A large decoy set of protein-protein complexes produced by flexible docking

Computational methods are needed to help characterize the structure and function of protein-protein complexes. To develop and improve such methods, standard test problems are essential. One important test is to identify experimental structures from among large sets of decoys. Here, a flexible docking procedure was used to produce such a large ensemble of decoy complexes. In addition to their use for structure prediction, they can serve as a proxy for the nonspecific, protein-protein complexes that occur transiently in the cell, which are hard to characterize experimentally, yet biochemically important. For 202 homodimers and 41 heterodimers with known X-ray structures, we produced an average of 1217 decoys each. The structures were characterized in detail. The decoys have rather large protein-protein interfaces, with at least 45 residue-residue contacts for every 100 contacts found in the experimental complex. They have limited intramonomer deformation and limited intermonomer steric conflicts. The decoys thoroughly sample each monomer's surface, with all the surface amino acids being part of at least one decoy interface. The decoys with the lowest intramonomer deformation were analyzed separately, as proxies for nonspecific protein-protein complexes. Their interfaces are less hydrophobic than the experimental ones, with an amino acid composition similar to the overall surface composition. They have a poorer shape complementarity and a weaker association energy, but are no more fragmented than the experimental interfaces, with 2.1 distinct patches of interacting residues on average, compared to 2.6 for the experimental interfaces. The decoys should be useful for testing and parameterizing docking methods and scoring functions; they are freely available as PDB files at http://biology.polytechnique.fr/decoys.