Enhanced sampling and applications in protein folding
dc.contributor.advisor | Ma, Jianpeng | |
dc.contributor.advisor | McNew, James A. | |
dc.contributor.advisor | Igoshin, Oleg A. | |
dc.creator | Zhang, Cheng | |
dc.date.accessioned | 2013-07-24T19:52:21Z | |
dc.date.accessioned | 2013-07-24T19:52:26Z | |
dc.date.available | 2013-07-24T19:52:21Z | |
dc.date.available | 2013-07-24T19:52:26Z | |
dc.date.created | 2012-12 | |
dc.date.issued | 2013-07-24 | |
dc.date.submitted | December 2012 | |
dc.date.updated | 2013-07-24T19:52:26Z | |
dc.description.abstract | We 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.mimetype | application/pdf | |
dc.identifier.citation | Zhang, 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.slug | 123456789/ETD-2012-12-221 | |
dc.identifier.uri | https://hdl.handle.net/1911/71707 | |
dc.language.iso | eng | |
dc.rights | Copyright 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.subject | Protein folding | |
dc.subject | Enhanced sampling | |
dc.subject | Integral identity | |
dc.subject | Statistical distribution | |
dc.title | Enhanced sampling and applications in protein folding | |
dc.type | Thesis | |
dc.type.material | Text | |
thesis.degree.department | Applied Physics | |
thesis.degree.discipline | Natural Sciences | |
thesis.degree.grantor | Rice University | |
thesis.degree.level | Doctoral | |
thesis.degree.name | Doctor of Philosophy |