Document Detail


Grouping of amino acid types and extraction of amino acid properties from multiple sequence alignments using variance maximization.
MedLine Citation:
PMID:  16184599     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Understanding of amino acid type co-occurrence in trusted multiple sequence alignments is a prerequisite for improved sequence alignment and remote homology detection algorithms. Two objective approaches were used to investigate co-occurrence, both based on variance maximization of the weighted residue frequencies in columns taken from a large alignment database. The first approach discretely grouped amino acid types, and the second approach extracted orthogonal properties of amino acids using principal components analysis. The grouping results corresponded to amino acid physical properties such as side chain hydrophobicity, size, or backbone flexibility, and an optimal arrangement of approximately eight groups was observed. However, interpretation of the orthogonal properties was more complex. Although the principal components accounting for the largest variances exhibited modest correlations with hydrophobicity and conservation of glycine, in general principal components did not correspond to physical properties of amino acids. Although not intuitive, these amino acid mathematical properties were demonstrated to be robust and to improve local pairwise alignment accuracy, relative to 20 amino acid frequencies alone, for a simple test case.
Authors:
James O Wrabl; Nick V Grishin
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, U.S. Gov't, P.H.S.    
Journal Detail:
Title:  Proteins     Volume:  61     ISSN:  1097-0134     ISO Abbreviation:  Proteins     Publication Date:  2005 Nov 
Date Detail:
Created Date:  2005-10-27     Completed Date:  2006-04-17     Revised Date:  2007-11-14    
Medline Journal Info:
Nlm Unique ID:  8700181     Medline TA:  Proteins     Country:  United States    
Other Details:
Languages:  eng     Pagination:  523-34     Citation Subset:  IM    
Copyright Information:
(c) 2005 Wiley-Liss, Inc.
Affiliation:
Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas 75390-9050, USA.
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MeSH Terms
Descriptor/Qualifier:
Amino Acids / chemistry*
Hydrophobicity
Models, Chemical
Pliability
Principal Component Analysis
Proteins / chemistry*
Sequence Alignment*
Grant Support
ID/Acronym/Agency:
GM67165/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
0/Amino Acids; 0/Proteins

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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