title: QUASAR--scoring and ranking of sequence-structure alignments.
abstract: 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.
authors.affiliation: Practical Informatics and Bioinformatics Group, Department of Informatics, Ludwig-Maximilians-University, Amalienstrasse 17, D-80333 Munich, Germany. fabian.birzele@ifi.lmu.de
authors.forename: Fabian
authors.initials: F
authors.lastname: Birzele
authors.forename: Jan E
authors.initials: JE
authors.lastname: Gewehr
authors.forename: Ralf
authors.initials: R
authors.lastname: Zimmer
mesh_terms: D019295:Computational Biology; D030562:Databases, Protein; D015394:Molecular Structure; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*; D016415:Sequence Alignment / Q000706:statistics & numerical data*; D012984:Software
chemical_list: D011506:Proteins