Document Detail

Sequence-structure homology recognition by iterative alignment refinement and comparative modeling.
MedLine Citation:
PMID:  11835486     Owner:  NLM     Status:  MEDLINE    
Our approach to fold recognition for the fourth critical assessment of techniques for protein structure prediction (CASP4) experiment involved the use of the FUGUE sequence-structure homology recognition program (, followed by model building. We treat models as hypotheses and examine these to determine whether they explain the available data. Our method depends heavily on environment-specific substitution tables derived from our database of structural alignments of homologous proteins (HOMSTRAD, FUGUE uses these tables to incorporate structural information into profiles created from HOMSTRAD alignments that are matched against a profile created for the target from multiple sequence alignment. In addition, environment-specific substitution tables are used throughout the modeling procedure and as part of the model evaluation. Annotation of sequence alignments with JOY, to reflect local structural features, proved valuable, both for modifying hypotheses, and for rejecting predictions when the expected pattern of conservation is not observed. Our stringency in rejecting incorrect predictions led us to submit a relatively small number of models, including only a low number of false positives, resulting in a high average score.
M G Williams; H Shirai; J Shi; H G Nagendra; J Mueller; K Mizuguchi; R N Miguel; S C Lovell; C A Innis; C M Deane; L Chen; N Campillo; D F Burke; T L Blundell; P I de Bakker
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Proteins     Volume:  Suppl 5     ISSN:  0887-3585     ISO Abbreviation:  Proteins     Publication Date:  2001  
Date Detail:
Created Date:  2002-02-08     Completed Date:  2002-08-27     Revised Date:  2006-11-15    
Medline Journal Info:
Nlm Unique ID:  8700181     Medline TA:  Proteins     Country:  United States    
Other Details:
Languages:  eng     Pagination:  92-7     Citation Subset:  IM    
Copyright Information:
Copyright 2002 Wiley-Liss, Inc.
Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
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MeSH Terms
Amino Acid Sequence
Carbohydrate Metabolism
Carboxylic Ester Hydrolases / chemistry
Computer Simulation
Cytoskeletal Proteins / chemistry
Models, Molecular*
Molecular Sequence Data
Polysaccharide-Lyases / chemistry
Protein Binding
Protein Folding
Protein Structure, Tertiary*
Sequence Analysis, Protein
Sequence Homology, Amino Acid*
alpha Catenin
Reg. No./Substance:
0/Cytoskeletal Proteins; 0/alpha Catenin; EC 3.1.1.-/Carboxylic Ester Hydrolases; EC; EC 4.2.2.-/Polysaccharide-Lyases; EC lyase

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