MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

被引:311
作者
Beauchamp, Kyle A. [1 ]
Bowman, Gregory R. [2 ]
Lane, Thomas J. [2 ]
Maibaum, Lutz [2 ]
Haque, Imran S. [3 ]
Pande, Vijay S. [1 ,2 ,3 ]
机构
[1] Stanford Univ, Biophys Program, Stanford, CA 94305 USA
[2] Stanford Univ, Dept Chem, Stanford, CA 94305 USA
[3] Stanford Univ, Dept Comp Sci, Stanford, CA 94305 USA
关键词
PROTEINS; KINETICS; NETWORK;
D O I
10.1021/ct200463m
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
Markov state models provide a framework for understanding the fundamental states and rates in the conformational dynamics of biomolecules. We describe an improved protocol for constructing Markov state models from molecular dynamics simulations. The new protocol includes advances in clustering, data preparation, and model estimation; these improvements lead to significant increases in model accuracy, as assessed by the ability to recapitulate equilibrium and kinetic properties of reference systems. A high-performance implementation of this protocol, provided in MSMBuilder2, is validated on dynamics ranging from picoseconds to milliseconds.
引用
收藏
页码:3412 / 3419
页数:8
相关论文
共 41 条
[1]   PRINCIPLES THAT GOVERN FOLDING OF PROTEIN CHAINS [J].
ANFINSEN, CB .
SCIENCE, 1973, 181 (4096) :223-230
[2]  
[Anonymous], 1995, Python reference manual
[3]  
[Anonymous], FINDING GROUPS DATA
[4]  
Ascher David., 1999, Numerical Python
[5]   Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint [J].
Bacallado, Sergio ;
Chodera, John D. ;
Pande, Vijay .
JOURNAL OF CHEMICAL PHYSICS, 2009, 131 (04)
[6]   PROTEIN-FOLDING INTERMEDIATES - NATIVE-STATE HYDROGEN-EXCHANGE [J].
BAI, YW ;
SOSNICK, TR ;
MAYNE, L ;
ENGLANDER, SW .
SCIENCE, 1995, 269 (5221) :192-197
[7]   Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models [J].
Bowman, Gregory R. ;
Ensign, Daniel L. ;
Pande, Vijay S. .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2010, 6 (03) :787-794
[8]   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)
[9]   Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations [J].
Buch, Ignasi ;
Giorgino, Toni ;
De Fabritiis, Gianni .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2011, 108 (25) :10184-10189
[10]   Coarse master equations for peptide folding dynamics [J].
Buchete, Nicolae-Viorel ;
Hummer, Gerhard .
JOURNAL OF PHYSICAL CHEMISTRY B, 2008, 112 (19) :6057-6069