism: Drosophila suzukii\n Sequence Length: 119 amino acids\n Sequence: MAIAYFIPDQAQLLAESYQQNGQQAATSPRTAATPAAAPQQPQQSQQQQQHQQQQNRPQFRANISVPLGSQQGSMTMSEFGCWDLLAQIFCYALRIYSYNSSQRRPTVIQISFEISSGS\n AlphaFold Structure: Available\n Structure Coverage: residues 1-119\n\nPROTEIN: obst-A\n UniProt ID: A0A0M4ETU9\n Organism: Drosophila busckii\n Sequence Length: 236 amino acids\n Sequence: MKLFLCAIAVMLCVSATTAAGSGFTCPKPDGQFPDEVQCDKYYLCDDGVAKAKLCPDGLVFDPLNRKINKCDQPFNVDCEDRTELQEPKSTKYCPRKNGFFAHPESSVCNIFYNCIEGDALEMKCTTGLHFDEYSGTCVWPDTAKREGCGITEKKSESGFSCPKDQPKTDVRGQVVTHPRYPHPTDCQKFYVCLNGEDPRDLGCQLGEVYNDVSEMCDAPENVPGCEDWYKDVDKN\n AlphaFold Structure: Available\n Structure Coverage: residues 1-236\n\nPROTEIN: ptc\n UniProt ID: A0A346A6L3\n Organism: Drosophila subpulchrella\n Sequence Length: 1047 amino acids\n Sequence: GKARGSRTAIYLRSVFQSHLETLGSSVQKHAGKVLFVAILVLSTFCVGLKSAQIHSKVHQLWIQEGGRLEAEMAYTQKTIGEDEAATHQLLIQTTHDPNASVLHPQALLAHLEVLVKATAVKVHL...MMLCSNVLISLGFMTSVGNRQRRVQLGMQMALGPLVHGMLTSGVAVFMLS\n AlphaFold Structure: Not available\n\nPROTEIN: serp\n UniProt ID: Q26017\n Organism: Plasmodium falciparum\n Sequence Length: 145 amino acids\n Sequence: MIFFNFKLNRMICPIFFLYIINVLFTQYFIKCEGNKVTVISHNNGHNDNLDVNKNGVISQENVFDTSESLNLPSNKKVGSDDLNTTTISFTVPDNLENEVKVVSSSESGKGATVSHTKVTSEGLSDTQPNVTQSVSSSTHTPGSL\n AlphaFold Structure: Available\n Structure Coverage: residues 1-145\n\nPROTEIN: verm\n UniProt ID: A0A3G5EAA8\n Organism: Actinomadura sp. XM-4-3\n Sequence Length: 223 amino acids\n Sequence: MAGQVELSERLLDYVRSVSLRDDAVLRDLVAETAAMPPLHAMVTMPEEGQLLALLVGLTGAGRVLEIGTFTGYSTLCMARALPPGGRIVTCDINARWTAVAERYWARAGVADRIELRLGDAAETMAKLLAERGPGTFDLVFVDADKTGYAHYYEQALTHLRPGGLVVLDNTLFFGRVADPEADDPDTEAIRALNASLHRDTRVDLSLLVMADGITLARKNTTS\n AlphaFold Structure: Available\n Structure Coverage: residues 1-223",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg12992\" name=\"CG12992\" uniprot=\"Q5BHV2\"/>\n <p id=\"sxl\" name=\"Sxl\" uniprot=\"A0A140B9G0\"/>\n <p id=\"ci\" name=\"ci\" uniprot=\"D4GNN4\"/>\n <p id=\"grim\" name=\"grim\" uniprot=\"A0A7S6VG14\"/>\n <p id=\"obst-a\" name=\"obst-A\" uniprot=\"A0A0M4ETU9\"/>\n <p id=\"ptc\" name=\"ptc\" uniprot=\"A0A346A6L3\"/>\n <p id=\"serp\" name=\"serp\" uniprot=\"Q26017\"/>\n <p id=\"verm\" name=\"verm\" uniprot=\"A0A3G5EAA8\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg12992\" b=\"serp\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"sxl\" b=\"serp\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg12992\" b=\"sxl\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"ci\" b=\"serp\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"ptc\" b=\"serp\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"grim\" b=\"serp\" type=\"Two-hybrid\"/>\n <i id=\"7\" a=\"ci\" b=\"verm\" type=\"Two-hybrid\"/>\n <i id=\"8\" a=\"ci\" b=\"ptc\" type=\"Phenotypic Enhancement\"/>\n <i id=\"9\" a=\"ci\" b=\"ptc\" type=\"Phenotypic Suppression\"/>\n <i id=\"10\" a=\"serp\" b=\"verm\" type=\"Phenotypic Enhancement\"/>\n <i id=\"11\" a=\"obst-a\" b=\"serp\" type=\"Affinity Capture-Western\"/>\n <i id=\"12\" a=\"sxl\" b=\"ptc\" type=\"Affinity Capture-Western\"/>\n <i id=\"13\" a=\"sxl\" b=\"ci\" type=\"Affinity Capture-Western\"/>\n <i id=\"14\" a=\"ci\" b=\"ptc\" type=\"Affinity Capture-Western\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Known protein network in compressed BioPAX format:\n<biopax>\n <proteins>\n <p id=\"cg15080\" name=\"CG15080\" uniprot=\"A0A0M4EI06\"/>\n <p id=\"cg7158\" name=\"CG7158\" uniprot=\"A0A0M4EN27\"/>\n <p id=\"rab30\" name=\"Rab30\" uniprot=\"Q9VM50\"/>\n <p id=\"sgf11\" name=\"Sgf11\" uniprot=\"A0A812ANH5\"/>\n <p id=\"tpc1\" name=\"Tpc1\" uniprot=\"A0A812PDN9\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg15080\" b=\"cg7158\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg7158\" b=\"sgf11\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg7158\" b=\"tpc1\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg7158\" b=\"rab30\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>\n\nNew protein to integrate:\nPROTEIN: Cpr11A\n UniProt ID: A0AB39YXT4\n Organism: Drosophila suzukii\n Sequence Length: 215 amino acids\n Sequence: MKSFLILLGLAALAAADVKHLTDRNLDLFKYNPSDVYTLPEDIDDDKPAVHFSGDVMKAKTETLQNYNSGKKFKLELKTQNGIQVSSVGKLKDDKTFVVSGSYSFTGADGKRYKTRYTADEFGYHPITELDLDIPEPQPLGVTAQRQTVDPSSLLGNKNRFQFLQQTLDSEQGPLRGSGQSGDDYSYTSPYGHGYDYQPPQVPLSTPSRLYLPTA\n AlphaFold Structure: Not available\n\nPredict the interactions for Cpr11A in compressed BioPAX format:",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg15080\" name=\"CG15080\" uniprot=\"A0A0M4EI06\"/>\n <p id=\"cg7158\" name=\"CG7158\" uniprot=\"A0A0M4EN27\"/>\n <p id=\"cpr11a\" name=\"Cpr11A\" uniprot=\"A0AB39YXT4\"/>\n <p id=\"rab30\" name=\"Rab30\" uniprot=\"Q9VM50\"/>\n <p id=\"sgf11\" name=\"Sgf11\" uniprot=\"A0A812ANH5\"/>\n <p id=\"tpc1\" name=\"Tpc1\" uniprot=\"A0A812PDN9\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg15080\" b=\"cpr11a\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg7158\" b=\"cpr11a\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Predict the protein interaction network for these proteins in compressed BioPAX format:\n\nPROTEIN: asd-2\n UniProt ID: A8XGG9\n Organism: Caenorhabditis briggsae\n Sequence Length: 397 amino acids\n Sequence: MTHASTEHLTPNGSTNGISTSQQQQYSVEYLSQLLKDKKQLAAFPNVFHHLERLADDEISKVRVALFQFEFTKDNVTLPDAEGDITVHTEKVFVPAKEHPDYNFVGRILGPRGMTAKQLEQETGC...AAQAQAQAQYGALAAAAANQAGGQQYAEYAGVDLTSQQGAHGGYYVRRWA\n AlphaFold Structure: Available\n Structure Coverage: residues 1-397\n\nPROTEIN: eya-1\n UniProt ID: O17670\n Full Name: Protein phosphatase eya-1\n Organism: Caenorhabditis elegans\n Sequence Length: 503 amino acids\n Sequence: MLPDSEGQKLKTFLLGTGTTLDPSLDPTGNSNFSMATTSDSSTIWTALPASQPGDKDIPTVDLAAISEAYGSTSSTTSLTSSVTSQYQYNSYPQYAMYTSANPANYYQQVTANLRAGTTAFPYSL...RFGKKCSFICITSGDTANSAKRLNIPVWPLNSNTDLDKLYSALDNFLLGG\n AlphaFold Structure: Available\n Structure Coverage: residues 1-503\n Function: Tyrosine protein phosphatase (By similarity). Acts probably as a transcription regulator in the embryonic and postembryonic development of several tissues including pharynx, vulva and gonads (PubMed:1...\n\nPROTEIN: let-7\n Full Name: let-7\n AlphaFold Structure: Not available\n\nPROTEIN: ptb-1\n UniProt ID: A8WSY1\n Organism: Caenorhabditis briggsae\n Sequence Length: 610 amino acids\n Sequence: QRGPDDLQLSLRNGGAAATAAVTSAGAPGAGYFANVMTADSEPKKAKLDPSLYSSQFYTTPLHHGLATSGAPVAVAPAATTAQLLTGNPITQIQGIQLSTLPQCNQTSSATTTPVSRVVHVRNIP...KAFKFFPKDHKMALCQLEDIETAIDALIKMHNHKLAENAHLRVSFSKSGI\n AlphaFold Structure: Available\n Structure Coverage: residues 1-610\n\nPROTEIN: shn-1\n UniProt ID: A8WT89\n Organism: Caenorhabditis briggsae\n Sequence Length: 1137 amino acids\n Sequence: MNQEEDPVNLQIFVPELNVRILESSINVFILFQKFLAVTQNDFIWDVKRKLLATLPQALPQAFNYGLFLPPCDGRAGKFLLEDRTIRDYPFTDCVPYLELKYKKRVYKMLNLDEKQLKAMHTKGQ...HLSEYSPAFRNQRIDGRCLRQCDRSRFTQLGVTRIAHRQIIEAALRGILQ\n AlphaFold Structure: Available\n Structure Coverage: residues 1-1137\n\nPROTEIN: tag-262\n UniProt ID: A0A0P1B745\n Organism: Plasmopara halstedii\n Sequence Length: 310 amino acids\n Sequence: MVNLDDEFARFEAEIQSLEQQTPNETTSIEDANDLPAKKIKLGLTAPSKEVVVKPKVYMAPPRPAPFKKTETSVDDSIEHIDGRSGLLNTLEDVAAHRGALSGFPAGTSGEHAAIASTNLMSGSY...DCAKALREMNGKYIGNRPVKLSKSKWQDRNIDVAKKKIRKRKRDKHHLFN\n AlphaFold Structure: Available\n Structure Coverage: residues 1-310",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"asd-2\" name=\"asd-2\" uniprot=\"A8XGG9\"/>\n <p id=\"eya-1\" name=\"eya-1\" uniprot=\"O17670\" fullname=\"Protein phosphatase eya-1\"/>\n <p id=\"let-7\" name=\"let-7\"/>\n <p id=\"ptb-1\" name=\"ptb-1\" uniprot=\"A8WSY1\"/>\n <p id=\"shn-1\" name=\"shn-1\" uniprot=\"A8WT89\"/>\n <p id=\"tag-262\" name=\"tag-262\" uniprot=\"A0A0P1B745\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"eya-1\" b=\"ptb-1\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"asd-2\" b=\"eya-1\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"asd-2\" b=\"ptb-1\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"ptb-1\" b=\"tag-262\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"asd-2\" b=\"tag-262\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"let-7\" b=\"ptb-1\" type=\"Protein-RNA\"/>\n <i id=\"7\" a=\"ptb-1\" b=\"shn-1\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Complete this partial protein network in compressed BioPAX format:\n<biopax>\n <proteins>\n <p id=\"act-5\" name=\"act-5\" uniprot=\"A8XS95\"/>\n <p id=\"agef-1\" name=\"agef-1\" uniprot=\"A8XWC0\"/>\n <p id=\"elb-1\" name=\"elb-1\" uniprot=\"A8XHD3\"/>\n <p id=\"elc-1\" name=\"elc-1\" uniprot=\"Q9BKS1\" fullname=\"Elongin-C\"/>\n <p id=\"lin-35\" name=\"lin-35\" uniprot=\"A8WW47\"/>\n <p id=\"lmn-1\" name=\"lmn-1\" uniprot=\"A8XF91\"/>\n <p id=\"lrr-1\" name=\"lrr-1\" uniprot=\"A8WUM8\"/>\n <p id=\"meg-3\" name=\"meg-3\" uniprot=\"A0A5K4EK08\"/>\n <p id=\"spk-1\" name=\"spk-1\" uniprot=\"Q03563\" fullname=\"Serine/threonine-protein kinase spk-1\"/>\n <p id=\"usp-33\" name=\"usp-33\" uniprot=\"A8X475\" fullname=\"Ubiquitin carboxyl-terminal hydrolase\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"elb-1\" b=\"elc-1\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"lin-35\" b=\"lmn-1\" type=\"Phenotypic Enhancement\"/>\n <i id=\"3\" a=\"elb-1\" b=\"lin-35\" type=\"Phenotypic Enhancement\"/>\n <i id=\"4\" a=\"lin-35\" b=\"lrr-1\" type=\"Phenotypic Enhancement\"/>\n <i id=\"5\" a=\"elc-1\" b=\"lrr-1\" type=\"Affinity Capture-Western\"/>\n <i id=\"6\" a=\"elb-1\" b=\"lrr-1\" type=\"Affinity Capture-Western\"/>\n <i id=\"7\" a=\"agef-1\" b=\"elb-1\" type=\"Two-hybrid\"/>\n <i id=\"8\" a=\"elb-1\" b=\"elc-1\" type=\"Co-fractionation\"/>\n <i id=\"9\" a=\"elb-1\" b=\"elc-1\" type=\"Co-purification\"/>\n <i id=\"10\" a=\"lin-35\" b=\"meg-3\" type=\"Affinity Capture-MS\"/>\n <i id=\"11\" a=\"meg-3\" b=\"spk-1\" type=\"Affinity Capture-MS\"/>\n <i id=\"12\" a=\"elc-1\" b=\"meg-3\" type=\"Affinity Capture-MS\"/>\n <i id=\"13\" a=\"elb-1\" b=\"meg-3\" type=\"Affinity Capture-MS\"/>\n <i id=\"14\" a=\"lmn-1\" b=\"meg-3\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"act-5\" name=\"act-5\" uniprot=\"A8XS95\"/>\n <p id=\"agef-1\" name=\"agef-1\" uniprot=\"A8XWC0\"/>\n <p id=\"elb-1\" name=\"elb-1\" uniprot=\"A8XHD3\"/>\n <p id=\"elc-1\" name=\"elc-1\" uniprot=\"Q9BKS1\" fullname=\"Elongin-C\"/>\n <p id=\"lin-35\" name=\"lin-35\" uniprot=\"A8WW47\"/>\n <p id=\"lmn-1\" name=\"lmn-1\" uniprot=\"A8XF91\"/>\n <p id=\"lrr-1\" name=\"lrr-1\" uniprot=\"A8WUM8\"/>\n <p id=\"meg-3\" name=\"meg-3\" uniprot=\"A0A5K4EK08\"/>\n <p id=\"spk-1\" name=\"spk-1\" uniprot=\"Q03563\" fullname=\"Serine/threonine-protein kinase spk-1\"/>\n <p id=\"usp-33\" name=\"usp-33\" uniprot=\"A8X475\" fullname=\"Ubiquitin carboxyl-terminal hydrolase\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"act-5\" b=\"elb-1\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"elb-1\" b=\"elc-1\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"lin-35\" b=\"lmn-1\" type=\"Phenotypic Enhancement\"/>\n <i id=\"4\" a=\"elb-1\" b=\"lin-35\" type=\"Phenotypic Enhancement\"/>\n <i id=\"5\" a=\"lin-35\" b=\"lrr-1\" type=\"Phenotypic Enhancement\"/>\n <i id=\"6\" a=\"elc-1\" b=\"lrr-1\" type=\"Affinity Capture-Western\"/>\n <i id=\"7\" a=\"elb-1\" b=\"lrr-1\" type=\"Affinity Capture-Western\"/>\n <i id=\"8\" a=\"elb-1\" b=\"spk-1\" type=\"Two-hybrid\"/>\n <i id=\"9\" a=\"elb-1\" b=\"lmn-1\" type=\"Two-hybrid\"/>\n <i id=\"10\" a=\"agef-1\" b=\"elb-1\" type=\"Two-hybrid\"/>\n <i id=\"11\" a=\"elb-1\" b=\"elc-1\" type=\"Co-fractionation\"/>\n <i id=\"12\" a=\"elb-1\" b=\"usp-33\" type=\"Co-fractionation\"/>\n <i id=\"13\" a=\"elb-1\" b=\"elc-1\" type=\"Co-purification\"/>\n <i id=\"14\" a=\"elc-1\" b=\"lrr-1\" type=\"Two-hybrid\"/>\n <i id=\"15\" a=\"lin-35\" b=\"meg-3\" type=\"Affinity Capture-MS\"/>\n <i id=\"16\" a=\"meg-3\" b=\"spk-1\" type=\"Affinity Capture-MS\"/>\n <i id=\"17\" a=\"act-5\" b=\"meg-3\" type=\"Affinity Capture-MS\"/>\n <i id=\"18\" a=\"elc-1\" b=\"meg-3\" type=\"Affinity Capture-MS\"/>\n <i id=\"19\" a=\"elb-1\" b=\"meg-3\" type=\"Affinity Capture-MS\"/>\n <i id=\"20\" a=\"lmn-1\" b=\"meg-3\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Generate a protein network in compressed BioPAX format with the following properties:\n- Proteins: CG10754, CG18522, CG30324, CG31955, Mst84Dd, Sgt, dar1, hale, kn, nudE\n- Network density: approximately 0.27\n- Hub proteins (highly connected): dar1, hale\n- Total interactions: approximately 12",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg10754\" name=\"CG10754\" uniprot=\"Q8I173\"/>\n <p id=\"cg18522\" name=\"CG18522\" uniprot=\"A0A0M4ENC1\"/>\n <p id=\"cg30324\" name=\"CG30324\" uniprot=\"A0A0M4EBB6\"/>\n <p id=\"cg31955\" name=\"CG31955\" uniprot=\"Q8IQ04\"/>\n <p id=\"mst84dd\" name=\"Mst84Dd\" uniprot=\"Q01645\" fullname=\"Male-specific sperm protein Mst84Dd\"/>\n <p id=\"sgt\" name=\"Sgt\" uniprot=\"A0A0H5C3I7\"/>\n <p id=\"dar1\" name=\"dar1\" uniprot=\"A0A0M4EP90\"/>\n <p id=\"hale\" name=\"hale\" uniprot=\"Q8T3W6\"/>\n <p id=\"kn\" name=\"kn\" uniprot=\"S5MGZ4\"/>\n <p id=\"nude\" name=\"nudE\" uniprot=\"A8JNQ0\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg10754\" b=\"dar1\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"dar1\" b=\"nude\" type=\"Phenotypic Suppression\"/>\n <i id=\"3\" a=\"dar1\" b=\"kn\" type=\"Phenotypic Suppression\"/>\n <i id=\"4\" a=\"cg31955\" b=\"dar1\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"sgt\" b=\"dar1\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"dar1\" b=\"hale\" type=\"Two-hybrid\"/>\n <i id=\"7\" a=\"mst84dd\" b=\"dar1\" type=\"Two-hybrid\"/>\n <i id=\"8\" a=\"mst84dd\" b=\"hale\" type=\"Two-hybrid\"/>\n <i id=\"9\" a=\"cg18522\" b=\"dar1\" type=\"Two-hybrid\"/>\n <i id=\"10\" a=\"cg18522\" b=\"hale\" type=\"Two-hybrid\"/>\n <i id=\"11\" a=\"cg30324\" b=\"dar1\" type=\"Two-hybrid\"/>\n <i id=\"12\" a=\"cg30324\" b=\"hale\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Generate a protein network in compressed BioPAX format with the following properties:\n- Proteins: CG9593, RpL34b, RpS13, Tequila, mRpL38\n- Network density: approximately 0.40\n- Hub proteins (highly connected): CG9593, RpS13\n- Total interactions: approximately 4",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg9593\" name=\"CG9593\" uniprot=\"A0A0M5J5H5\"/>\n <p id=\"rpl34b\" name=\"RpL34b\" uniprot=\"A0A812UYZ1\"/>\n <p id=\"rps13\" name=\"RpS13\" uniprot=\"G9HRG1\"/>\n <p id=\"tequila\" name=\"Tequila\" uniprot=\"Q9VST9\"/>\n <p id=\"mrpl38\" name=\"mRpL38\" uniprot=\"A0A8S3UCH7\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg9593\" b=\"rps13\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg9593\" b=\"mrpl38\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg9593\" b=\"tequila\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg9593\" b=\"rpl34b\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Predict the protein interaction network for these proteins in compressed BioPAX format:\n\nPROTEIN: CG2678\n UniProt ID: A0A6I8VZQ2\n Organism: Drosophila pseudoobscura pseudoobscura\n Sequence Length: 329 amino acids\n Sequence: MECVCRVCLDGSVPLVDIFAEISDLRLNLYESSPACVISKLAPEHSVVRGDSMPQFICLSCIHGVQTAYRYKLLLDKSFANYQQLSLNNTKQKHYSLVLLSVSGNEETYTIENIYEEEDRMRAND...SNLEVLGKKLNLTCQECGRIFLLKRSLDKHTCHHSTNVRRTSFPVHAVRR\n AlphaFold Structure: Available\n Structure Coverage: residues 1-329\n\nPROTEIN: CG4061\n UniProt ID: X2JI07\n Full Name: RNA 3'-terminal phosphate cyclase\n Organism: Drosophila melanogaster\n Sequence Length: 361 amino acids\n Sequence: MDAEKMLEIDGSYLEGGGQALRNALSLSCILGKPVRVVKIRASRPSPGLSHQHLHGLNLLRDITNADVVGNYLLSSTVEFTPRTILDNTYRVETHTAASITLIYQMALPVLLFAGRPSRLIVSGG...TMRTGKLTNHTRTAINVAEQMTGVKFDVAMEPGGQMLVSCKGLGHVNKLI\n AlphaFold Structure: Available\n Structure Coverage: residues 1-361\n\nPROTEIN: CG4853\n UniProt ID: A0A0M4E8K2\n Organism: Drosophila busckii\n Sequence Length: 714 amino acids\n Sequence: MDENILNAVESLFGKDVKIVDCETSSSVQQEEVLLINGVPVKLDGMPEDDASAIKSALLDGQMPAVEHLNQLLFRAGLAQQPIEVETSLTVKSSLTTTEEVLVSRNGHVLDERTVETKEHFNHHS...PYEQLPSVLAYLQKTEVLTDASLMKASYDCELPEGPGEKDHYKTLKASKK\n AlphaFold Structure: Available\n Structure Coverage: residues 1-714\n\nPROTEIN: CG6353\n UniProt ID: A0A0M4EH88\n Organism: Drosophila busckii\n Sequence Length: 156 amino acids\n Sequence: MEVEFSKENFLLPETKYEYLDHTADVQLHGWGSSLQEAFEQCGVAMFGYMTELEYVSVESCFEIEAKGDDIEGLLFHFLDELLYLFSVEPFLVCKKLEITKFDLDNFEIVCRCYGEPFELGKHPQGTEVKAITYSAMQVVQDKERNHYEVFVIIDI\n AlphaFold Structure: Available\n Structure Coverage: residues 1-156\n Function: Belongs to the archease family\n\nPROTEIN: Pten\n UniProt ID: Q9V3L4\n Full Name: Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN\n Organism: Drosophila melanogaster\n Sequence Length: 509 amino acids\n Sequence: MANTISLMSNVIRNVVSKKRIRYKEKGYDLDLTYINDNIIAMGYPAPDKLEGLFRNRLEDVFKLLEENHAQHYKIYNLCSERSYDVAKFRGRVAVYPFDDHNPPTIELIQRFCSDVDMWLKEDSS...WQNSEVHITSDTRSINENKNINYNSYITCKQSSPKFNCGTEDGEEDWESE\n AlphaFold Structure: Available\n Structure Coverage: residues 1-509\n\nPROTEIN: Rac1\n UniProt ID: M9PBH7\n Organism: Drosophila melanogaster\n Sequence Length: 192 amino acids\n Sequence: MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDAKPINLGLWDTAGQEDYDRLRPLSYPQTDVFLICFSLVNPASFENVRAKWYPEVRHHCPSTPIILVGTKLDLRDDKNTIEKLRDKKLAPITYPQGLAMAKEIGAVKYLECSALTQKGLKTVFDEAIRSVLCPVLQPKSKRKCALL\n AlphaFold Structure: Available\n Structure Coverage: residues 1-192\n\nPROTEIN: Tom20\n UniProt ID: E3TEB4\n Organism: Ictalurus punctatus\n Sequence Length: 146 amino acids\n Sequence: MMGGRTSAIAAGVGAALLVGYCIYFDRKRRSDPNFKSKLRERRKKQKAAQEKAGLSRLPDLKDAEAVQKFFLEEIQLGEELLAQGDYEKGVDHLTNAIAVCGQPQQLLQVLQQTLPPPVFQMLLTKLPTISQRIVSAQSLSDDDIE\n AlphaFold Structure: Available\n Structure Coverage: residues 1-146\n\nPROTEIN: Xbp1\n UniProt ID: A2T718\n Organism: Pan troglodytes\n Sequence Length: 75 amino acids\n Sequence: VVVAAAAPNPADGTPKVLLLSGQPASAAGAPAGQALPLMVPAQRGASPEAASGGLPQARKRQRLTHLSPEEKALR\n AlphaFold Structure: Available\n Structure Coverage: residues 1-75",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg2678\" name=\"CG2678\" uniprot=\"A0A6I8VZQ2\"/>\n <p id=\"cg4061\" name=\"CG4061\" uniprot=\"X2JI07\" fullname=\"RNA 3'-terminal phosphate cyclase\"/>\n <p id=\"cg4853\" name=\"CG4853\" uniprot=\"A0A0M4E8K2\"/>\n <p id=\"cg6353\" name=\"CG6353\" uniprot=\"A0A0M4EH88\"/>\n <p id=\"pten\" name=\"Pten\" uniprot=\"Q9V3L4\" fullname=\"Phosphatidylinositol 3,4,5-trisphosphate 3-phosphatase and dual-specificity protein phosphatase PTEN\"/>\n <p id=\"rac1\" name=\"Rac1\" uniprot=\"M9PBH7\"/>\n <p id=\"tom20\" name=\"Tom20\" uniprot=\"E3TEB4\"/>\n <p id=\"xbp1\" name=\"Xbp1\" uniprot=\"A2T718\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"cg2678\" b=\"cg4061\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg4061\" b=\"cg4853\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"cg4061\" b=\"rac1\" type=\"Phenotypic Suppression\"/>\n <i id=\"4\" a=\"cg4061\" b=\"cg6353\" type=\"Phenotypic Suppression\"/>\n <i id=\"5\" a=\"cg4061\" b=\"pten\" type=\"Phenotypic Suppression\"/>\n <i id=\"6\" a=\"cg4061\" b=\"xbp1\" type=\"Phenotypic Suppression\"/>\n <i id=\"7\" a=\"pten\" b=\"rac1\" type=\"Phenotypic Suppression\"/>\n <i id=\"8\" a=\"cg4061\" b=\"tom20\" type=\"Proximity Label-MS\"/>\n <i id=\"9\" a=\"rac1\" b=\"tom20\" type=\"Proximity Label-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "You are a protein interaction prediction system. Given a known protein network in compressed BioPAX format and a new protein with sequence and structural information, predict which proteins in the network the new protein will interact with. Generate the interactions in compressed BioPAX format.",
"role": "system"
},
{
"content": "Network:\n<biopax>\n <proteins>\n <p id=\"cg30089\" name=\"CG30089\" uniprot=\"A0A0M5JAD0\"/>\n <p id=\"cg32809\" name=\"CG32809\" uniprot=\"A0A8X7CTA0\"/>\n <p id=\"cg8065\" name=\"CG8065\" uniprot=\"Q5BHV0\"/>\n <p id=\"ckiialpha-i3\" name=\"CkIIalpha-i3\" uniprot=\"A0AB39ZGT3\"/>\n <p id=\"e2f2\" name=\"E2f2\" uniprot=\"A0A250YI81\"/>\n <p id=\"epac\" name=\"Epac\" uniprot=\"A8YPR5\"/>\n <p id=\"nimc1\" name=\"NimC1\" uniprot=\"A0A0M3QTV7\"/>\n </proteins>\n <interactions/>\n</biopax>\n\nNew to integrate:\nPROTEIN: janA\n UniProt ID: A0A836EXL9\n Organism: Pseudoatta argentina\n Sequence Length: 1138 amino acids\n Sequence: MNLSSVESSENAEALLVRTVVIGQTILVNPRRPRRNDQVNELDAFVVATITTLFQWSTVLHAMLAILNMKSKGRTKCDMHDQRLSLKKVVTQLARQSCETSTSLYGELRLLVSTHTERACTFLVN...PAEPKNSSCGPPEGPCQPVEPPGYPSKPKPQKKSFSVQCPPKKPCKKEKC\n AlphaFold Structure: Available\n Structure Coverage: residues 1-1138\n Function: JanA and janB regulate somatic sex differentiation\n\nPredict for janA:",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"cg30089\" name=\"CG30089\" uniprot=\"A0A0M5JAD0\"/>\n <p id=\"cg32809\" name=\"CG32809\" uniprot=\"A0A8X7CTA0\"/>\n <p id=\"cg8065\" name=\"CG8065\" uniprot=\"Q5BHV0\"/>\n <p id=\"ckiialpha-i3\" name=\"CkIIalpha-i3\" uniprot=\"A0AB39ZGT3\"/>\n <p id=\"e2f2\" name=\"E2f2\" uniprot=\"A0A250YI81\"/>\n <p id=\"epac\" name=\"Epac\" uniprot=\"A8YPR5\"/>\n <p id=\"nimc1\" name=\"NimC1\" uniprot=\"A0A0M3QTV7\"/>\n <p id=\"jana\" name=\"janA\" uniprot=\"A0A836EXL9\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"e2f2\" b=\"jana\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"cg30089\" b=\"jana\" type=\"Two-hybrid\"/>\n <i id=\"3\" a=\"ckiialpha-i3\" b=\"jana\" type=\"Two-hybrid\"/>\n <i id=\"4\" a=\"cg32809\" b=\"jana\" type=\"Two-hybrid\"/>\n <i id=\"5\" a=\"epac\" b=\"jana\" type=\"Two-hybrid\"/>\n <i id=\"6\" a=\"cg8065\" b=\"jana\" type=\"Two-hybrid\"/>\n <i id=\"7\" a=\"nimc1\" b=\"jana\" type=\"Two-hybrid\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
[
{
"content": "Predict the protein interaction network:\n\nPROTEIN: C44C10.4\n UniProt ID: Q18616\n Full Name: Structural maintenance of chromosomes-like protein 1\n Organism: Caenorhabditis elegans\n Sequence Length: 537 amino acids\n Sequence: MTYPQQRLLTVDILNFKCYQHHKSFGPFDHVTTFIGMNGCGKSIMIEAIAFVFGEDLPDPKNPHNEHLFYDYNIRCVVSLKFEMPDGSTKRFTRIGLKTTYTYMIFNKYVTEEEYLLELGKMNFR...VIDDIDRNLYHEASKKIEPYLSRQKQTQFIVTTKEDSYFTEVTKTITLEN\n AlphaFold Structure: Available\n Structure Coverage: residues 1-537\n Function: Acts as a modulator of condensin function, possibly by binding to the condensin SMC subunits and thereby inhibiting their function. Negatively regulates the condensin I complex in mitotic chromosome s...\n\nPROTEIN: dpff-1\n UniProt ID: A8X7Y2\n Organism: Caenorhabditis briggsae\n Sequence Length: 377 amino acids\n Sequence: MISENGYMDLMRNCIKWNSRQMEDRKKRLRFPYYEHQTATAQREARFATRTADHAYSSNDPNCVMQFSTERWKKSKSHQPSDAIEMNMFLRENPSIQVAIDHLTPQAPTSTMVRFAESVSDNSND...DDKLLFCDDCDRGYHLYCLNPPLEKAPDDEYSCRLCQIEFGDKASAPAKK\n AlphaFold Structure: Available\n Structure Coverage: residues 1-377\n\nPROTEIN: dpy-27\n UniProt ID: A8XX62\n Organism: Caenorhabditis briggsae\n Sequence Length: 1575 amino acids\n Sequence: MSAAKRRAVSAEPTDPDGPEGPPVAVDMPDVNLSDDQRAMYKYKLNIADPLNEKNLEAEFELGKKTIEMQLNENDSLLDIVVGPKYKDFEADPDGKRVIIQDIIVHNFKSYKGSHQLGPFHKNLT...FDEEGDEPIRKKKRRKVAKEYEDASDLESTPTPTRDPSPVVQTRSRRSRL\n AlphaFold Structure: Not available\n\nPROTEIN: meg-3\n UniProt ID: A0A5K4EK08\n Organism: Schistosoma mansoni\n Sequence Length: 150 amino acids\n Sequence: YLLCKKEYSIMNRFFWTVTQCTILLVIICNLNTMKATSANSRTHGATSTSTHGATSTAKPAASTPPKAAATSTIKPTVTTPKAAATSTIKPTVTTKPSPAKPAASNTAKPAASTPKKPHDERAVLAAAAVPIVLGVIGEVIGFILQYIAS\n AlphaFold Structure: Available\n Structure Coverage: residues 1-150\n\nPROTEIN: mix-1\n UniProt ID: A8WT04\n Organism: Caenorhabditis briggsae\n Sequence Length: 1296 amino acids\n Sequence: MHIKSIQLDGFKSYQKHTEIAPFSPQFNAITGYNGSGKSNVLDSICFLLGISKLDNIRAKSMNELISHGGSKAVVQIRFDNRDKKQSPFGMDHLDELVVQRHITALPTGKSCYTGYTLNGHSATT...MSGAELKKLQTDKKLAAQATEVAEAEKEATKKPSKKSAKKAVQNTDDEME\n AlphaFold Structure: Not available\n\nPROTEIN: smc-4\n UniProt ID: Q20060\n Full Name: Structural maintenance of chromosomes protein 4\n Organism: Caenorhabditis elegans\n Sequence Length: 1549 amino acids\n Sequence: MPPKTSAAPPQSDESDSDFDDAPVKKPQKKTTKPVNRHKEGSKDPEEELQRAVNEKFDGSDGEDDDSDLFSLQLPSRPDFLTKPNRADRLMIRNVEVDNFKSYFGKASIGPFHKSFTSIIGPNGS...KARNIEADETTPPSKRSNSASTPKRSPMKPLTPSSKKKEKAIVDDDDDME\n AlphaFold Structure: Available\n Structure Coverage: residues 1-1549\n Function: Central component of the condensin I complex, a complex required for conversion of interphase chromatin into mitotic-like condense chromosomes (PubMed:11914278, PubMed:19781752). The condensin I compl...",
"role": "user"
},
{
"content": "<biopax>\n <proteins>\n <p id=\"c44c10.4\" name=\"C44C10.4\" uniprot=\"Q18616\" fullname=\"Structural maintenance of chromosomes-like protein 1\"/>\n <p id=\"dpff-1\" name=\"dpff-1\" uniprot=\"A8X7Y2\"/>\n <p id=\"dpy-27\" name=\"dpy-27\" uniprot=\"A8XX62\"/>\n <p id=\"meg-3\" name=\"meg-3\" uniprot=\"A0A5K4EK08\"/>\n <p id=\"mix-1\" name=\"mix-1\" uniprot=\"A8WT04\"/>\n <p id=\"smc-4\" name=\"smc-4\" uniprot=\"Q20060\" fullname=\"Structural maintenance of chromosomes protein 4\"/>\n </proteins>\n <interactions>\n <i id=\"1\" a=\"c44c10.4\" b=\"dpff-1\" type=\"Two-hybrid\"/>\n <i id=\"2\" a=\"c44c10.4\" b=\"dpy-27\" type=\"Affinity Capture-MS\"/>\n <i id=\"3\" a=\"c44c10.4\" b=\"smc-4\" type=\"Affinity Capture-MS\"/>\n <i id=\"4\" a=\"c44c10.4\" b=\"mix-1\" type=\"Affinity Capture-MS\"/>\n <i id=\"5\" a=\"mix-1\" b=\"smc-4\" type=\"Affinity Capture-Western\"/>\n <i id=\"6\" a=\"dpy-27\" b=\"mix-1\" type=\"Affinity Capture-Western\"/>\n <i id=\"7\" a=\"dpy-27\" b=\"mix-1\" type=\"Affinity Capture-MS\"/>\n <i id=\"8\" a=\"mix-1\" b=\"smc-4\" type=\"Affinity Capture-MS\"/>\n <i id=\"9\" a=\"meg-3\" b=\"mix-1\" type=\"Affinity Capture-MS\"/>\n <i id=\"10\" a=\"meg-3\" b=\"smc-4\" type=\"Affinity Capture-MS\"/>\n <i id=\"11\" a=\"dpff-1\" b=\"meg-3\" type=\"Affinity Capture-MS\"/>\n <i id=\"12\" a=\"c44c10.4\" b=\"meg-3\" type=\"Affinity Capture-MS\"/>\n </interactions>\n</biopax>",
"role": "assistant"
}
] |
End of preview.