Enhanced sampling and applications in protein folding

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dc.contributor.advisorMa, Jianpengen_US
dc.contributor.advisorMcNew, James A.en_US
dc.contributor.advisorIgoshin, Oleg A.en_US
dc.creatorZhang, Chengen_US
dc.date.accessioned2013-07-24T19:52:21Zen_US
dc.date.accessioned2013-07-24T19:52:26Zen_US
dc.date.available2013-07-24T19:52:21Zen_US
dc.date.available2013-07-24T19:52:26Zen_US
dc.date.created2012-12en_US
dc.date.issued2013-07-24en_US
dc.date.submittedDecember 2012en_US
dc.date.updated2013-07-24T19:52:26Zen_US
dc.description.abstractWe show that a single-copy tempering method is useful in protein-folding simulations of large scale and high accuracy (explicit solvent, atomic representation, and physics-based potential). The method uses a runtime estimate of the average potential energy from an integral identity to guide a random walk in the continuous temperature space. It was used for folding three mini-proteins, trpzip2 (PDB ID: 1LE1), trp-cage (1L2Y), and villin headpiece (1VII) within atomic accuracy. Further, using a modification of the method with a dihedral bias potential added on the roof temperature, we were able to fold four larger helical proteins: α3D (2A3D), α3W (1LQ7), Fap1-NRα (2KUB) and S-836 (2JUA). We also discuss how to optimally use simulation data through an integral identity. With the help of a general mean force formula, the identity makes better use of data collected in a molecular dynamics simulation and is more accurate and precise than the common histogram approach.en_US
dc.format.mimetypeapplication/pdfen_US
dc.identifier.citationZhang, Cheng. "Enhanced sampling and applications in protein folding." (2013) Diss., Rice University. <a href="https://hdl.handle.net/1911/71707">https://hdl.handle.net/1911/71707</a>.en_US
dc.identifier.slug123456789/ETD-2012-12-221en_US
dc.identifier.urihttps://hdl.handle.net/1911/71707en_US
dc.language.isoengen_US
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.en_US
dc.subjectProtein foldingen_US
dc.subjectEnhanced samplingen_US
dc.subjectIntegral identityen_US
dc.subjectStatistical distributionen_US
dc.titleEnhanced sampling and applications in protein foldingen_US
dc.typeThesisen_US
dc.type.materialTexten_US
thesis.degree.departmentApplied Physicsen_US
thesis.degree.disciplineNatural Sciencesen_US
thesis.degree.grantorRice Universityen_US
thesis.degree.levelDoctoralen_US
thesis.degree.nameDoctor of Philosophyen_US
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