Nucleic Acids Research Advance Access originally published online on May 22, 2009
Nucleic Acids Research 2009 37(Web Server issue):W612-W616; doi:10.1093/nar/gkp417
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W612-W616
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Articles |
SEPPA: a computational server for spatial epitope prediction of protein antigens
1Department of Biomedical Engineering, School of Life Sciences and Technology, Tongji University, Shanghai 200092, 2Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai 200235 and 3Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
*To whom correspondence should be addressed. Tel: +86 21 5406 5003; Fax: +86 21 5406 5058; Email: zwcao{at}tongji.edu.cn
Correspondence may also be addressed to Y.X. Li. Tel: +86 21 5406 5001; Fax: +86 21 5406 5058; Email: yxli{at}scbit.org
Received February 4, 2009. Revised April 24, 2009. Accepted May 6, 2009.
In recent years, a lot of efforts have been made in conformational epitope prediction as antigen proteins usually bind antibodies with an assembly of sequentially discontinuous and structurally compact surface residues. Currently, only a few methods for spatial epitope prediction are available with focus on single residue propensity scales or continual segments clustering. In the method of SEPPA, a concept of ‘unit patch of residue triangle’ was introduced to better describe the local spatial context in protein surface. Besides that, SEPPA incorporated clustering coefficient to describe the spatial compactness of surface residues. Validated by independent testing datasets, SEPPA gave an average AUC value over 0.742 and produced a successful pick-up rate of 96.64%. Comparing with peers, SEPPA shows significant improvement over other popular methods like CEP, DiscoTope and BEpro. In addition, the threshold scores for certain accuracy, sensitivity and specificity are provided online to give the confidence level of the spatial epitope identification. The web server can be accessed at http://lifecenter.sgst.cn/seppa/index.php. Batch query is supported.