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

Authors:
Niklas Von Öhsen;Ingolf Sommer;Ralf Zimmer;Thomas Lengauer
Affiliations:
Institute for Algorithms and Scientific Computing (SCAI), Fraunhofer Gesellschaft, Schloss Birlinghoven, Sankt Augustin, 53754, Germany,;Max-Planck-Institut für Informatik, Stuhlsatzenhausweg 85, Saarbrücken, 66123, Germany;Institut für Informatik, Ludwig-Maximilians-Universität München, Amalienstrasse 17, München, 80333, Germany;Max-Planck-Institut für Informatik, Stuhlsatzenhausweg 85, Saarbrücken, 66123, Germany
Venue:
Bioinformatics
Year:
2004

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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.