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CASTp Information
 
About CASTp
Background
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Examples
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PyMOL plugin
   
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  Jmol - Jmol is a free, open source molecule viewer. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. It only requires that you have a Java enabled browser. Works best in Internet Explorer.
  Chime Plugin - Chime is a broswer plugin that runs under Windows, MacOS, and IRIX. This is the best choice for Windows 95/98/NT/2000/XP or IRIX. Linux user can also use this plugin by running a virtual windows environment( VMware). Chime is available from MDL's website.
  E-mail only - This option allows you to get results back via email only. No visualizations will be provided.
 
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About CASTp
Binding sites and active sites of proteins and DNAs are often associated with structural pockets and cavities. castP server uses the weighted Delaunay triangulation and the alpha complex for shape measurements. It provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules. It measures analytically the area and volume of each pocket and cavity, both in solvent accessible surface (SA, Richards' surface) and molecular surface (MS, Connolly's surface). It also measures the number of mouth openings, area of the openings, circumference of mouth lips, in both SA and MS surfaces for each pocket.

You can request calculation for a particular molecule. The results will be shown on the screen or emailed to you. The emailed results include measured parameters for pockets, cavities and mouth openings, as well as listing of wall atoms and mouth atoms for each pocket. In addition, a downloadable PyMOL plugin will help you to visualize the pocket of your interest.
About CASTp Server
This server was developed by Joe Dundas and Zheng Ouyang as an update to the CASTp server developed by Andrew Binkowski and Shapor Naghibzadeh, under the guidance of Prof. Jie Liang, who developed the castP program and the original server. The computation is based on the pocket algorithm of the alpha shape theory, and its core is the alpha shape API developed in Edelsbrunner's group and the NCSA. We would like to thank Dr. Herbert Edelsbrunner for the alpha shape API and Dr. Clare K. Woodward for encouragement.
Reference
Please cite the following if you publish or present results using castP analysis:
Joe Dundas, Zheng Ouyang, Jeffery Tseng, Andrew Binkowski, Yaron Turpaz, and Jie Liang. 2006. CASTp: computed atas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucl. Acids Res., 34:W116-W118.
Additional background reading
Jie Liang, Herbert Edelsbrunner, and Clare Woodward. 1998. Anatomy of Protein Pockets and Cavities: Measurement of Binding Site Geometry and Implications for Ligand Design. Protein Sciene, 7:1884-1897.

© 2005 All rights reserved.
Acknowledgement
The CASTp server is partially funded by support from National Science Foundation (DBI0078270, CAREER DBI-0133856)