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Nucleic Acids Research Advance Access published online on May 3, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm252
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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.

Web Server Issue

PAR-3D: a server to predict protein active site residues

Kshama Goyal1, Debasisa Mohanty2 and Shekhar C. Mande1,*

1Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad 500 076 and 2National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India

*To whom correspondence should be addressed. Tel: +91-40-27171442; Fax: +91-40-27155610; Email: shekhar{at}cdfd.org.in

Received January 17, 2007. Revised March 10, 2007. Accepted April 8, 2007.

PAR-3D (http://sunserver.cdfd.org.in:8080/protease/PAR_3D/index.html) is a web-based tool that exploits the fact that relative juxtaposition of active site residues is a conserved feature in functionally related protein families. The server uses previously calculated and stored values of geometrical parameters of a set of known proteins (training set) for prediction of active site residues in a query protein structure. PAR-3D stores motifs for different classes of proteases, the ten glycolytic pathway enzymes and metal-binding sites. The server accepts the structures in the pdb format. The first step during the prediction is the extraction of probable active site residues from the query structure. Spatial arrangement of the probable active site residues is then determined in terms of geometrical parameters. These are compared with stored geometries of the different motifs. Its speed and efficiency make it a beneficial tool for structural genomics projects, especially when the biochemical function of the protein has not been characterized.


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