Scooby-domain: prediction of globular domains in protein sequence | Zendy

R. A. George | Zendy; K. Lin | Zendy; Jaap Heringa | Zendy

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Scooby-domain: prediction of globular domains in protein sequence

Author(s) -

R. A. George,

K. Lin,

Jaap Heringa

Publication year - 2005

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gki381

Subject(s) - biology , sequence (biology) , domain (mathematical analysis) , peptide sequence , protein domain , computational biology , globular protein , sequence alignment , protein sequencing , homology modeling , protein structure , loop modeling , sequence logo , protein structure prediction , sequence homology , genetics , biochemistry , mathematics , gene , mathematical analysis , enzyme

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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