VMD-SS

The investigation on the types of secondary structure (SS) of a protein is important. The evolution of secondary structures during molecular dynamics simulations is a useful parameter to analyze protein structures. Therefore, it is of interest to describe VMD-SS (a software program) for the identification of secondary structure elements and its trajectories during simulation for known structures available at the Protein Data Bank (PDB). The program helps to calculate (1) percentage SS, (2) SS occurrence in each residue, (3) percentage SS during simulation, and (4) percentage residues in all SS types during simulation. The VMD-SS plug-in was designed using TCL script and stride to calculate secondary structure features

蛋白质二级结构（Secondary Structure，SS）类型的相关研究具有重要意义。分子动力学模拟过程中二级结构的演化是分析蛋白质结构的有效参数。因此，本文旨在介绍一款用于识别二级结构元件的软件程序VMD-SS，以及针对蛋白质数据银行（Protein Data Bank，PDB）中收录的已知结构开展模拟轨迹分析的相关方法。该程序可实现四项核心功能：(1) 二级结构占比计算；(2) 各残基的二级结构出现情况统计；(3) 模拟过程中二级结构占比分析；(4) 模拟过程中各类二级结构对应的残基占比计算。VMD-SS插件采用TCL脚本（TCL script）与Stride（stride）工具开发，用于计算蛋白质二级结构特征。