Skip Navigation



Nucleic Acids Research Advance Access published online on June 21, 2007
Nucleic Acids Research, doi:10.1093/nar/gkm297
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (2371K) Freely available
Right arrow Screen PDF (639K) Freely available
Right arrowOA All Versions of this Article:
35/suppl_2/W573    most recent
gkm297v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by López, G.
Right arrow Articles by Tress, M. L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by López, G.
Right arrow Articles by Tress, M. L.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© 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

firestar—prediction of functionally important residues using structural templates and alignment reliability

Gonzalo López*, Alfonso Valencia and Michael L. Tress

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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
C. Kauffman and G. Karypis
LIBRUS: combined machine learning and homology information for sequence-based ligand-binding residue prediction
Bioinformatics, December 1, 2009; 25(23): 3099 - 3107.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
N. Tuncbag, G. Kar, O. Keskin, A. Gursoy, and R. Nussinov
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces
Brief Bioinform, May 1, 2009; 10(3): 217 - 232.
[Abstract] [Full Text] [PDF]

Home page
 J R Soc InterfaceHome page
G. A Reeves, D. Talavera, and J. M Thornton
Genome and proteome annotation: organization, interpretation and integration
J R Soc Interface, February 6, 2009; 6(31): 129 - 147.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
M. L. Tress, J.-J. Wesselink, A. Frankish, G. Lopez, N. Goldman, A. Loytynoja, T. Massingham, F. Pardi, S. Whelan, J. Harrow, et al.
Determination and validation of principal gene products
Bioinformatics, January 1, 2008; 24(1): 11 - 17.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.