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