ProPairs: A Data Set for Protein–Protein Docking

ProPairs is a data set of crystal structures of protein complexes defined as biological assemblies in the protein data bank (PDB), which are classified as legitimate protein-protein docking complexes by also identifying the corresponding unbound protein structures in the PDB. The underlying program selecting suitable protein complexes, also called ProPairs, is an automated method to extract structures of legitimate protein docking complexes and their unbound partner proteins from the PDB which fulfill specific criteria. In this way a total of 5,642 protein complexes have been identified with 11,600 different decompositions in unbound protein pairs yielding legitimate protein docking partners. After removing sequence redundancy (requiring a sequence identity of the residues in the interface of less than 40%), 2,070 different legitimate protein docking complexes remain. For 810 of these protein docking complexes, both docking partners possess corresponding unbound structures in the PDB. From the 2,070 nonredundant protein docking complexes there are 417 which possess a cofactor at the interface. From the 176 protein docking complexes of the Protein-Protein Docking Benchmark 4.0 (DB4.0) data set, 13 differ from the ProPairs data set. Twelve of them differ with respect to the composition of the unbound structures but are contained in the large redundant ProPairs data set. One protein docking complex of the DB4.0 data set is not contained in ProPairs since the biological assembly specified in the PDB is wrong (PDB id 1d6r ). For one protein complex (PDB id 1bgx ) the DB4.0 data set uses a fabricated unbound structure. For public use interactive online access is provided to the ProPairs data set of nonredundant protein docking complexes along with the source code of the underlying method [ http://propairs.github.io].