The ABCs of molecular dynamics simulations on B-DNA, circa 2012
The ABCs of molecular dynamics simulations on B-DNA, circa 2012
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DOI：
10.1007/s12038-012-9222-6
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发表时间：
2012-07-01
影响因子：
2.9
通讯作者：
Mezei, Mihaly
中科院分区：
文献类型：
--
作者：
Beveridge, David L.;Cheatham, Thomas E., III;Mezei, Mihaly
本文回顾了ABC在全原子分子动力学（MD）模拟领域的研究进展，包括双链体B型DNA双链体的所有四核苷酸步骤的显式溶剂。2012. ABC联盟已经完成了两个阶段的模拟，最新的是一组50-100轨道的基础上，琥珀ff 99力场与parmbsc 0修改。MD对DNA和DNA结构的序列效应的领域提供了一些一般性的观点，其次是我们的MD结果的概述，包括详细比较的ff 99/parmbsc 0结果与晶体和NMR结构可用于d（CGCGAATTCGCG）。本文还介绍了受ABC倡议和数据库启发或与之相关的一些研究项目，包括轨迹分析方法、处理大型结果数据库的信息学、轨迹的分布效率压缩、水和离子对DNA的溶剂化、粗粒模型的参数化及其应用、基因发现和基因组注释等。
This article provides a retrospective on the ABC initiative in the area of all-atom molecular dynamics (MD) simulations including explicit solvent on all tetranucleotide steps of duplex B-form DNA duplex, ca. 2012. The ABC consortium has completed two phases of simulations, the most current being a set of 50-100 trajectories based on the AMBER ff99 force field together with the parmbsc0 modification. Some general perspectives on the field of MD on DNA and sequence effects on DNA structure are provided, followed by an overview our MD results, including a detailed comparison of the ff99/parmbsc0 results with crystal and NMR structures available for d(CGCGAATTCGCG). Some projects inspired by or related to the ABC initiative and database are also reviewed, including methods for the trajectory analyses, informatics of dealing with the large database of results, compressions of trajectories for efficacy of distribution, DNA solvation by water and ions, parameterization of coarse-grained models with applications and gene finding and genome annotation.