American Chemical Society, Journal of Chemical Information and Modeling, 8(54), p. 2275-2285
DOI: 10.1021/ci500261z
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We provide evidence supporting that protein-protein and protein-ligand docking poses are functions of protein shape and intrinsic dynamics. Over sets of 68 protein-protein complexes and 240 non-homologous enzymes, we recognize common predispositions for binding sites to have minimal vibrations and angular momenta while two interacting proteins orient so as to maximize the angle between their rotation/bending axes (> 65°). The findings are then used to define quantitative criteria to filter out docking decoys less likely to be the near-native poses, hence the chances to find near-native hits can be doubled. With the novel approach to partition a protein into 'domains' of robust but disparate intrinsic dynamics, 90% of catalytic residues in enzymes can be found within the first 50% of the residues closest to the interface of these dynamics domains. The results suggest an anisotropic rather than isotropic distribution of catalytic residues near the mass centers of enzymes.