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Title |
VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program
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Authors |
Masoumeh Yahyavi1, Sajad Falsafi-Zadeh2*, Zahra Karimi2, Giti Kalatarian3 & Hamid Galehdari2
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Affiliation |
1Department of Laboratory Science, faculty of Para-medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; 2Department of Genetics, faculty of Sciences, Shahid Chamran University, Ahvaz, Iran; 3Biochemistry faculty, Hamedan University of Medical Sciences, Hamedan, Iran
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sajad.falsafi@yahoo.com; *Corresponding authors
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Article Type |
Software
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Date |
Received January 08, 2013; Accepted January 15, 2013; Published August 30, 2014
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Abstract |
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.
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Availability |
http://science.scu.ac.ir/HomePage.aspx?TabID=13755
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Keywords |
Secondary Structure, PDB, Trajectory, VMD, VMD-SS Plug-in, Stride.
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Citation |
Yahyavi et al.
Bioinformation 10(8): 548-550 (2014) |
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Edited by |
P Kangueane
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ISSN |
0973-2063
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Publisher |
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License |
This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License. |