Literature DB >> 11909330

Using novel variable transformations to enhance conformational sampling in molecular dynamics.

Zhongwei Zhu1, Mark E Tuckerman, Shane O Samuelson, Glenn J Martyna.   

Abstract

One of the computational "grand challenges" is to develop methodology capable of sampling conformational equilibria in systems with rough energy landscapes. Here, a significant step forward is made by combining molecular dynamics with a novel variable transformation designed to enhance sampling by reducing barriers without introducing bias and, thus, to preserve, perfectly, equilibrium properties.

Mesh:

Year:  2002        PMID: 11909330     DOI: 10.1103/PhysRevLett.88.100201

Source DB:  PubMed          Journal:  Phys Rev Lett        ISSN: 0031-9007            Impact factor:   9.161


  6 in total

1.  A self-learning algorithm for biased molecular dynamics.

Authors:  Gareth A Tribello; Michele Ceriotti; Michele Parrinello
Journal:  Proc Natl Acad Sci U S A       Date:  2010-09-27       Impact factor: 11.205

2.  Multiscale simulation of microbe structure and dynamics.

Authors:  Harshad Joshi; Abhishek Singharoy; Yuriy V Sereda; Srinath C Cheluvaraja; Peter J Ortoleva
Journal:  Prog Biophys Mol Biol       Date:  2011-07-23       Impact factor: 3.667

3.  Influence of solvent and intramolecular hydrogen bonding on the conformational properties of o-linked glycopeptides.

Authors:  Sairam S Mallajosyula; Alexander D MacKerell
Journal:  J Phys Chem B       Date:  2011-08-31       Impact factor: 2.991

Review 4.  Equilibrium sampling in biomolecular simulations.

Authors:  Daniel M Zuckerman
Journal:  Annu Rev Biophys       Date:  2011       Impact factor: 12.981

5.  Evolutionary Divergence of the C-terminal Domain of Complexin Accounts for Functional Disparities between Vertebrate and Invertebrate Complexins.

Authors:  Rachel T Wragg; Daniel A Parisotto; Zhenlong Li; Mayu S Terakawa; David Snead; Ishani Basu; Harel Weinstein; David Eliezer; Jeremy S Dittman
Journal:  Front Mol Neurosci       Date:  2017-05-26       Impact factor: 5.639

6.  Folding of Trp-cage mini protein using temperature and biasing potential replica-exchange molecular dynamics simulations.

Authors:  Srinivasaraghavan Kannan; Martin Zacharias
Journal:  Int J Mol Sci       Date:  2009-03-12       Impact factor: 5.923

  6 in total

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