| ## How to use the data sets | |
| This dataset contains more about 80,000 unique pairs of protein sequences and ligand SMILES, and the coordinates | |
| of their complexes from the PDB. Only ligands with a molecular weight >= 100 Da are included. | |
| 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/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 | |
| ``` | |