Document Detail

Property-based sequence representations do not adequately encode local protein folding information.
MedLine Citation:
PMID:  17387739     Owner:  NLM     Status:  MEDLINE    
We examine the informatic characteristics of amino acid representations based on physical properties. We demonstrate that sequences rewritten using contracted alphabets based on physical properties do not encode local folding information well. The best four-character alphabet can only encode approximately 57% of the maximum possible amount of structural information. This result suggests that property-based representations that operate on a local length scale are not likely to be useful in homology searches and fold-recognition exercises.
A D Solis; S Rackovsky
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural    
Journal Detail:
Title:  Proteins     Volume:  67     ISSN:  1097-0134     ISO Abbreviation:  Proteins     Publication Date:  2007 Jun 
Date Detail:
Created Date:  2007-05-11     Completed Date:  2007-06-07     Revised Date:  2007-12-03    
Medline Journal Info:
Nlm Unique ID:  8700181     Medline TA:  Proteins     Country:  United States    
Other Details:
Languages:  eng     Pagination:  785-8     Citation Subset:  IM    
Copyright Information:
2007 Wiley-Liss, Inc.
Department of Pharmacology and Biological Chemistry, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, New York 10029, USA.
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MeSH Terms
Amino Acid Sequence
Cluster Analysis
Molecular Sequence Data
Protein Folding*
Proteins / chemistry*,  metabolism*
Grant Support
2R01 LM-06789/LM/NLM NIH HHS
Reg. No./Substance:

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