VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program

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 identifi...

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Detalles Bibliográficos
Autores principales: Yahyavi, Masoumeh, Falsafi-Zadeh, Sajad, Karimi, Zahra, Kalatarian, Giti, Galehdari, Hamid
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Biomedical Informatics 2014
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166777/
https://www.ncbi.nlm.nih.gov/pubmed/25258493
http://dx.doi.org/10.6026/97320630010548
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author Yahyavi, Masoumeh
Falsafi-Zadeh, Sajad
Karimi, Zahra
Kalatarian, Giti
Galehdari, Hamid
author_facet Yahyavi, Masoumeh
Falsafi-Zadeh, Sajad
Karimi, Zahra
Kalatarian, Giti
Galehdari, Hamid
author_sort Yahyavi, Masoumeh
collection PubMed
description 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
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spelling pubmed-41667772014-09-25 VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program Yahyavi, Masoumeh Falsafi-Zadeh, Sajad Karimi, Zahra Kalatarian, Giti Galehdari, Hamid Bioinformation Software 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 Biomedical Informatics 2014-08-30 /pmc/articles/PMC4166777/ /pubmed/25258493 http://dx.doi.org/10.6026/97320630010548 Text en © 2014 Biomedical Informatics This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.
spellingShingle Software
Yahyavi, Masoumeh
Falsafi-Zadeh, Sajad
Karimi, Zahra
Kalatarian, Giti
Galehdari, Hamid
VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program
title VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program
title_full VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program
title_fullStr VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program
title_full_unstemmed VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program
title_short VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program
title_sort vmd-ss: a graphical user interface plug-in to calculate the protein secondary structure in vmd program
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166777/
https://www.ncbi.nlm.nih.gov/pubmed/25258493
http://dx.doi.org/10.6026/97320630010548
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