Four-body contact potentials derived from two protein datasets to discriminate native structures from decoys |
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Authors: | Feng Yaping Kloczkowski Andrzej Jernigan Robert L |
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Institution: | Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011-0320, USA. |
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Abstract: | 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. |
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Keywords: | contact potential two‐body potential four‐body potential Delauney tessellation (DT) |
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