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Bioinformatics Advance Access published online on July 19, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti575
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received May 23, 2005
Revised June 16, 2005
Accepted July 6, 2005

Applications note

HTH-query: a method for detecting DNA-binding proteins with a Helix-Turn-Helix structural motif

C. Ferrer-Costa 1, H. P. Shanahan 2*, S. Jones 3, and J. M. Thornton 4

1 Molecular Modelling and Bioinformatics, IRBB-Parc Cientific de Barcelona. UB, Josep Samitier, 1-5 08028 Barcelona, Catalonia, Spain
2 Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK
3 Department of Biochemistry, School of Life Sciences, John Maynard Smith Building, University of Sussex, Falmer, Brighton, BN1 9QG, UK
4 EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

* To whom correspondence should be addressed.
H. P. Shanahan, E-mail: Hugh.Shanahan{at}physics.org


  Abstract

Summary: HTH-query is web based service to determine if a protein structure has a Helix-Turn-Helix structural motif which could bind to DNA. It is based on a similarity with a set of structural templates, the accessibility of a putative structural motif and a positive electrostatic potential in the neighbourhood of the putative motif. A set of scores are computed, based on each template, using a linear predictor. From the training set used the predictor has a true positive rate of 83.5% and a false positive rate of 0.8%. The emphasis for the web site is on providing a straightforward interface which can be easily used by a bench-based scientist.

Availability: HTHquery is implemented using a set of Perl scripts and C program and can be accessed freely on the web site http://www.ebi.ac.uk/thornton-srv/databases/HTHquery.


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