process_data.rst

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
  • DAVIS
  • KIBA

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
  • Broad 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

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