Enhanced sampling and applications in protein folding

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dc.contributor.advisorMa, Jianpeng
dc.contributor.advisorMcNew, James A.
dc.contributor.advisorIgoshin, Oleg A.
dc.creatorZhang, Cheng
dc.date.accessioned2013-07-24T19:52:21Z
dc.date.accessioned2013-07-24T19:52:26Z
dc.date.available2013-07-24T19:52:21Z
dc.date.available2013-07-24T19:52:26Z
dc.date.created2012-12
dc.date.issued2013-07-24
dc.date.submittedDecember 2012
dc.date.updated2013-07-24T19:52:26Z
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.
dc.format.mimetypeapplication/pdf
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>.
dc.identifier.slug123456789/ETD-2012-12-221
dc.identifier.urihttps://hdl.handle.net/1911/71707
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 folding
dc.subjectEnhanced sampling
dc.subjectIntegral identity
dc.subjectStatistical distribution
dc.titleEnhanced sampling and applications in protein folding
dc.typeThesis
dc.type.materialText
thesis.degree.departmentApplied Physics
thesis.degree.disciplineNatural Sciences
thesis.degree.grantorRice University
thesis.degree.levelDoctoral
thesis.degree.nameDoctor of Philosophy
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