Ma, Jianpeng2019-05-172019-05-172018-082018-05-31August 201Ma, Tianqi. "OPUS-DOSP: A Distance- and Orientation-dependent All-atom Potential Derived from Side-chain Packing." (2018) Master’s Thesis, Rice University. <a href="https://hdl.handle.net/1911/105797">https://hdl.handle.net/1911/105797</a>.https://hdl.handle.net/1911/105797In this thesis, 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, 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.application/pdfengCopyright is held by the author, unless otherwise indicated. Permission to reuse, publish, or reproduce the work beyond the bounds of fair use or other exemptions to copyright law must be obtained from the copyright holder.protein structure predictionempirical potential functiondecoy recognitionside-chain packingThesis2019-05-17