The Global Protein Surface Survey allows for the visualization of surface features from three dimensional protein structures using PyMOL. In addition to CASTp surface pockets and voids (http://cast.engr.uic.edu) , contact surfaces for ligands, metals, peptides and DNA bindings surfaces are available for viewing.

The following publically available sources contribute data for the plugin:

Computed Atlas of Surface Topography of Proteins (CASTp, http://cast.engr.uic.edu)

Catalytic Site Atlas (CSA, http://www.ebi.ac.uk/thornton-srv/databases/CSA/)

Download/Install

Version 0.3: Simply place this file into the following directory: $PYMOLPATH/module/pmg_tk/startup/
This version makes a significant reliability fix in the upload file service. Update released July 9, 2007.

Version 0.2: Simply place this file into the following directory: $PYMOLPATH/module/pmg_tk/startup/
The latest version (v0.2) of the plugin allows users to upload their own PDB files directly from the PyMOL interface.

Version 0.1: Simply place this file into the following directory: $PYMOLPATH/module/pmg_tk/startup/

This version of the plugin has been tested with PyMOL v0.98 and v0.99.

Using the Plugin

Under the "Plugin" menu, select Global Protein Surface Survey. The option "GPSS Surfaces All" shows all CASTp and ligand, metal, and peptide surfaces..



Enter a PDB identification code:



The plugin will load the PDB and all the associated surfaces. All pockets are shown in surface mode. Simply click on the surface name to toggle on/off.

Upload A Structure

As of Version 0.2, users may upload a structure in .pdb format directly from the plugin or via the WWW interface. The results will be viewable from both sources. You must supply a valid email address, as you will be contacted when all surfaces of your structure have been calculated. It is the GPSS policy, that all uploaded files submitted are stored anonymously and will be deleted weekly on Sunday at 11:59 PM (CST).If you have any questions please contact abinkowski@anl.gov.

This functionality is experimental, but it should work reliably.

What about CASTPyMOL Plugin?

The GPSS Plugin is an enhanced version of the CASTpyMOL plugin previously developed. There will be no further releases of the CASTpyMOL plugin. It is still available at (http://cast.engr.uic.edu), but will only work with PyMOL v0.98. All CASTp surface data will be accessible from the GPSS plugin, as well as new data that was not previously available.

Acknowledgements

I would like to thank Warren DeLano for the PyMOL software, Jie Liang for access to the CASTp data and Sebastien Moretti for suggesting the plugin.

Questions, Comments, Feedback, Suggestions

Andrew Binkowski (abinkowski@anl.gov)