Refinement of Protein Docking with Atom-Atom Contact Potentials, Backbone Flexibility and Side-Chain Repacking

Abstract

Protein-protein docking is a challenging task for proteins with large conformational changes upon binding (unbound/bound interface RMSD g (ii) a neighbor-dependent Ramachandran probability distributions for the backbone loops torsional degrees of freedom; and (iii) our library of protein-protein interface side-chain rotamers. The procedure was benchmarked on the Dockground (http://dockground.compbio.ku.edu) X-ray unbound set 4.0, which contains 396 co-crystallized protein-protein complexes and corresponding unbound structures for both proteins. The procedure was evaluated by CAPRI assessment criteria for its ability to refine docking predictions with ligand RMSD < 10 A, classified as incorrect, to the acceptable or better quality category, using only the atom-atom contact potentials and the rotational/translational degrees of freedom.