Literature DB >> 17382533

Improved sampling methods for molecular simulation.

Hongxing Lei1, Yong Duan.   

Abstract

Molecular simulation has broad application in the biological sciences. One of the greatest challenges in molecular simulation is the limited conformational sampling due to slow barrier crossing on the rugged energy landscape of complex biomolecules and to the relatively short simulation time. Many enhanced sampling techniques have been developed over the years to alleviate this problem. Significant progress has been made in the past couple of years, with emerging methods targeting specific aspects of the potential energy surface and new variants of the replica exchange method.

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Year:  2007        PMID: 17382533     DOI: 10.1016/j.sbi.2007.03.003

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  27 in total

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2.  Structural analysis of protein dynamics by MD simulations and NMR spin-relaxation.

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Journal:  Proteins       Date:  2008-05-01

Review 3.  Computational techniques for efficient conformational sampling of proteins.

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Journal:  Curr Opin Struct Biol       Date:  2008-01-22       Impact factor: 6.809

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Journal:  J Comput Aided Mol Des       Date:  2017-03-20       Impact factor: 3.686

7.  Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method.

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Journal:  J Chem Phys       Date:  2014-05-07       Impact factor: 3.488

8.  Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations.

Authors:  Ron O Dror; Morten Ø Jensen; David W Borhani; David E Shaw
Journal:  J Gen Physiol       Date:  2010-06       Impact factor: 4.086

9.  An improved strategy for generating forces in steered molecular dynamics: the mechanical unfolding of titin, e2lip3 and ubiquitin.

Authors:  Bosco K Ho; David A Agard
Journal:  PLoS One       Date:  2010-09-29       Impact factor: 3.240

10.  An Analysis of Biomolecular Force Fields for Simulations of Polyglutamine in Solution.

Authors:  Aaron M Fluitt; Juan J de Pablo
Journal:  Biophys J       Date:  2015-09-01       Impact factor: 4.033

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