Document Detail


Robustness of the residue conservation score reflecting both frequencies and physicochemistries.
MedLine Citation:
PMID:  18175048     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Measuring residue conservation at aligned positions has many applications in biology. Recently, a new conservation score has been defined. Unlike the previous methods, the new approach considers both residue frequencies and physicochemistries. Specifically, it measures physicochemistries based on BLOSUM matrices disregarding the meaning of the entries in such matrices, which may involve the problem of log-log probability. In this paper we present a conservation measure that also reflects both frequencies and physicochemistries while considering the fact that the entries of BLOSUM matrices are already interpreted as log probability. When the supposed score is applied to 14 protein examples, the results show that these two conservation scores are equivalent aside from the different score ranges. The method is also used to score the functional sites of three protein families. Compared with the widely used entropy-based methods, the resulting scores are more robust and consistent in the sense that the functional sites are much more conserved because of functional constraints.
Authors:
X-S Liu; W-L Guo
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2008-01-04
Journal Detail:
Title:  Amino acids     Volume:  34     ISSN:  1438-2199     ISO Abbreviation:  Amino Acids     Publication Date:  2008 May 
Date Detail:
Created Date:  2008-05-06     Completed Date:  2008-08-15     Revised Date:  2008-11-21    
Medline Journal Info:
Nlm Unique ID:  9200312     Medline TA:  Amino Acids     Country:  Austria    
Other Details:
Languages:  eng     Pagination:  643-52     Citation Subset:  IM    
Affiliation:
Institute of Nanoscience, Academy of Frontier Science, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China. xsliu@nuaa.edu.cn
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MeSH Terms
Descriptor/Qualifier:
Amino Acid Sequence
Amino Acids / chemistry*
Chemistry, Physical
Computational Biology*
Conserved Sequence
Physicochemical Phenomena
Protein Folding
Proteins / chemistry*
Reproducibility of Results
Sensitivity and Specificity
Sequence Alignment
Sequence Analysis, Protein
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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