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Nucleic Acids Research Advance Access originally published online on November 28, 2006
Nucleic Acids Research 2007 35(Database issue):D219-D223; doi:10.1093/nar/gkl897
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Nucleic Acids Research, 2007, Vol. 35, Database issue D219-D223
© 2006 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.

Articles

FireDB—a database of functionally important residues from proteins of known structure

Gonzalo Lopez*, A. Valencia and M. Tress

Computational and Structural Biology Program, Spanish National Cancer Research Centre (CNIO) Melchor Fernández Almagro, 3, E-28029, Madrid, Spain

*To whom correspondence should be addressed. Tel: +34 917 328 000; Fax: +34 912 246 980; Email: glopez{at}cnio.es

Received August 18, 2006. Revised October 9, 2006. Accepted October 10, 2006.

The FireDB database is a databank for functional information relating to proteins with known structures. It contains the most comprehensive and detailed repository of known functionally important residues, bringing together both ligand binding and catalytic residues in one site. The platform integrates biologically relevant data filtered from the close atomic contacts in Protein Data Bank crystal structures and reliably annotated catalytic residues from the Catalytic Site Atlas. The interface allows users to make queries by protein, ligand or keyword. Relevant biologically important residues are displayed in a simple and easy to read manner that allows users to assess binding site similarity across homologous proteins. Binding site residue variations can also be viewed with molecular visualization tools. The database is available at http://firedb.bioinfo.cnio.es


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[Abstract] [Full Text] [PDF]


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