Datasets for Evaluation of Small-Molecule Binding Site Prediction Methods on Membrane-Embedded Protein Interfaces

The dataset contains PDB files of protein-ligand complexes for two major membrane protein classes - GPCRs and ion channels. In addition, it contains PDB files for a subset of 420 protein-ligand structures from the PDBBind dataset. For each GPCR or ion channel a directory with the following content is provided: a PDB file downloaded from the OPM database (https://opm.phar.umich.edu) and a 'cleaned' PDB file in which all ligands, ions or lipids, except for the small molecule whose binding site should be predicted, were removed. For each protein in the BDBBind set a directory with the following content is provided: a PDB file of the protein, a PDB and MOL2 file of the ligand and a PDB file of the combined protein-ligand complex. A Scripts directory contains several Python scripts which were used to perform the calculations in this study, including the downloading and handling of PDB files, the conversion of method output files, the calculation of method results and the plotting of results.