title: VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program.
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.
  
  
  BACKGROUND
  The database is available for free at http://science.scu.ac.ir/HomePage.aspx?TabID=13755.
authors.affiliation: Department of Laboratory Science, faculty of Para-medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
authors.forename: Masoumeh
authors.initials: M
authors.lastname: Yahyavi
authors.affiliation: Department of Genetics, faculty of Sciences, Shahid Chamran University, Ahvaz, Iran.
authors.forename: Sajad
authors.initials: S
authors.lastname: Falsafi-Zadeh
authors.affiliation: Department of Genetics, faculty of Sciences, Shahid Chamran University, Ahvaz, Iran.
authors.forename: Zahra
authors.initials: Z
authors.lastname: Karimi
authors.affiliation: Biochemistry faculty, Hamedan University of Medical Sciences, Hamedan, Iran.
authors.forename: Giti
authors.initials: G
authors.lastname: Kalatarian
authors.affiliation: Department of Genetics, faculty of Sciences, Shahid Chamran University, Ahvaz, Iran.
authors.forename: Hamid
authors.initials: H
authors.lastname: Galehdari
keywords: PDB; Secondary Structure; Stride; Trajectory; VMD; VMD-SS Plug-in