Supporting the CIF file format of proteins in molecular dynamics simulations
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.
Protein Data BankPDB formatCIF formatmolecular dynamics simulationGROMACS
王恒越、张志勇
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中国科学技术大学物理系,安徽合肥 230026
蛋白质数据库 PDB格式 CIF格式 分子动力学模拟 GROMACS
国家重点研发计划国家自然科学基金Chinese Academy of Sciences Strategic Priority Research Program
NETL
NSTL
万方数据
维普
