spice-dataset/amino-acid-ligand at main · openmm/spice-dataset · GitHub

Name		Name	Last commit message	Last commit date
parent directory ..
Components-smiles-oe.smi		Components-smiles-oe.smi
README.md		README.md
amino-acid-ligand-21-25.hdf5.gz		amino-acid-ligand-21-25.hdf5.gz
amino-acid-ligand-26-30.hdf5.gz		amino-acid-ligand-26-30.hdf5.gz
amino-acid-ligand-31-33.hdf5.gz		amino-acid-ligand-31-33.hdf5.gz
amino-acid-ligand-34-36.hdf5.gz		amino-acid-ligand-34-36.hdf5.gz
amino-acid-ligand-5-20.hdf5.gz		amino-acid-ligand-5-20.hdf5.gz
cc-to-pdb.tdd		cc-to-pdb.tdd
createAminoAcidLigand.py		createAminoAcidLigand.py

README.md

This collection consists of dimers, each involving of a ligand and a single amino acid. The conformations are drawn from PDB files.

The files Components-smiles-oe.smi and cc-to-pdb.tdd were downloaded from Ligand Expo.

The conformations were generated using OpenMM 8.0, RDKit 2023.03.2, OpenFF Toolkit 0.14.0, and openmmforcefields 0.11.2.