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Four‐body contact potentials derived from two protein datasets to discriminate native structures from decoys
Author(s) -
Feng Yaping,
Kloczkowski Andrzej,
Jernigan Robert L.
Publication year - 2007
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.21362
Subject(s) - threading (protein sequence) , computer science , delaunay triangulation , contact order , low resolution , protein structure , resolution (logic) , biological system , high resolution , algorithm , crystallography , chemistry , native state , biology , artificial intelligence , biochemistry , remote sensing , geology
Two‐body inter‐residue contact potentials for proteins have often been extracted and extensively used for threading. Here, we have developed a new scheme to derive four‐body contact potentials as a way to consider protein interactions in a more cooperative model. We use several datasets of protein native structures to demonstrate that around 500 chains are sufficient to provide a good estimate of these four‐body contact potentials by obtaining convergent threading results. We also have deliberately chosen two sets of protein native structures differing in resolution, one with all chains' resolution better than 1.5 Å and the other with 94.2% of the structures having a resolution worse than 1.5 Å to investigate whether potentials from well‐refined protein datasets perform better in threading. However, potentials from well‐refined proteins did not generate statistically significant better threading results. Our four‐body contact potentials can discriminate well between native structures and partially unfolded or deliberately misfolded structures. Compared with another set of four‐body contact potentials derived by using a Delaunay tessellation algorithm, our four‐body contact potentials appear to offer a better characterization of the interactions between backbones and side chains and provide better threading results, somewhat complementary to those found using other potentials. Proteins 2007. © 2007 Wiley‐Liss, Inc.