Crevasse: Companion Pocket Finding Software for FADE
Crevasse is a pocket finding package designed as companion software for FADE. Crevasse segments FADE output into individual pockets on the protein surface. Crevasse is not focused as strictly on so-called druggable pockets as other pocket finding software. Instead it can be tuned to find varying degrees of concavity on the protein surface.
Crevasse has been successfully applied to compare conserved surface features on the protein kinase family. Pockets computed with FADE and Crevasse were spatially clustered using standard methods to map similarities and differences on a set of aligned protein kinase cores.
Crevasse and FADE also provide a fast, simple solution to rapidly find pockets and surface concavities on large sets of proteins. Crevasse and FADE operate from the command line and are designed to be easy to script for high-througput computations. The output is both visualization and database-friendly. Pockets are written in a PDB-like format that can be loaded into common viewers such as PyMol or VMD. They are also output as a list and in release 1.1 they will be written out as boxes enclosing the protein surface where the pocket was identified.
Please consult the following documentation:
Please complete this registration form to download Crevasse. You will receive a link to a page containing documentation and source code.
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Crevasse is companion software for FADE. You must be using a recent version FADE, downloaded any time after October 8, 2009. Download FADE from Julie Mitchell at UW.
Elaine E. Thompson, Alexandr P. Kornev, Natarajan Kannan, Choel Kim, Lynn F. Ten Eyck, Susan S. Taylor Comparative surface geometry of the protein kinase family, Protein Science, 18(10): 2016-2026, 2009. View Abstract
J. C. Mitchell, R. Kerr and L. F. Ten Eyck, Rapid atomic density measures for molecular shape characterization, J. Mol. Graph. Model., 19(3): 324-329, 2001. View Abstract
|Last revision: October 21 2009||San Diego Supercomputer Center|
|URL: http://www.sdsc.edu/CCMS/Crevasse||© Copyright 2007 University of California at San Diego|