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Bioinformatics Advance Access originally published online on October 10, 2005
Bioinformatics 2005 21(24):4425-4426; doi:10.1093/bioinformatics/bti712
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

QUASAR—scoring and ranking of sequence–structure alignments

Fabian Birzele *,{dagger}, Jan E. Gewehr {dagger} and Ralf Zimmer

Practical Informatics and Bioinformatics Group, Department of Informatics, Ludwig-Maximilians-University Amalienstrasse 17, D-80333 Munich, Germany

*To whom correspondence should be addressed.

Summary: Sequence–structure alignments are a common means for protein structure prediction in the fields of fold recognition and homology modeling, and there is a broad variety of programs that provide such alignments based on sequence similarity, secondary structure or contact potentials. Nevertheless, finding the best sequence–structure alignment in a pool of alignments remains a difficult problem. QUASAR (quality of sequence–structure alignments ranking) provides a unifying framework for scoring sequence–structure alignments that aids finding well-performing combinations of well-known and custom-made scoring schemes. Those scoring functions can be benchmarked against widely accepted quality scores like MaxSub, TMScore, Touch and APDB, thus enabling users to test their own alignment scores against ‘standard-of-truth’ structure-based scores. Furthermore, individual score combinations can be optimized with respect to benchmark sets based on known structural relationships using QUASAR's in-built optimization routines.

Availability: The software, examples, the Java documentation and a tutorial are available at http://www.bio.ifi.lmu.de/QUASAR

Contact: fabian.birzele{at}ifi.lmu.de

Received on August 19, 2005; revised on September 27, 2005; accepted on October 6, 2005

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F. Birzele, J. E. Gewehr, G. Csaba, and R. Zimmer
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