title: Improving the orientation-dependent statistical potential using a reference state.
abstract: Statistical potentials are frequently engaged in the protein structural prediction and protein folding for conformational evaluation. Theoretically, to describe the many-body effect, pairwise interaction between two atom groups should be corrected by their relative geometric orientation. The potential functions developed by this means are called orientation-dependent statistical potentials and have exhibited substantially improved performance. However, none of the currently available orientation-dependent statistical potentials use any reference state, which has been proven to greatly enhance the power of distance-dependent statistical potentials in numerous previous studies. In this work, we designed a reasonable reference state for the orientation-dependent statistical potentials: using the average geometric relationship between atom pairs in known structures by neglecting their residue identities. The statistical potential developed using this reference state (called ORDER_AVE) prevails most available rival potentials in a series of tests on the decoy sets, although the information of side chain atoms (except the β-carbon) is absent in its construction.
authors.affiliation: MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Liu
authors.forename: Jianyang
authors.initials: J
authors.lastname: Zeng
authors.forename: Haipeng
authors.initials: H
authors.lastname: Gong
mesh_terms: D019295:Computational Biology / Q000379:methods*; D006801:Humans; D008958:Models, Molecular; D015233:Models, Statistical; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011506:Proteins
keywords: decoy sets; energy function; orientation-dependent statistical potential; reference state