|
--- |
|
tags: |
|
- proteins |
|
- molecules |
|
- chemistry |
|
- SMILES |
|
- complex structures |
|
--- |
|
|
|
## How to use the data sets |
|
|
|
This dataset contains 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 |
|
|
|
``` |
|
import pandas as pd |
|
train = pd.read_pickle('data/pdb_train.p') |
|
test = pd.read_pickle('data/pdb_test.p') |
|
``` |
|
|
|
### 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 |
|
``` |
|
|
