基于文库的 Monte Carlo 方法对全原子肽进行有效的平衡采样。
Efficient equilibrium sampling of all-atom peptides using library-based Monte Carlo.
机构信息
Department of Computational Biology, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA.
出版信息
J Phys Chem B. 2010 May 6;114(17):5870-7. doi: 10.1021/jp910112d.
Abstract
We applied our previously developed library-based Monte Carlo (LBMC) to equilibrium sampling of several implicitly solvated all-atom peptides. LBMC can perform equilibrium sampling of molecules using precalculated statistical libraries of molecular-fragment configurations and energies. For this study, we employed residue-based fragments distributed according to the Boltzmann factor of the optimized potential for liquid simulations all-atom (OPLS-AA) forcefield describing the individual fragments. Two solvent models were employed: a simple uniform dielectric and the generalized Born/surface area (GBSA) model. The efficiency of LBMC was compared to standard Langevin dynamics (LD) using three different statistical tools. The statistical analyses indicate that LBMC is more than 100 times faster than LD not only for the simple solvent model but also for GBSA.
摘要
我们应用了先前开发的基于库的蒙特卡罗（LBMC）方法对几个隐式溶剂化的全原子肽进行平衡采样。LBMC 可以使用预先计算的分子片段构象和能量统计库对分子进行平衡采样。在这项研究中，我们根据优化的液体模拟势能（OPLS-AA）力场描述的各个片段的玻尔兹曼因子分布使用基于残基的片段。我们使用了两种溶剂模型：简单的均匀介电模型和广义 Born/表面积（GBSA）模型。使用三种不同的统计工具比较了 LBMC 和标准朗之万动力学（LD）的效率。统计分析表明，LBMC 不仅对于简单的溶剂模型，而且对于 GBSA 模型，其速度比 LD 快 100 多倍。
相似文献
1
Efficient equilibrium sampling of all-atom peptides using library-based Monte Carlo.基于文库的 Monte Carlo 方法对全原子肽进行有效的平衡采样。
J Phys Chem B. 2010 May 6;114(17):5870-7. doi: 10.1021/jp910112d.
2
General library-based Monte Carlo technique enables equilibrium sampling of semi-atomistic protein models.基于通用库的蒙特卡罗技术能够对半原子蛋白质模型进行平衡采样。
J Phys Chem B. 2009 Aug 6;113(31):10891-904. doi: 10.1021/jp901322v.
3
Rapid sampling of all-atom peptides using a library-based polymer-growth approach.使用基于文库的聚合物生长方法对全原子肽进行快速采样。
J Comput Chem. 2011 Feb;32(3):396-405. doi: 10.1002/jcc.21626. Epub 2010 Aug 23.
4
Extending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction space.运用库模拟蒙特卡罗法拓展基于片段的自由能计算：在相互作用空间中的退火。
J Comput Chem. 2011 Apr 30;32(6):1135-43. doi: 10.1002/jcc.21695. Epub 2010 Nov 29.
5
Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units.使用基于库的蒙特卡罗方法和图形处理单元进行可调谐的混合分辨率建模。
J Chem Theory Comput. 2012 Aug 14;8(8):2921-2929. doi: 10.1021/ct300263z. Epub 2012 Jun 15.
6
Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics-Monte Carlo Simulations Guided by a Coarse-Grained Model.由粗粒度模型引导的混合非平衡分子动力学-蒙特卡罗模拟对原子模型的增强采样
J Chem Theory Comput. 2015 Aug 11;11(8):3572-83. doi: 10.1021/acs.jctc.5b00372.
7
Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems.多肽链联合残基模型的分子动力学。II. 朗之万动力学和贝伦德森热浴动力学以及对模型α-螺旋系统的测试。
J Phys Chem B. 2005 Jul 21;109(28):13798-810. doi: 10.1021/jp058007w.
8
DICE: A Monte Carlo Code for Molecular Simulation Including the Configurational Bias Monte Carlo Method.DICE：一种包含构象偏差蒙特卡罗方法的分子模拟的蒙特卡罗代码。
J Chem Inf Model. 2020 Jul 27;60(7):3472-3488. doi: 10.1021/acs.jcim.0c00077. Epub 2020 Jun 18.
9
Polypeptide folding using Monte Carlo sampling, concerted rotation, and continuum solvation.使用蒙特卡罗抽样、协同旋转和连续溶剂化的多肽折叠。
J Am Chem Soc. 2004 Feb 18;126(6):1849-57. doi: 10.1021/ja0378862.
10
Simulation of peptide folding with explicit water--a mean solvation method.用显式水模拟肽折叠——一种平均溶剂化方法。
Proteins. 1999 Feb 15;34(3):295-302. doi: 10.1002/(sici)1097-0134(19990215)34:3<295::aid-prot3>3.0.co;2-t.
引用本文的文献
1
Tunable, mixed-resolution modeling using library-based Monte Carlo and graphics processing units.使用基于库的蒙特卡罗方法和图形处理单元进行可调谐的混合分辨率建模。
J Chem Theory Comput. 2012 Aug 14;8(8):2921-2929. doi: 10.1021/ct300263z. Epub 2012 Jun 15.
2
Expanding the conformational selection paradigm in protein-ligand docking.拓展蛋白质-配体对接中的构象选择范式。
Methods Mol Biol. 2012;819:59-74. doi: 10.1007/978-1-61779-465-0_5.
3
Accelerating molecular Monte Carlo simulations using distance and orientation-dependent energy tables: tuning from atomistic accuracy to smoothed "coarse-grained" models.使用距离和方向相关的能量表加速分子蒙特卡罗模拟：从原子精度调整到平滑的“粗粒化”模型。
J Comput Chem. 2012 Jan 30;33(3):268-75. doi: 10.1002/jcc.21970. Epub 2011 Nov 25.
4
Extending fragment-based free energy calculations with library Monte Carlo simulation: annealing in interaction space.运用库模拟蒙特卡罗法拓展基于片段的自由能计算：在相互作用空间中的退火。
J Comput Chem. 2011 Apr 30;32(6):1135-43. doi: 10.1002/jcc.21695. Epub 2010 Nov 29.
5
Equilibrium sampling in biomolecular simulations.生物分子模拟中的平衡采样。
Annu Rev Biophys. 2011;40:41-62. doi: 10.1146/annurev-biophys-042910-155255.
6
Automated sampling assessment for molecular simulations using the effective sample size.使用有效样本量进行分子模拟的自动抽样评估。
J Chem Theory Comput. 2010 Sep 1;6(10):3048-3057. doi: 10.1021/ct1002384.
本文引用的文献
1
Kinetics from Implicit Solvent Simulations of Biomolecules as a Function of Viscosity.生物分子隐式溶剂模拟动力学与粘度的关系
J Chem Theory Comput. 2007 Sep;3(5):1734-48. doi: 10.1021/ct7000705.
2
Efficient Generalized Born Models for Monte Carlo Simulations.用于蒙特卡罗模拟的高效广义玻恩模型
J Chem Theory Comput. 2006 May;2(3):732-9. doi: 10.1021/ct600069r.
3
Resolution Exchange Simulation with Incremental Coarsening.采用增量粗化的分辨率交换模拟
J Chem Theory Comput. 2006 May;2(3):656-66. doi: 10.1021/ct050337x.
4
Generalized Born model with a simple, robust molecular volume correction.具有简单、稳健分子体积校正的广义玻恩模型。
J Chem Theory Comput. 2007 Jan 1;3(1):156-169. doi: 10.1021/ct600085e.
5
Quantifying uncertainty and sampling quality in biomolecular simulations.量化生物分子模拟中的不确定性和采样质量。
Annu Rep Comput Chem. 2009 Jan 1;5:23-48. doi: 10.1016/S1574-1400(09)00502-7.
6
Absolute free energies and equilibrium ensembles of dense fluids computed from a nondynamic growth method.基于非动态增长方法计算稠密流体的绝对自由能和平衡系综。
J Chem Phys. 2009 Dec 7;131(21):214110. doi: 10.1063/1.3269674.
7
General library-based Monte Carlo technique enables equilibrium sampling of semi-atomistic protein models.基于通用库的蒙特卡罗技术能够对半原子蛋白质模型进行平衡采样。
J Phys Chem B. 2009 Aug 6;113(31):10891-904. doi: 10.1021/jp901322v.
8
Absolute free energies estimated by combining precalculated molecular fragment libraries.通过合并预先计算的分子片段库估算的绝对自由能。
J Comput Chem. 2009 Aug;30(11):1680-91. doi: 10.1002/jcc.21337.
9
Efficient and direct generation of multidimensional free energy surfaces via adiabatic dynamics without coordinate transformations.通过无坐标变换的绝热动力学高效直接地生成多维自由能面。
J Phys Chem B. 2008 Dec 11;112(49):15742-57. doi: 10.1021/jp805039u.
10
ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions.苦艾精：一种用于模拟水溶液中多肽的新型连续介质溶剂化模型。
J Comput Chem. 2009 Apr 15;30(5):673-99. doi: 10.1002/jcc.21005.
Zotero 插件