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EPCES and EPSVR: Prediction of B-Cell Antigenic Epitopes on Protein Surfaces with Conformational Information

  • Shide Liang
  • Dandan Zheng
  • Bo Yao
  • Chi ZhangEmail author
Protocol
  • 99 Downloads
Part of the Methods in Molecular Biology book series (MIMB, volume 2131)

Abstract

Accurate prediction of discontinuous antigenic epitopes is important for immunologic research and medical applications, but it is not an easy problem. Currently, there are only a few prediction servers available, though discontinuous epitopes constitute the majority of all B-cell antigenic epitopes. In this chapter, we describe two online servers, EPCES and EPSVR, for discontinuous epitope prediction. All methods were benchmarked by a curated independent test set, in which all antigens had no complex structures with the antibody, and their epitopes were identified by various biochemical experiments. The servers and all datasets are available at http://sysbio.unl.edu/EPCES/ and http://sysbio.unl.edu/EPSVR/.

Key words

B-cell epitope prediction Support vector machine 

Notes

Acknowledgments

The work is supported by funding under C.Z.’s startup funds from the University of Nebraska, Lincoln, NE. This work was completed utilizing the Holland Computing Center of the University of Nebraska.

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Department of R&DBio-Thera SolutionsGuangzhouChina
  2. 2.Department of Radiation OncologyUniversity of Nebraska Medical CenterOmahaUSA
  3. 3.Quantitative Biomedical Research CenterUniversity of Texas Southwestern Medical CenterDallasUSA
  4. 4.School of Biological SciencesUniversity of Nebraska – LincolnLincolnUSA

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