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Nucleic Acids Research 2005 33(Web Server Issue):W160-W163; doi:10.1093/nar/gki381
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Article

Scooby-domain: prediction of globular domains in protein sequence

Richard A. George1,2, Kuang Lin3 and Jaap Heringa4,*

1Inpharmatica Ltd 60 Charlotte Street, London W1T 2NU UK 2European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK 3Division of Mathematical Biology, National Institute for Medical Research The Ridgeway, Mill Hill NW7 1AA, UK 4Centre for Integrative Bioinformatics (IBIVU), Faculty of Sciences and Faculty of Earth and Life Sciences, Vrije Universiteit De Boelelaan 1081a, 1081HV Amsterdam, The Netherlands

*To whom correspondence should be addressed. Tel: +31 2059 87649; Fax: +31 2059 87653; Email: heringa{at}cs.vu.nl

Received February 14, 2005. Revised March 8, 2005. Accepted March 8, 2005.

Scooby-domain (sequence hydrophobicity predicts domains) is a fast and simple method to identify globular domains in protein sequence, based on the observed lengths and hydrophobicities of domains from proteins with known tertiary structure. The prediction method successfully identifies sequence regions that will form a globular structure and those that are likely to be unstructured. The method does not rely on homology searches and, therefore, can identify previously unknown domains for structural elucidation. Scooby-domain is available as a Java applet at http://ibivu.cs.vu.nl/programs/scoobywww. It may be used to visualize local properties within a protein sequence, such as average hydrophobicity, secondary structure propensity and domain boundaries, as well as being a method for fast domain assignment of large sequence sets.


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