How to use the data sets

This dataset contains more than 16,000 unique pairs of protein sequences and ligand SMILES, and the coordinates of their complexes.

SMILES are assumed to be tokenized by the regex from P. Schwaller

Every (x,y,z) ligand coordinate maps onto a SMILES token, and is nan if the token does not represent an atom

Every receptor coordinate maps onto the Calpha coordinate of that residue.

The dataset can be used to fine-tune a language model, all data comes from PDBind-cn.

Use the already preprocessed data

Load a test/train split using

from datasets import load_dataset
train = load_dataset("jglaser/pdbbind_complexes",split='train[:90%]')
validation = load_dataset("jglaser/pdbbind_complexes",split='train[90%:]')

Pre-process yourself

To manually perform the preprocessing, download the data sets from P.DBBind-cn

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/data

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