OPUS-DOSP: A Distance- and Orientation-dependent All-atom Potential Derived from Side-chain Packing

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dc.contributor.advisorMa, Jianpeng
dc.creatorMa, Tianqi
dc.date.accessioned2019-05-17T15:39:35Z
dc.date.available2019-05-17T15:39:35Z
dc.date.created2018-08
dc.date.issued2018-05-31
dc.date.submittedAugust 2018
dc.date.updated2019-05-17T15:39:35Z
dc.description.abstractIn 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.
dc.format.mimetypeapplication/pdf
dc.identifier.citationMa, 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>.
dc.identifier.urihttps://hdl.handle.net/1911/105797
dc.language.isoeng
dc.rightsCopyright 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.
dc.subjectprotein structure prediction
dc.subjectempirical potential function
dc.subjectdecoy recognition
dc.subjectside-chain packing
dc.titleOPUS-DOSP: A Distance- and Orientation-dependent All-atom Potential Derived from Side-chain Packing
dc.typeThesis
dc.type.materialText
thesis.degree.departmentApplied Physics
thesis.degree.disciplineNatural Sciences
thesis.degree.grantorRice University
thesis.degree.levelMasters
thesis.degree.majorApplied Physics/Bioengineering
thesis.degree.nameMaster of Science
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