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| Search CASTp database |
Visualization options |
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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 is developed and maintained 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.
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| 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.
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| Acknowledgement |
The CASTp
server is partially funded by support from National Science Foundation
(DBI0078270, CAREER DBI-0133856)
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