Paper Info
Title
SSEP-Domain: protein domain prediction by alignment of secondary structure elements and profiles
Abstract
Motivation: 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. Results: A preliminary version of SSEP-Domain was ranked among the top-performing domain prediction servers in the CASP 6 and CAFASP 4 experiments. Evaluation of the final version shows further improvement over these results together with a significant speed-up. Availability: The server is available at http://www.bio.ifi.lmu.de/SSEP/ Contact: jan.gewehr@bio.ifi.lmu.de Supplementary information: The supplementary data are available at http://www.bio.ifi.lmu.de/SSEP/
Year
DOI
Venue
2006
10.1093/bioinformatics/bti751
Bioinformatics
Keywords
Field
DocType
protein domains,structural genomics,secondary structure,pattern search
CAFASP,Data mining,Protein domain,Structural genomics,Ranking,Computer science,Server,Bioinformatics,Protein secondary structure,CASP,InterPro
Journal
Volume
Issue
ISSN
22
2
1367-4803
Citations 
PageRank 
References 
16
0.81
17
Authors
2
Name
Order
Citations
PageRank
Jan E. Gewehr18117.19
Ralf Zimmer2160.81