Arby: automatic protein structure prediction using profile-profile alignment and confidence measures

Publication Type		Journal Article
Authors		Niklas von Öhsen, Ingolf Sommer, Ralf Zimmer
Year of Publication		2004
Journal		Bioinformatics
Volume		20
Number		14
Pages		2228-35
DOI		10.1093/bioinformatics/bth232
Citation Key		bioinflmu-573
Document visibility		Global publication list
PDF		PDF
Export		BibTex

Abstract

MOTIVATION: Arby is a new server for protein structure prediction that combines several homology-based methods for predicting the three-dimensional structure of a protein, given its sequence. The methods used include a threading approach, which makes use of structural information, and a profile-profile alignment approach that incorporates secondary structure predictions. The combination of the different methods with the help of empirically derived confidence measures affords reliable template selection. RESULTS: According to the recent CAFASP3 experiment, the server is one of the most sensitive methods for predicting the structure of single domain proteins. The quality of template selection is assessed using a fold-recognition experiment. AVAILABILITY: The Arby server is available through the portal of the Helmholtz Network for Bioinformatics at http://www.hnbioinfo.de under the protein structure category.