Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools

Jason A. Greenbaum, Pernille Haste Andersen, Martin Blythe, Huynh Hoa Bui, Raul E. Cachau, James Crowe, Matthew Davies, A. S. Kolaskar, Ole Lund, Sherrie Morrison, Brendan Mumey, Yanay Ofran, Jean Luc Pellequer, Clemencia Pinilla, Julia V. Ponomarenko, G. P.S. Raghava, Marc H.V. Van Regenmortel, Erwin L. Roggen, Alessandro Sette, Avner SchlessingerJohannes Sollner, Martin Zand, Bjoern Peters

Research output: Contribution to journalReview articlepeer-review

206 Scopus citations

Abstract

A B-cell epitope is the three-dimensional structure within an antigen that can be bound to the variable region of an antibody. The prediction of B-cell epitopes is highly desirable for various immunological applications, but has presented a set of unique challenges to the bioinformatics and immunology communities. Improving the accuracy of B-cell epitope prediction methods depends on a community consensus on the data and metrics utilized to develop and evaluate such tools. A workshop, sponsored by the National Institute of Allergy and Infectious Disease (NIAID), was recently held in Washington, DC to discuss the current state of the B-cell epitope prediction field. Many of the currently available tools were surveyed and a set of recommendations was devised to facilitate improvements in the currently existing tools and to expedite future tool development. An underlying theme of the recommendations put forth by the panel is increased collaboration among research groups. By developing common datasets, standardized data formats, and the means with which to consolidate information, we hope to greatly enhance the development of B-cell epitope prediction tools.

Original languageEnglish
Pages (from-to)75-82
Number of pages8
JournalJournal of Molecular Recognition
Volume20
Issue number2
DOIs
StatePublished - Mar 2007
Externally publishedYes

Keywords

  • Algorithms
  • B-cell epitopes
  • Bioinformatics
  • Data standardization
  • Epitope prediction
  • Immunology databases
  • Software tools
  • Tool development

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