Enhanced, targeted sampling of high-dimensional free-energy landscapes using variationally enhanced sampling, with an application to chignolin

被引:47
|
作者
Shaffer, Patrick [1 ,2 ]
Valsson, Omar [1 ,2 ,3 ]
Parrinello, Michele [1 ,2 ,3 ]
机构
[1] Univ Svizzera Italiana, ETH, Dept Chem & Appl Biosci, CH-6900 Lugano, Switzerland
[2] Univ Svizzera Italiana, Inst Sci Computaz, Fac Informat, CH-6900 Lugano, Switzerland
[3] Univ Svizzera Italiana, Natl Ctr Computat Design & Discovery Novel Mat MA, CH-6900 Lugano, Switzerland
关键词
enhanced sampling; protein folding; free-energy calculation; biomolecular simulation; REPLICA-EXCHANGE; EFFICIENT; SIMULATIONS; ALGORITHM; PROTEINS; PEPTIDE; SYSTEMS;
D O I
10.1073/pnas.1519712113
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
The capabilities of molecular simulations have been greatly extended by a number of widely used enhanced sampling methods that facilitate escaping from metastable states and crossing large barriers. Despite these developments there are still many problems which remain out of reach for these methods which has led to a vigorous effort in this area. One of the most important problems that remains unsolved is sampling high-dimensional free-energy landscapes and systems that are not easily described by a small number of collective variables. In this work we demonstrate a new way to compute free-energy landscapes of high dimensionality based on the previously introduced variationally enhanced sampling, and we apply it to the miniprotein chignolin.
引用
收藏
页码:1150 / 1155
页数:6
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