Processing Data
======================================================================================================

We have downloaded most of the small dataset in the repository. 

Drug-Target Binding Benchmark Dataset
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^


We list public **Drug-Target Binding Benchmark Dataset** 
that is supported by DeepPurpose and 
corresponding downloading and processing function. 

===============   ===============================================================================================================
   Dataset                                        downloading and processing Function
===============   ===============================================================================================================
   BindingDB                         download_BindingDB() to download the data and process_BindingDB() to process the data
   DAVIS                             load_process_DAVIS() to download and process the data
   KIBA                               load_process_KIBA() to download and process the data
===============   ===============================================================================================================

* **Download Link**

	* `BindingDB <https://www.bindingdb.org/bind/index.jsp>`_ 
	* `DAVIS <http://staff.cs.utu.fi/~aatapa/data/DrugTarget/>`_
	* `KIBA <https://jcheminf.biomedcentral.com/articles/10.1186/s13321-017-0209-z>`_



















Repurposing Dataset
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

We list public **Repurposing Dataset** 
that is supported by DeepPurpose and 
corresponding downloading and processing function. 


=======================================   =====================================================================
           Dataset                                           downloading and processing Function   
=======================================   =====================================================================
     Curated Antiviral Drugs Library	          load_antiviral_drugs() to load and process the data  
       Broad Repurposing Hub	               load_broad_repurposing_hub() downloads and process the data  
=======================================   =====================================================================

* **Download Link**

	* `Curated Antiviral Drugs Library <https://en.wikipedia.org/wiki/List_of_antiviral_drugs>`_ 
	* `Broad Repurposing Hub <https://www.broadinstitute.org/drug-repurposing-hub>`_






















Bioassay Data for COVID-19
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

=========================   =====================================================================
           Dataset                       downloading and processing Function   
=========================   =====================================================================
           AID1706		          load_AID1706_SARS_CoV_3CL() to load and process 
=========================   =====================================================================



* **Download Link**

	* `AID1706 <https://pubchem.ncbi.nlm.nih.gov/bioassay/1706>`_ 



















COVID-19 Targets
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

===============================   =====================================================================
           Dataset                       downloading and processing Function   
===============================   =====================================================================
  SARS-CoV 3CL Protease		          load_SARS_CoV_Protease_3CL()
  SARS-CoV2 3CL Protease	          load_SARS_CoV2_Protease_3CL()
  SARS_CoV2 RNA Polymerase	          load_SARS_CoV2_RNA_polymerase()
  SARS-CoV2 Helicase	              load_SARS_CoV2_Helicase()
  SARS-CoV2 3to5_exonuclease	      load_SARS_CoV2_3to5_exonuclease()
  SARS-CoV2 endoRNAse	               load_SARS_CoV2_endoRNAse()
===============================   =====================================================================










.. toctree::
   :glob:
   :maxdepth: 1
   :caption: Technical Details of Function

   data/read_file_training_dataset_bioassay  
   data/read_file_training_dataset_drug_target_pairs
   data/read_file_virtual_screening_drug_target_pairs
   data/read_file_repurposing_library
   data/read_file_target_sequence
   data/download_BindingDB
   data/process_BindingDB
   data/load_process_DAVIS
   data/load_process_KIBA
   data/load_AID1706_txt_file 
   data/load_AID1706_SARS_CoV_3CL
   data/load_antiviral_drugs
   data/load_broad_repurposing_hub