title: Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices.
abstract: Wurst is a protein threading program with an emphasis on high quality sequence to structure alignments (http://www.zbh.uni-hamburg.de/wurst). Submitted sequences are aligned to each of about 3000 templates with a conventional dynamic programming algorithm, but using a score function with sophisticated structure and sequence terms. The structure terms are a log-odds probability of sequence to structure fragment compatibility, obtained from a Bayesian classification procedure. A simplex optimization was used to optimize the sequence-based terms for the goal of alignment and model quality and to balance the sequence and structural contributions against each other. Both sequence and structural terms operate with sequence profiles.
authors.affiliation: University of Hamburg, Zentrum für Bioinformatik, Bundesstrasse 43, D-20146 Hamburg, Germany.
authors.forename: Andrew E
authors.initials: AE
authors.lastname: Torda
authors.forename: James B
authors.initials: JB
authors.lastname: Procter
authors.forename: Thomas
authors.initials: T
authors.lastname: Huber
mesh_terms: D019943:Amino Acid Substitution; D020407:Internet; D008958:Models, Molecular; D011487:Protein Conformation; D020539:Sequence Analysis, Protein; D012984:Software; D014584:User-Computer Interface