SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles | Zendy

Jan E. Gewehr | Zendy; Ralf Zimmer | Zendy

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SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles

Author(s) -

Jan E. Gewehr,

Ralf Zimmer

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/bti751

Subject(s) - casp , domain (mathematical analysis) , computer science , protein structure prediction , protein domain , data mining , computational biology , sequence alignment , template , artificial intelligence , machine learning , protein structure , pattern recognition (psychology) , biology , peptide sequence , mathematics , genetics , mathematical analysis , biochemistry , gene , programming language

The prediction of protein domains is a crucial task for functional classification, homology-based structure prediction and structural genomics. In this paper, we present the SSEP-Domain protein domain prediction approach, which is based on the application of secondary structure element alignment (SSEA) and profile-profile alignment (PPA) in combination with InterPro pattern searches. SSEA allows rapid screening for potential domain regions while PPA provides us with the necessary specificity for selecting significant hits. The combination with InterPro patterns allows finding domain regions without solved structural templates if sequence family definitions exist.

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