Journal
BIOINFORMATION
Volume 10, Issue 8, Pages 548-550Publisher
BIOMEDICAL INFORMATICS
DOI: 10.6026/97320630010548
Keywords
Secondary Structure; PDB; Trajectory; VMD; VMD-SS Plug-in; Stride
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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: http://science.scu.ac.ir/HomePage.aspx?TabID=13755
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