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Current Protein & Peptide Science

Editor-in-Chief

ISSN (Print): 1389-2037
ISSN (Online): 1875-5550

Homology-Free Prediction of Functional Class of Proteins and Peptides by Support Vector Machines

Author(s): Y. Z. Chen, F. Zhu, L. Y. Han, X. Chen, H. H. Lin, S. Ong, B. Xie and H. L. Zhang

Volume 9, Issue 1, 2008

Page: [70 - 95] Pages: 26

DOI: 10.2174/138920308783565697

Price: $65

Abstract

Protein and peptide sequences contain clues for functional prediction. A challenge is to predict sequences that show low or no homology to proteins or peptides of known function. A machine learning method, support vector machines (SVM), has recently been explored for predicting functional class of proteins and peptides from sequence-derived properties irrespective of sequence similarity, which has shown impressive performance for predicting a wide range of protein and peptide classes including certain low- and non- homologous sequences. This method serves as a new and valuable addition to complement the extensively-used alignment-based, clustering-based, and structure-based functional prediction methods. This article evaluates the strategies, current progresses, reported prediction performances, available software tools, and underlying difficulties in using SVM for predicting the functional class of proteins and peptides.

Keywords: Machine learning method, peptide, peptide function, protein family, protein function, protein function prediction, protein sequence, support vector machine

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