Document Detail


Optimizing amino acid groupings for GPCR classification.
MedLine Citation:
PMID:  18676973     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
MOTIVATION: There is much interest in reducing the complexity inherent in the representation of the 20 standard amino acids within bioinformatics algorithms by developing a so-called reduced alphabet. Although there is no universally applicable residue grouping, there are numerous physiochemical criteria upon which one can base groupings. Local descriptors are a form of alignment-free analysis, the efficiency of which is dependent upon the correct selection of amino acid groupings.
RESULTS: Within the context of G-protein coupled receptor (GPCR) classification, an optimization algorithm was developed, which was able to identify the most efficient grouping when used to generate local descriptors. The algorithm was inspired by the relatively new computational intelligence paradigm of artificial immune systems. A number of amino acid groupings produced by this algorithm were evaluated with respect to their ability to generate local descriptors capable of providing an accurate classification algorithm for GPCRs.
Authors:
Matthew N Davies; Andrew Secker; Alex A Freitas; Edward Clark; Jon Timmis; Darren R Flower
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2008-08-01
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  24     ISSN:  1367-4811     ISO Abbreviation:  Bioinformatics     Publication Date:  2008 Sep 
Date Detail:
Created Date:  2008-09-08     Completed Date:  2008-10-31     Revised Date:  2013-05-20    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  England    
Other Details:
Languages:  eng     Pagination:  1980-6     Citation Subset:  IM    
Affiliation:
Edward Jenner Institute, Compton, Newbury, Berkshire, UK.
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MeSH Terms
Descriptor/Qualifier:
Algorithms*
Amino Acids / classification*
Artificial Intelligence
Computational Biology / methods
Databases, Protein
Receptors, G-Protein-Coupled / chemistry*,  classification*,  metabolism
Sequence Analysis, Protein / methods
Chemical
Reg. No./Substance:
0/Amino Acids; 0/Receptors, G-Protein-Coupled

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


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