標題: Incorporating Structural Characteristics for Identification of Protein Methylation Sites
作者: Shien, Dray-Ming
Lee, Tzong-Yi
Chang, Wen-Chi
Hsu, Justin Bo-Kai
Horng, Jorng-Tzong
Hsu, Po-Chiang
Wang, Ting-Yuan
Huang, Hsien-Da
生物科技學系
生物資訊及系統生物研究所
Department of Biological Science and Technology
Institude of Bioinformatics and Systems Biology
關鍵字: protein methylation;solvent accessible surface area (ASA);support vector machine (SVM)
公開日期: 15-Jul-2009
摘要: Studies over the last few years have identified protein methylation on histones and other proteins that are involved in the regulation of gene transcription. Several works have developed approaches to identify computationally the potential methylation sites on lysine and arginine. Studies of protein tertiary structure have demonstrated that the sites of protein methylation are preferentially in regions that are easily accessible. However, previous studies have not taken into account the solvent-accessible surface area (ASA) that surrounds the methylation sites. This work presents a method named MASA that combines the support vector machine with the sequence and structural characteristics of proteins to identify methylation sites on lysine, arginine, glutamate, and asparagine. Since most experimental methylation sites are not associated with corresponding protein tertiary structures in the Protein Data Bank, the effective solvent-accessible prediction tools have been adopted to determine the potential ASA values of amino acids in proteins. Evaluation of predictive performance by cross-validation indicates that the ASA values around the methylation sites can improve the accuracy of prediction. Additionally, an independent test reveals that the prediction accuracies for methylated lysine and arginine are 80.8 and 85.0%, respectively. Finally, the proposed method is implemented as an effective system for identifying protein methylation sites. The developed web server is freely available at http:/IMASA.mbc.nctu.edu.tw/. (C) 2009 Wiley Periodicals, Inc. J Comput Chem 30: 1532-1543, 2009
URI: http://dx.doi.org/10.1002/jcc.21232
http://hdl.handle.net/11536/6956
ISSN: 0192-8651
DOI: 10.1002/jcc.21232
期刊: JOURNAL OF COMPUTATIONAL CHEMISTRY
Volume: 30
Issue: 9
起始頁: 1532
結束頁: 1543
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