Nucleic Acids Research Advance Access originally published online on April 30, 2009
Nucleic Acids Research 2009 37(Web Server issue):W384-W389; doi:10.1093/nar/gkp308
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W384-W389
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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SplitPocket: identification of protein functional surfaces and characterization of their spatial patterns
1Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, 2Center for Computational Biology and Bioinformatics, University of Texas at Austin, One University Station, C4500, Austin, TX 78712, USA and 3Biodiversity Research Center, Academia Sinica, Taipei 115 Taiwan
*To whom correspondence should be addressed. Tel: +1 773 702 3104; Fax: +1 773 702 9740; Email: whli{at}uchicago.edu.
Received February 20, 2009. Revised April 13, 2009. Accepted April 16, 2009.
SplitPocket (http://pocket.uchicago.edu/) is a web server to identify functional surfaces of protein from structure coordinates. Using the Alpha Shape Theory, we previously developed an analytical approach to identify protein functional surfaces by the geometric concept of a split pocket, which is a pocket split by a binding ligand. Our geometric approach extracts site-specific spatial information from coordinates of structures. To reduce the search space, probe radii are designed according to the physicochemical textures of molecules. The method uses the weighted Delaunay triangulation and the discrete flow algorithm to obtain geometric measurements and spatial patterns for each predicted pocket. It can also measure the hydrophobicity on a surface patch. Furthermore, we quantify the evolutionary conservation of surface patches by an index derived from the entropy scores in HSSP (homology-derived secondary structure of proteins). We have used the method to examine 
1.16 million potential pockets and identified the split pockets in >26 000 structures in the Protein Data Bank. This integrated web server of functional surfaces provides a source of spatial patterns to serve as templates for predicting the functional surfaces of unbound structures involved in binding activities. These spatial patterns should also be useful for protein functional inference, structural evolution and drug design.
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  Y. Y. Tseng, Z. J. Chen, and W.-H. Li fPOP: footprinting functional pockets of proteins by comparative spatial patterns Nucleic Acids Res., October 30, 2009; (2009) gkp900v1. [Abstract] [Full Text] [PDF]
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