Understanding Protein Folding Using Markov State Models

被引：9

作者：

Pande, Vijay S. ^{[1
]}

机构：

[1] Stanford Univ, Stanford, CA 94305 USA

来源：

INTRODUCTION TO MARKOV STATE MODELS AND THEIR APPLICATION TO LONG TIMESCALE MOLECULAR SIMULATION | 2014年 / 797卷

关键词：

SIMULATION;

D O I：

10.1007/978-94-007-7606-7_8

中图分类号：

R-3 [医学研究方法]; R3 [基础医学];

学科分类号：

1001 ;

摘要：

引用

页码：101 / 106

页数：6

共 10 条

[1] Simple few-state models reveal hidden complexity in protein folding [J].

Beauchamp, Kyle A. ;

McGibbon, Robert ;

Lin, Yu-Shan ;

Pande, Vijay S. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2012, 109 (44) :17807-17813

[2] Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements [J].

Beauchamp, Kyle A. ;

Lin, Yu-Shan ;

Das, Rhiju ;

Pande, Vijay S. .

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2012, 8 (04) :1409-1414

[3] Atomistic Folding Simulations of the Five-Helix Bundle Protein λ6-85 [J].

Bowman, Gregory R. ;

Voelz, Vincent A. ;

Pande, Vijay S. .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2011, 133 (04) :664-667

[4] Protein folded states are kinetic hubs [J].

Bowman, Gregory R. ;

Pande, Vijay S. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (24) :10890-10895

[5] Progress and challenges in the automated construction of Markov state models for full protein systems [J].

Bowman, Gregory R. ;

Beauchamp, Kyle A. ;

Boxer, George ;

Pande, Vijay S. .

JOURNAL OF CHEMICAL PHYSICS, 2009, 131 (12)

[6] Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories [J].

Lane, Thomas J. ;

Bowman, Gregory R. ;

Beauchamp, Kyle ;

Voelz, Vincent A. ;

Pande, Vijay S. .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2011, 133 (45) :18413-18419

[7] Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW [J].

Morcos, Faruck ;

Chatterjee, Santanu ;

McClendon, Christopher L. ;

Brenner, Paul R. ;

Lopez-Rendon, Roberto ;

Zintsmaster, John ;

Ercsey-Ravasz, Maria ;

Sweet, Christopher R. ;

Jacobson, Matthew P. ;

Peng, Jeffrey W. ;

Izaguirre, Jesus A. .

PLOS COMPUTATIONAL BIOLOGY, 2010, 6 (12)

[8] Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations [J].

Noe, Frank ;

Schuette, Christof ;

Vanden-Eijnden, Eric ;

Reich, Lothar ;

Weikl, Thomas R. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (45) :19011-19016

[9] Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment [J].

Voelz, Vincent A. ;

Jaeger, Marcus ;

Yao, Shuhuai ;

Chen, Yujie ;

Zhu, Li ;

Waldauer, Steven A. ;

Bowman, Gregory R. ;

Friedrichs, Mark ;

Bakajin, Olgica ;

Lapidus, Lisa J. ;

Weiss, Shimon ;

Pande, Vijay S. .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2012, 134 (30) :12565-12577

[10] Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1-39) [J].

Voelz, Vincent A. ;

Bowman, Gregory R. ;

Beauchamp, Kyle ;

Pande, Vijay S. .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2010, 132 (05) :1526-+

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