| Literature DB >> 28864201 |
Gang Xu1, Tianqi Ma2, Tianwu Zang2, Weitao Sun3, Qinghua Wang4, Jianpeng Ma5.
Abstract
We report a new distance- and orientation-dependent, all-atom statistical potential derived from side-chain packing, named OPUS-DOSP, for protein structure modeling. The framework of OPUS-DOSP is based on OPUS-PSP, previously developed by us [JMB (2008), 376, 288-301], with refinement and new features. In particular, distance or orientation contribution is considered depending on the range of contact distance. A new auxiliary function in energy function is also introduced, in addition to the traditional Boltzmann term, in order to adjust the contributions of extreme cases. OPUS-DOSP was tested on 11 decoy sets commonly used for statistical potential benchmarking. Among 278 native structures, 239 and 249 native structures were recognized by OPUS-DOSP without and with the auxiliary function, respectively. The results show that OPUS-DOSP has an increased decoy recognition capability comparing with those of other relevant potentials to date.Entities:
Keywords: decoy recognition; empirical potential function; protein folding; protein structure prediction; side-chain packing
Mesh：
Year: 2017 PMID： 28864201 PMCID： PMC6193766 DOI： 10.1016/j.jmb.2017.08.013
Source DB: PubMed Journal: J Mol Biol ISSN： 0022-2836 Impact factor: 5.469