Nucleic Acids Research Advance Access originally published online on June 21, 2007
Nucleic Acids Research 2007 35(Web Server issue):W573-W577; doi:10.1093/nar/gkm297
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Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W573-W577
© 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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firestar—prediction of functionally important residues using structural templates and alignment reliability
Structural Biology and Biocomputing 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 February 5, 2007. Revised April 2, 2007. Accepted April 12, 2007.
Here we present firestar, an expert system for predicting ligand-binding residues in protein structures. The server provides a method for extrapolating from the large inventory of functionally important residues organized in the FireDB database and adds information about the local conservation of potential-binding residues. The interface allows users to make queries by protein sequence or structure. The user can access pairwise and multiple alignments with structures that have relevant functionally important binding sites. The results are presented in a series of easy to read displays that allow users to compare binding residue conservation across homologous proteins. The binding site residues can also be viewed with molecular visualization tools. One feature of firestar is that it can be used to evaluate the biological relevance of small molecule ligands present in PDB structures. With the server it is easy to discern whether small molecule binding is conserved in homologous structures. We found this facility particularly useful during the recent assessment of CASP7 function prediction. Availability: http://firedb.bioinfo.cnio.es/Php/FireStar.php.
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