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Nucleic Acids Research, 2003, Vol. 31, No. 13 3324-3327
© 2003 Oxford University Press

WebFEATURE: an interactive web tool for identifying and visualizing functional sites on macromolecular structures

Mike P. Liang, D. Rey Banatao, Teri E. Klein, Douglas L. Brutlag1 and Russ B. Altman*

Department of Genetics and Stanford Medical Informatics, 251 Campus Drive, Stanford University, Stanford, CA 94305, USA 1 Department of Biochemistry and Stanford Medical Informatics, Beckman Center B400 MC 5307, Stanford University, Stanford, CA 94305, USA

*To whom correspondence should be addressed. Tel: +1 6507253394; Fax: +1 6507257944; Email: russ.altman{at}stanford.edu
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

WebFEATURE (http://feature.stanford.edu/webfeature/) is a web-accessible structural analysis tool that allows users to scan query structures for functional sites in both proteins and nucleic acids. WebFEATURE is the public interface to the scanning algorithm of the FEATURE package, a supervised learning algorithm for creating and identifying 3D, physicochemical motifs in molecular structures. Given an input structure or Protein Data Bank identifier (PDB ID), and a statistical model of a functional site, WebFEATURE will return rank-scored ‘hits’ in 3D space that identify regions in the structure where similar distributions of physicochemical properties occur relative to the site model. Users can visualize and interactively manipulate scored hits and the query structure in web browsers that support the Chime plug-in. Alternatively, results can be downloaded and visualized through other freely available molecular modeling tools, like RasMol, PyMOL and Chimera. A major application of WebFEATURE is in rapid annotation of function to structures in the context of structural genomics.


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