Document Detail


EHPred: an SVM-based method for epoxide hydrolases recognition and classification.
MedLine Citation:
PMID:  16365918     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
A two-layer method based on support vector machines (SVMs) has been developed to distinguish epoxide hydrolases (EHs) from other enzymes and to classify its subfamilies using its primary protein sequences. SVM classifiers were built using three different feature vectors extracted from the primary sequence of EHs: the amino acid composition (AAC), the dipeptide composition (DPC), and the pseudo-amino acid composition (PAAC). Validated by 5-fold cross tests, the first layer SVM classifier can differentiate EHs and non-EHs with an accuracy of 94.2% and has a Matthew's correlation coefficient (MCC) of 0.84. Using 2-fold cross validation, PAAC-based second layer SVM can further classify EH subfamilies with an overall accuracy of 90.7% and MCC of 0.87 as compared to AAC (80.0%) and DPC (84.9%). A program called EHPred has also been developed to assist readers to recognize EHs and to classify their subfamilies using primary protein sequences with greater accuracy.
Authors:
Jia Jia; Liang Yang; Zi-Zhang Zhang
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Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't    
Journal Detail:
Title:  Journal of Zhejiang University. Science. B     Volume:  7     ISSN:  1673-1581     ISO Abbreviation:  J Zhejiang Univ Sci B     Publication Date:  2006 Jan 
Date Detail:
Created Date:  2005-12-20     Completed Date:  2006-02-01     Revised Date:  2013-06-07    
Medline Journal Info:
Nlm Unique ID:  101236535     Medline TA:  J Zhejiang Univ Sci B     Country:  China    
Other Details:
Languages:  eng     Pagination:  1-6     Citation Subset:  IM    
Affiliation:
James. D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China.
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MeSH Terms
Descriptor/Qualifier:
Algorithms*
Amino Acid Sequence
Artificial Intelligence*
Computing Methodologies
Epoxide Hydrolases / chemistry*,  classification*
Molecular Sequence Data
Pattern Recognition, Automated / methods*
Sequence Alignment / methods*
Sequence Analysis, Protein / methods*
Sequence Homology, Amino Acid
Chemical
Reg. No./Substance:
EC 3.3.2.-/Epoxide Hydrolases
Comments/Corrections

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


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