Abstract
The early determination of family for a newly found enzyme molecule becomes important because it is directly related to the detail information about which specific target it acts on, as well as to its catalytic process and biological function. Unfortunately, it is still a hard work to distinguish enzyme classes by experiments. With an enormous amount of protein sequences uncovered in the genome research, it is both challenging and indispensable to develop an automatic method for fast and reliably classifying the enzyme family. Using the concept of Chous pseudo amino acid composition, we developed a new method that coupled discrete wavelet transform with support vector machine based on the amino acid hydrophobicity to predict enzyme family. The overall success rate obtained by the 10-cross-validation for the identification of the six enzyme families was 91.9%, indicating the current method could be an effective and promising highthroughput method in the enzyme research.
Keywords: Discrete wavelet transform, Support vector machine, Enzyme family classes, Hydrophobicity, 10-cross-validation, Chou's pseudo amino acid composition
Protein & Peptide Letters
Title: Using the Concept of Chous Pseudo Amino Acid Composition to Predict Enzyme Family Classes: An Approach with Support Vector Machine Based on Discrete Wavelet Transform
Volume: 17 Issue: 6
Author(s): Jian-Ding Qiu, Jian-Hua Huang, Shao-Ping Shi and Ru-Ping Liang
Affiliation:
Keywords: Discrete wavelet transform, Support vector machine, Enzyme family classes, Hydrophobicity, 10-cross-validation, Chou's pseudo amino acid composition
Abstract: The early determination of family for a newly found enzyme molecule becomes important because it is directly related to the detail information about which specific target it acts on, as well as to its catalytic process and biological function. Unfortunately, it is still a hard work to distinguish enzyme classes by experiments. With an enormous amount of protein sequences uncovered in the genome research, it is both challenging and indispensable to develop an automatic method for fast and reliably classifying the enzyme family. Using the concept of Chous pseudo amino acid composition, we developed a new method that coupled discrete wavelet transform with support vector machine based on the amino acid hydrophobicity to predict enzyme family. The overall success rate obtained by the 10-cross-validation for the identification of the six enzyme families was 91.9%, indicating the current method could be an effective and promising highthroughput method in the enzyme research.
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Cite this article as:
Qiu Jian-Ding, Huang Jian-Hua, Shi Shao-Ping and Liang Ru-Ping, Using the Concept of Chous Pseudo Amino Acid Composition to Predict Enzyme Family Classes: An Approach with Support Vector Machine Based on Discrete Wavelet Transform, Protein & Peptide Letters 2010; 17 (6) . https://dx.doi.org/10.2174/092986610791190372
DOI https://dx.doi.org/10.2174/092986610791190372 |
Print ISSN 0929-8665 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5305 |
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Plants are still the major repository of biologically active substances. In the last two decades, however, natural peptides and proteins of plant origin have gained increasing attention due to their pharmacological activities over a variety of human illness, including those mediated by infections and parasitosis and those involving different cellular ...read more
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