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Nucleic Acids Research 2004 32(16):4732-4741; doi:10.1093/nar/gkh803
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Published online 8 September 2004

Nucleic Acids Research, Vol. 32 No. 16 © Oxford University Press 2004; all rights reserved

Identifying DNA-binding proteins using structural motifs and the electrostatic potential

Hugh P. Shanahan*, Mario A. Garcia1, Susan Jones2 and Janet M. Thornton

EMBL–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, 1 Departamento de Ciencias Quimicas, Facultad de Ciencias Experimentales y de la Salud, Universidad San Pablo CEU, Urb Monteprincipe, 28668, Boadilla del Monte, Madrid, Spain and 2 Department of Biochemistry, School of Life Sciences, John Maynard Smith Building, University of Sussex, Falmer, Brighton BN1 9QG, UK

* To whom correspondence should be addressed. Tel: +44 1223 492540; Fax: +44 1223 494444; Email: Hugh.Shanahan{at}physics.org
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

Received May 20, 2004; Revised and Accepted August 17, 2004

Robust methods to detect DNA-binding proteins from structures of unknown function are important for structural biology. This paper describes a method for identifying such proteins that (i) have a solvent accessible structural motif necessary for DNA-binding and (ii) a positive electrostatic potential in the region of the binding region. We focus on three structural motifs: helix–turn-helix (HTH), helix–hairpin–helix (HhH) and helix–loop–helix (HLH). We find that the combination of these variables detect 78% of proteins with an HTH motif, which is a substantial improvement over previous work based purely on structural templates and is comparable to more complex methods of identifying DNA-binding proteins. Similar true positive fractions are achieved for the HhH and HLH motifs. We see evidence of wide evolutionary diversity for DNA-binding proteins with an HTH motif, and much smaller diversity for those with an HhH or HLH motif.


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