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Open Access Research article

Efficacy of different protein descriptors in predicting protein functional families

Serene AK Ong1, Hong Huang Lin1, Yu Zong Chen1, Ze Rong Li2 and Zhiwei Cao3*

Author Affiliations

1 Department of Pharmacy, National University of Singapore, Blk S16, Level 8, 08-14, 3 Science Drive 2, Singapore 117543, Singapore

2 College of Chemistry, Sichuan University, Chengdu, 610064, P.R. China

3 Shanghai Center for Bioinformatics Technology, 100, Qinzhou Road, Shanghai 200235 P.R. China

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BMC Bioinformatics 2007, 8:300  doi:10.1186/1471-2105-8-300

Published: 17 August 2007



Sequence-derived structural and physicochemical descriptors have frequently been used in machine learning prediction of protein functional families, thus there is a need to comparatively evaluate the effectiveness of these descriptor-sets by using the same method and parameter optimization algorithm, and to examine whether the combined use of these descriptor-sets help to improve predictive performance. Six individual descriptor-sets and four combination-sets were evaluated in support vector machines (SVM) prediction of six protein functional families.


The performance of these descriptor-sets were ranked by Matthews correlation coefficient (MCC), and categorized into two groups based on their performance. While there is no overwhelmingly favourable choice of descriptor-sets, certain trends were found. The combination-sets tend to give slightly but consistently higher MCC values and thus overall best performance such that three out of four combination-sets show slightly better performance compared to one out of six individual descriptor-sets.


Our study suggests that currently used descriptor-sets are generally useful for classifying proteins and the prediction performance may be enhanced by exploring combinations of descriptors.