Protocol for calculating binding free energy of RNA:RNA interactions through molecular dynamics simulations using adaptive biasing force technique

被引：0

作者：

Kameda, Takeru ^{[1
]}

Saha, Daniel K. ^{[2
]}

Ray, Sourav ^{[2
]}

Togashi, Yuichi ^{[1
,3
]}

Asano, Katsura ^{[2
,4
,5
]}

机构：

[1] Ritsumeikan Univ, Coll Life Sci, Kusatsu, Shiga 5258577, Japan

[2] Kansas State Univ, Mol Cellular & Dev Biol Program, Div Biol, Manhattan, KS 66506 USA

[3] RIKEN, Ctr Biosyst Dynam Res, Kobe, Hyogo 6500047, Japan

[4] Hiroshima Univ, Grad Sch Integrated Sci Life, Program Biotechnol, Higashihiroshima, Hiroshima 7398530, Japan

[5] Hiroshima Univ, Hiroshima Res Ctr Hlth Aging HiHA, Higashihiroshima, 7398530, Japan

来源：

STAR PROTOCOLS | 2024年 / 5卷 / 03期

关键词：

TRANSLATION; PSEUDOKNOT;

D O I：

10.1016/j.xpro.2024.103223

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

The adaptive biasing force (ABF) technique allows sampling to proceed in a flat free energy surface when performing molecular dynamics (MD) simulations. Here, we present a protocol to perform MD simulations using the ABF technique and apply it to calculate the binding free energy of an RNA:RNA interaction. We describe steps for server setup, test running software, and building molecular models. We then detail procedures for running and configuring ABF-MD simulations and analyzing binding free energy and structural change. For complete details on the use and execution of this protocol, please refer to Fujita et al.1 1 and Kameda et al.2 2

引用

页数：15

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