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

页数：5

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