分子动力学模拟中支持CIF蛋白质文件格式
Supporting the CIF file format of proteins in molecular dynamics simulations
王恒越 1张志勇1
作者信息
- 1. 中国科学技术大学物理系,安徽合肥 230026
- 折叠
摘要
分子动力学(MD)模拟能够以非常精细的时间分辨率捕捉蛋白质的全原子动态行为,因此它已经成为蛋白质动力学研究的重要工具.当前有多种MD软件包被广泛使用.MD模拟需要从一个蛋白质初始结构开始,而初始结构一般来自蛋白质数据库(PDB).直到 2014 年,PDB文件格式一直是蛋白质结构的标准格式.然而,PDB格式存在一些内在缺陷,例如以固定宽度存储结构信息,这对于超大型蛋白质复合物来说存在问题.因此,CIF文件格式被提出来替代PDB格式,前者的特点是具有出色的扩展性.据我们所知,目前主流的MD软件包只支持PDB格式,而不直接支持CIF 格式.在本研究中,我们修改了一个MD软件包GROMACS 的源代码,使其能够支持输入CIF格式的蛋白质结构文件,并生成拓扑文件.这项工作将简化大型蛋白质复合物MD模拟中的预处理过程.
Abstract
Molecular dynamics(MD)simulations can capture the dynamic behavior of proteins in full atomic detail and at very fine temporal resolution,so they have become an important tool in the study of protein dynamics.To date,several MD packages are widely used.An MD simulation starts from an initial structure that is generally taken from the Protein Data Bank(PDB).Until 2014,the PDB format was the standard file format for protein structures.However,there are cer-tain intrinsic limitations in the PDB format,such as the storage of structural information in a fixed-width format,which is an issue for very large protein complexes.Therefore,the CIF(crystallographic information framework)format has been proposed,which is characterized by its superior expansibility.To our knowledge,the current mainstream MD packages support only the PDB format but do not support the CIF format directly.In this study,we modified the source code of one of the MD packages,GROMACS,which enables it to support CIF-formatted structure files as input and subsequently gen-erate molecular topology files.This work simplifies the preprocessing of large protein complexes for MD simulations.
关键词
蛋白质数据库/PDB格式/CIF格式/分子动力学模拟/GROMACSKey words
Protein Data Bank/PDB format/CIF format/molecular dynamics simulation/GROMACS引用本文复制引用
基金项目
国家重点研发计划(2021YFA1301504)
国家自然科学基金(91953101)
Chinese Academy of Sciences Strategic Priority Research Program(XDB37040202)
出版年
2024
NETL
NSTL
维普
万方数据