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...

Descripción completa

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
Descripción
Sumario: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

Ejemplares similares