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Ligands data

  • davis/ligand_to_graph.pkl | kiba/ligand_to_graph.pkl - python dictionary with ligand SMILES strings as keys and ligand graphs (nodes features, edges, edges features) as values
  • davis/ligand_to_ecfp.pkl | kiba/ligand_to_ecfp.pkl - python dictionary with ligand isomorphic SMILES strings as keys and Morgan fingerprints (2048-bit vector) as values

Proteins data

  • davis/protein_to_graph.pkl | kiba/protein_to_graph.pkl - python dictionary with unique protein identifiers as keys and protein graphs (nodes features, edges, edges features) as values

Other data

  • davis/full.csv | kiba/full.csv - tables with the protein-ligand pairs and corresponding affinity values (labels)
  • davis/folds/ | kiba/folds/ - train and test folds of the datasets used for cross-validation and testing
  • prot_3d_for_Davis.tar.gz | prot_3d_for_KIBA.tar.gz - filtered PDB structures generated with AlphaFold and used to create protein graphs