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Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices.

Andrew E Torda·James B Procter·Thomas Huber
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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.

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Amino Acid SubstitutionInternetModels, MolecularProtein ConformationSequence Analysis, ProteinSoftwareUser-Computer InterfaceJournal Article

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Andrew E Torda, James B Procter, Thomas Huber. 2004-07-01. Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices.. https://doi.org/10.1093/nar%2Fgkh357

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