A post-process to estimate an approximated minimal free energy path based on local centroids

被引：5
|
作者：
Morita, Rikuri [1 ]
Shigeta, Yasuteru [1 ]
Harada, Ryuhei [1 ]
机构：
[1] Univ Tsukuba, Ctr Computat Sci, 1-1-1 Tennodai, Tsukuba, Ibaraki 3058577, Japan
来源：
CHEMICAL PHYSICS LETTERS | 2021年 / 782卷
基金：
日本科学技术振兴机构; 日本学术振兴会;
关键词：
Molecular dynamics; Minimal free energy path; RIBOSE-BINDING PROTEIN; STRING METHOD; MOLECULAR-DYNAMICS; MONTE-CARLO; SOLVENT; SWARMS;
D O I：
10.1016/j.cplett.2021.139003
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：
Free energy calculations are indispensable for characterizing the conformational transitions of proteins. The dominant transition path can be regarded as a minimal free energy path (MFEP) on a free energy landscape (FEL). However, it takes computational costs to find an MFEP. In this study, we propose a post-process to estimate an approximated MFEP. In our method, an initial string consisting of beads is generated and relaxed using local centroids on the pre-prepared FEL to estimate the MFEP. The implementation in Python is available as a jupyter notebook from the website https://github.com/riquri/post-string.
引用
收藏
页数：5
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