HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif | Zendy

Carles FerrerCosta | Zendy; Hugh Shanahan | Zendy; Susan R. Jones | Zendy; Janet M. Thornton | Zendy

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HTHquery: a method for detecting DNA-binding proteins with a helix-turn-helix structural motif

Author(s) -

Carles FerrerCosta,

Hugh Shanahan,

Susan R. Jones,

Janet M. Thornton

Publication year - 2005

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bti575

Subject(s) - perl , scripting language , motif (music) , structural motif , alpha helix , computer science , template , helix (gastropod) , computational biology , helix turn helix , protein structure , crystallography , biology , chemistry , dna binding protein , genetics , programming language , biochemistry , transcription factor , physics , ecology , snail , acoustics , gene

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.

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