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Nucleic Acids Research Advance Access published online on June 6, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm422
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© 2007 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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siteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins

C. Axel Innis*

Howard Hughes Medical Institute/Yale University, Department of Molecular Biophysics and Biochemistry, New Haven, CT 06520-8114, USA

*To whom correspondence should be addressed. Tel: 203 432 5627; Email: axel.innis{at}yale.edu

Received January 30, 2007. Revised May 6, 2007. Accepted May 9, 2007.

Although knowledge of a protein's functional site is a key requirement for understanding its mode of action at the molecular level, our ability to locate such sites experimentally is far exceeded by the rate at which sequence and structural information is being accumulated. siteFiNDER|3D is an online tool for the prediction of functionally important regions in proteins of known structure. At the core of the server lies the CFG analysis algorithm, which uses a moving 3D window to correlate patterns of functional/chemical group conservation in the query protein with the location of functional sites. Here, we give a general overview of the functionality offered by the siteFiNDER|3D server, along with general recommendations aimed at maximizing the accuracy and predictive value of this tool in a variety of contexts. siteFiNDER|3D can be accessed at: ‘http://sage.csb.yale.edu/sitefinder3d’ and requires, at a minimum, the atomic coordinates of a query protein in PDB format.


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