Identification of amino acid propensities that are strong determinants of linear B-cell epitope using neural networks

Chun Hung Su, Nikhil R. Pal, Ken Li Lin, I. Fang Chung*

*此作品的通信作者

研究成果: Article同行評審

16 引文 斯高帕斯(Scopus)

摘要

Background: Identification of amino acid propensities that are strong determinants of linear B-cell epitope is very important to enrich our knowledge about epitopes. This can also help to obtain better epitope prediction. Typical linear B-cell epitope prediction methods combine various propensities in different ways to improve prediction accuracies. However, fewer but better features may yield better prediction. Moreover, for a propensity, when the sequence length is k, there will be k values, which should be treated as a single unit for feature selection and hence usual feature selection method will not work. Here we use a novel Group Feature Selecting Multilayered Perceptron, GFSMLP, which treats a group of related information as a single entity and selects useful propensities related to linear B-cell epitopes, and uses them to predict epitopes. Methodology/ Principal Findings: We use eight widely known propensities and four data sets. We use GFSMLP to rank propensities by the frequency with which they are selected. We find that Chou's beta-turn and Ponnuswamy's polarity are better features for prediction of linear B-cell epitope. We examine the individual and combined discriminating power of the selected propensities and analyze the correlation between paired propensities. Our results show that the selected propensities are indeed good features, which also cooperate with other propensities to enhance the discriminating power for predicting epitopes. We find that individually polarity is not the best predictor, but it collaborates with others to yield good prediction. Usual feature selection methods cannot provide such information. Conclusions/ Significance: Our results confirm the effectiveness of active (group) feature selection by GFSMLP over the traditional passive approaches of evaluating various combinations of propensities. The GFSMLP-based feature selection can be extended to more than 500 remaining propensities to enhance our biological knowledge about epitopes and to obtain better prediction. A graphical-user-interface version of GFSMLP is available at: http://bio.classcloud.org/GFSMLP/.

原文English
文章編號e30617
期刊PLoS ONE
7
發行號2
DOIs
出版狀態Published - 8 2月 2012

指紋

深入研究「Identification of amino acid propensities that are strong determinants of linear B-cell epitope using neural networks」主題。共同形成了獨特的指紋。

引用此