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Bioinformatics Advance Access originally published online on July 19, 2005
Bioinformatics 2005 21(18):3679-3680; 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{at}oupjournals.org

HTHquery: 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

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

*To whom correspondence should be addressed.

Summary: HTHquery is a 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 website 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 website http://www.ebi.ac.uk/thornton-srv/databases/HTHquery

Contact: Hugh.Shanahan{at}physics.org

Received on May 23, 2005; revised on June 16, 2005; accepted on July 6, 2005

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