VMD-SS：VMD程序中用于计算蛋白质二级结构的图形用户界面插件。
VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program.
作者信息
Yahyavi Masoumeh, Falsafi-Zadeh Sajad, Karimi Zahra, Kalatarian Giti, Galehdari Hamid
机构信息
Department of Laboratory Science, faculty of Para-medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
Department of Genetics, faculty of Sciences, Shahid Chamran University, Ahvaz, Iran.
出版信息
Bioinformation. 2014 Aug 30;10(8):548-50. doi: 10.6026/97320630010548. eCollection 2014.
UNLABELLED
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.
AVAILABILITY
The database is available for free at http://science.scu.ac.ir/HomePage.aspx?TabID=13755.
未标注
对蛋白质二级结构（SS）类型的研究很重要。分子动力学模拟过程中二级结构的演变是分析蛋白质结构的一个有用参数。因此，描述VMD - SS（一个软件程序）以识别二级结构元件及其在模拟过程中的轨迹（针对蛋白质数据库（PDB）中可用的已知结构）是很有意义的。该程序有助于计算：（1）二级结构百分比，（2）每个残基中二级结构的出现情况，（3）模拟过程中的二级结构百分比，以及（4）模拟过程中所有二级结构类型中的残基百分比。VMD - SS插件是使用TCL脚本和stride设计的，用于计算二级结构特征。
可用性
该数据库可在http://science.scu.ac.ir/HomePage.aspx?TabID = 13755免费获取。
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