Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys.
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 A and the other with 94.2% of the structures having a resolution worse than 1.5 A 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.
Feng
Yaping
Y
Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011-0320, USA.
Kloczkowski
Andrzej
A
Jernigan
Robert L
RL
D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
D011506:Proteins