MSMExplorer: visualizing Markov state models for biomolecule folding simulations

被引：20

作者：

Cronkite-Ratcliff, Bryce ^{[1
]}

Pande, Vijay ^{[1
,2
,3
]}

机构：

[1] Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA

[2] Stanford Univ, Dept Chem, Stanford, CA 94305 USA

[3] Stanford Univ, Dept Biol Struct, Stanford, CA 94305 USA

来源：

BIOINFORMATICS | 2013年 / 29卷 / 07期

关键词：

D O I：

10.1093/bioinformatics/btt051

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

A: Markov state models (MSMs) for the study of biomolecule folding simulations have emerged as a powerful tool for computational study of folding dynamics. MSMExplorer is a visualization application purpose-built to visualize these MSMs with an aim to increase the efficacy and reach of MSM science.

引用

页码：950 / 952

页数：3

共 12 条

[1]

[Anonymous], 1984, Congr Numer

[2]

Bastian M., 2009, INT AAAI C WEBL SOC, DOI DOI 10.13140/2.1.1341.1520

[3] Using generalized ensemble simulations and Markov state models to identify conformational states [J].

Bowman, Gregory R. ;

Huang, Xuhui ;

Pande, Vijay S. .

METHODS, 2009, 49 (02) :197-201

[4]

Dijkstra E. W., 1959, NUMER MATH, V1, P269

[5] Transition-Path Theory and Path-Finding Algorithms for the Study of Rare Events [J].

E, Weinan ;

Vanden-Eijnden, Eric .

ANNUAL REVIEW OF PHYSICAL CHEMISTRY, VOL 61, 2010, 61 :391-420

[6] GRAPH DRAWING BY FORCE-DIRECTED PLACEMENT [J].

FRUCHTERMAN, TMJ ;

REINGOLD, EM .

SOFTWARE-PRACTICE & EXPERIENCE, 1991, 21 (11) :1129-1164

[7]

Heer J., 2005, P ACM SIGCHI

[8] Illustration of transition path theory on a collection of simple examples [J].

Metzner, Philipp ;

Schuette, Christof ;

Vanden-Eijnden, Eric .

JOURNAL OF CHEMICAL PHYSICS, 2006, 125 (08)

[9] Transition networks for modeling the kinetics of conformational change in macromolecules [J].

Noe, Frank ;

Fischer, Stefan .

CURRENT OPINION IN STRUCTURAL BIOLOGY, 2008, 18 (02) :154-162

[10]

Schrodinger LLC, The PyMOL molecular graphics system

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