Document Detail


Accuracy of sequence alignment and fold assessment using reduced amino acid alphabets.
MedLine Citation:
PMID:  16506243     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Reduced or simplified amino acid alphabets group the 20 naturally occurring amino acids into a smaller number of representative protein residues. To date, several reduced amino acid alphabets have been proposed, which have been derived and optimized by a variety of methods. The resulting reduced amino acid alphabets have been applied to pattern recognition, generation of consensus sequences from multiple alignments, protein folding, and protein structure prediction. In this work, amino acid substitution matrices and statistical potentials were derived based on several reduced amino acid alphabets and their performance assessed in a large benchmark for the tasks of sequence alignment and fold assessment of protein structure models, using as a reference frame the standard alphabet of 20 amino acids. The results showed that a large reduction in the total number of residue types does not necessarily translate into a significant loss of discriminative power for sequence alignment and fold assessment. Therefore, some definitions of a few residue types are able to encode most of the relevant sequence/structure information that is present in the 20 standard amino acids. Based on these results, we suggest that the use of reduced amino acid alphabets may allow to increasing the accuracy of current substitution matrices and statistical potentials for the prediction of protein structure of remote homologs.
Authors:
Francisco Melo; Marc A Marti-Renom
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Proteins     Volume:  63     ISSN:  1097-0134     ISO Abbreviation:  Proteins     Publication Date:  2006 Jun 
Date Detail:
Created Date:  2006-05-16     Completed Date:  2006-07-20     Revised Date:  2006-11-15    
Medline Journal Info:
Nlm Unique ID:  8700181     Medline TA:  Proteins     Country:  United States    
Other Details:
Languages:  eng     Pagination:  986-95     Citation Subset:  IM    
Copyright Information:
2006 Wiley-Liss, Inc.
Affiliation:
Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile. fmelo@bio.puc.cl
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MeSH Terms
Descriptor/Qualifier:
Amino Acid Sequence
Amino Acids / chemistry*,  classification,  metabolism*
Consensus Sequence
Molecular Sequence Data
Oxidation-Reduction
Protein Folding*
Proteins / chemistry*,  metabolism*
Sequence Alignment / methods*
Structural Homology, Protein
Chemical
Reg. No./Substance:
0/Amino Acids; 0/Proteins

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