PSS - Protein Structural Statistics

• Presentation
• Citation
• Download
• Documentation
• Example
• Screenshots
• Support
• Copyright

Presentation

PSS is a protein structural statistics program for Unix-like environments. It is written in Perl, has a command-line interface, and is distributed under the GNU General Public License.

PSS reads an ensemble of PDB files of protein structures, performs a multiple sequence alignment, and computes structural statistics for each position of the alignment. Different optional functionalities are proposed: structure superposition, Cartesian coordinate statistics, dihedral angle calculation and statistics, and a cluster analysis based on dihedral angles. An HTML report containing a summary of results and figures can also be generated.

Citation

Please cite the following article in a publication using PSS:

Protein structural statistics with PSS
Thomas Gaillard, Benjamin B.L. Schwarz, Yassmine Chebaro, Roland H. Stote, and Annick Dejaegere
J. Chem. Inf. Model. 2013, 53, 2471-2482.
doi:10.1021/ci400233j

Download

• PSS.1.2.tar.gz
• PSS.1.2.tar.gz.md5sum

Documentation

• PSS.pl.html (main program)
• PSS.pm.html (object-oriented classes and methods)

Example

• Description:
  • 7 structures listed in the structlist.dat file are read from the pdb folder
  • The multiple sequence alignment is derived from PDB numbering
  • Structures are superposed on the A chain of the 1GZ8 structure
  • Structural statistics in Cartesian coordinates are calculated
  • Structural statistics in dihedral coordinates are calculated
  • A cluster analysis is performed based on positions and dihedrals defined in the poslist.dat file
  • A report in HTML format is produced including 3D visualization of superposed structures (dihedral distribution plots are limited to positions defined in poslist.dat)
• Command-line:
  pss --pdb pdb --structlist structlist.dat --poslist poslist.dat --align pdbnum --firstalignpos -2 --superp theseus --superpref 1GZ8:A --superp3d --cartstat --dihestat --clust --radius 60 --report
• PSS log
• HTML report

Screenshots

• 3D visualization of superposed structures:
  

  

• Cartesian fluctuation superposable figure:
  

  

• Cartesian fluctuation sortable and scrollable table:
  

  

• Dihedral fluctuation superposable figure:
  

  

• Dihedral fluctuation sortable and scrollable table:
  

  

• Dihedral distribution figures:
  

  

• Clustering dendrogram:
  

  

Support

We appreciate if users report bugs, feature requests, improvements, or patches to <thomas.gaillard@polytechnique.edu>.

Copyright

Copyright (c) 2006-2016 Thomas Gaillard, Benjamin Schwarz, Roland H. Stote, Annick Dejaegere

written by Thomas Gaillard <thomas.gaillard@polytechnique.edu>
with contributions from Benjamin Schwarz, Roland H. Stote, and Annick Dejaegere

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.