PPB-Affinity: Protein-Protein Binding Affinity dataset for AI-based protein drug discovery

Prediction of protein-protein binding (PPB) affinity plays an important role in large-molecular drug discovery. Deep learning (DL) has been adopted to predict the changes of PPB binding affinities upon mutations, but there was a scarcity of studies predicting the PPB affinity itself. The major reason is the paucity of open-source dataset with PPB affinity data. To address this gap, the current study introduced a large comprehensive PPB affinity (PPB-Affinity) dataset. The PPB-Affinity dataset contains key information such as crystal structures of protein-protein complexes (with or without protein mutation patterns), PPB affinity, receptor protein chain, ligand protein chain, etc. To the best of our knowledge, this is the largest publicly available PPB affinity dataset, and we believe it will significantly advance drug discovery by streamlining the screening of potential large-molecule drugs. We also developed a deep-learning benchmark model with this dataset to predict the PPB affinity, providing a foundational comparison for the research community.

Codes for PPB-Affinity database preparation is  disclosed at https://github.com/Huatsing-Lau/PPB-Affinity-DataPrepWorkflow.
Codes for the benchmark algorithm is disclosed at https://github.com/ChenPy00/PPB-Affinity.

The article related to the PPB-Affinity dataset can be found at https://doi.org/10.1038/s41597-024-03997-4.

Files are orginized as follows:

- PPB-Affinity.xlsx

- samples_deleted.zip

- PPB-Affinity-AF.zip

- PDB/

  - Affinity Benchmark v5.5/

    - file1.pdb

    - file2.pdb

    - ...

    - filek.pdb

  - ATLAS/

  - PDBbind v2020/

  - SAbDab/

  - SKEMPIv2.0/