Biochemistry, Biophysics and Molecular Biology, Roy J. Carver Department of
Journal or Book Title
Proteins: Structure, Function, and Bioinformatics
Multi-body potentials have been of much interest recently because they take into account three dimensional interactions related to residue packing and capture the cooperativity of these interactions in protein structures. Our goal was to combine long range multi-body potentials and short range potentials to improve recognition of native structure among misfolded decoys. We optimized the weights for four-body non-sequential, four-body sequential and short range potentials in order to obtain optimal model ranking results for threading and have compared these data against results obtained with other potentials. (Twenty six different coarse-grained potentials from the Potentials ‘R’Us web server have been used.) Our optimized multi-body potentials outperform all other contact potentials in the recognition of the native structure among decoys, both for models from homology template-based modeling and from template-free modeling in CASP8 decoy sets. We have compared the results obtained for this optimized coarse-grained potentials, where each residue is represented by a single point, with results obtained by using the DFIRE potential, which takes into account atomic level information of proteins. We found that for all proteins larger than 80 amino acids our optimized coarse-grained potentials yield results comparable to those obtained with the atomic DFIRE potential.
Gniewek, Pawel; Leelananda, Sumudu P.; Kolinski, Andrzej; Jernigan, Robert L.; and Kloczkowski, Andrzej, "MultiBody Coarse-Grained Potentials for Native Structure Recognition and Quality Assessment of Protein Models" (2011). Biochemistry, Biophysics and Molecular Biology Publications. 147.