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

Torda, A. E., Procter, J. B. and Huber, T. (2004) Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices. Nucleic Acids Research, 32 Web server issue: W532-W535.


Author Torda, A. E.
Procter, J. B.
Huber, T.
Title Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices
Journal name Nucleic Acids Research   Check publisher's open access policy
ISSN 0305-1048
Publication date 2004
Sub-type Article (original research)
DOI 10.1093/nar/gkh357
Volume 32
Issue Web server issue
Start page W532
End page W535
Total pages 4
Editor R. T. Walker
D. Soll
A. S. Jones
Place of publication Oxford, UK
Publisher Oxford University Press
Collection year 2004
Language eng
Subject C1
250699 Theoretical and Computational Chemistry not elsewhere classified
250502 Physical Chemistry of Macromolecules
250503 Characterisation of Macromolecules
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.
Keyword Biochemistry & Molecular Biology
Hidden Markov-models
Structure Prediction Servers
Fold Recognition
Twilight-zone
Alignments
Quality
Genthreader
Generation
Q-Index Code C1

 
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