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OPUS-DOSP: A Distance- and Orientation-dependent All-atom Potential Derived from Side-chain Packing
- Xu, Gang, Ma, Tianqi, Zang, Tianwu, Sun, Weitao, Wang, Qinghua, Ma, Jianpeng
- Journal of Molecular Biology 2017
- energy, models, protein structure
- 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.