README.md

---
tags:
- proteins
- molecules
- chemistry
- SMILES
- complex structures
---

## How to use the data sets

This dataset contains more about 36,000 unique pairs of protein sequences and ligand SMILES, and the coordinates
of their complexes from the PDB.

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.

## Ligand selection criteria

Only ligands

- that have at least 3 atoms,
- a molecular weight >= 100 Da,
- and which are not among the 280 most common ligands in the PDB (this includes common additives like PEG, ADP, ..)

are considered.

### Use the already preprocessed data

Load a test/train split using

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

### Manual update from PDB

```
# download the PDB archive into folder pdb/
sh rsync.sh 24 # number of parallel download processes

# extract sequences and coordinates in parallel
sbatch pdb.slurm
# or
mpirun -n 42 parse_complexes.py # desired number of tasks
```