README.md

metadata

tags:
  - molecules
  - Chemistry
  - SMILES
  - Protein
  - Ligand
  - Complexes

To generate the dataset

Register for an account at https://www.pdbbind.org.cn/, confirm the validation email, then login and download

the Index files (1) the general protein-ligand complexes (2) the refined protein-ligand complexes (3) Extract those files in pdbbind_complex_GB2022/data

Run the script pdbbind.py in a compute job on an MPI-enabled cluster (e.g., mpirun -n 64 pdbbind.py).

Output will be tar files in train/, val/ and test/ folders, following the split direction which is from EquiBind manuscript.