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 Schlessinger; Johannes Sollner; Martin Zand; Bjoern Peters

doi:10.1002/jmr.815

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

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

211 Citationer (Scopus)

Abstract

Udgivelsesdato: null-null

Originalsprog	Engelsk
Tidsskrift	Journal of Molecular Recognition
Vol/bind	20
Udgave nummer	2
Sider (fra-til)	75-82
Antal sider	7
ISSN	0952-3499
DOI	https://doi.org/10.1002/jmr.815
Status	Udgivet - 2007

Bibliografisk note

Adgang til dokumentet

10.1002/jmr.815

Citationsformater

Greenbaum, J. A., Andersen, P. H., Blythe, M., Bui, H-H., Cachau, R. E., Crowe, J., Davies, M., Kolaskar, A. S., Lund, O., Morrison, S., Mumey, B., Ofran, Y., Pellequer, J-L., Pinilla, C., Ponomarenko, J. V., Raghava, G. P. S., van Regenmortel, M. H. V., Roggen, E. L., Sette, A., ... Peters, B. (2007). Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. Journal of Molecular Recognition, 20(2), 75-82. https://doi.org/10.1002/jmr.815

Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. / Greenbaum, Jason A; Andersen, Pernille Haste; Blythe, Martin; Bui, Huynh-Hoa; Cachau, Raul E; Crowe, James; Davies, Matthew; Kolaskar, A S; Lund, Ole; Morrison, Sherrie; Mumey, Brendan; Ofran, Yanay; Pellequer, Jean-Luc; Pinilla, Clemencia; Ponomarenko, Julia V; Raghava, G P S; van Regenmortel, Marc H V; Roggen, Erwin L; Sette, Alessandro; Schlessinger, Avner; Sollner, Johannes; Zand, Martin; Peters, Bjoern.

I: Journal of Molecular Recognition, Bind 20, Nr. 2, 2007, s. 75-82.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

Greenbaum, JA, Andersen, PH, Blythe, M, Bui, H-H, Cachau, RE, Crowe, J, Davies, M, Kolaskar, AS, Lund, O, Morrison, S, Mumey, B, Ofran, Y, Pellequer, J-L, Pinilla, C, Ponomarenko, JV, Raghava, GPS, van Regenmortel, MHV, Roggen, EL, Sette, A, Schlessinger, A, Sollner, J, Zand, M & Peters, B 2007, 'Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools', Journal of Molecular Recognition, bind 20, nr. 2, s. 75-82. https://doi.org/10.1002/jmr.815

Greenbaum, Jason A ; Andersen, Pernille Haste ; Blythe, Martin ; Bui, Huynh-Hoa ; Cachau, Raul E ; Crowe, James ; Davies, Matthew ; Kolaskar, A S ; Lund, Ole ; Morrison, Sherrie ; Mumey, Brendan ; Ofran, Yanay ; Pellequer, Jean-Luc ; Pinilla, Clemencia ; Ponomarenko, Julia V ; Raghava, G P S ; van Regenmortel, Marc H V ; Roggen, Erwin L ; Sette, Alessandro ; Schlessinger, Avner ; Sollner, Johannes ; Zand, Martin ; Peters, Bjoern. / Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. I: Journal of Molecular Recognition. 2007 ; Bind 20, Nr. 2. s. 75-82.

@article{8cbd9b10b62e11ddae57000ea68e967b,

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

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.",

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

note = "Keywords: Animals; Consensus; Databases, Protein; Epitopes, B-Lymphocyte; Evaluation Studies as Topic; Health Planning Guidelines; Humans; Models, Biological; Models, Molecular; Peptide Library; Protein Structure, Secondary; Sequence Analysis, Protein; Software",

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T1 - Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools

AU - Greenbaum, Jason A

AU - Andersen, Pernille Haste

AU - Blythe, Martin

AU - Bui, Huynh-Hoa

AU - Cachau, Raul E

AU - Crowe, James

AU - Davies, Matthew

AU - Kolaskar, A S

AU - Lund, Ole

AU - Morrison, Sherrie

AU - Mumey, Brendan

AU - Ofran, Yanay

AU - Pellequer, Jean-Luc

AU - Pinilla, Clemencia

AU - Ponomarenko, Julia V

AU - Raghava, G P S

AU - van Regenmortel, Marc H V

AU - Roggen, Erwin L

AU - Sette, Alessandro

AU - Schlessinger, Avner

AU - Sollner, Johannes

AU - Zand, Martin

AU - Peters, Bjoern

N1 - Keywords: Animals; Consensus; Databases, Protein; Epitopes, B-Lymphocyte; Evaluation Studies as Topic; Health Planning Guidelines; Humans; Models, Biological; Models, Molecular; Peptide Library; Protein Structure, Secondary; Sequence Analysis, Protein; Software

PY - 2007

Y1 - 2007

N2 - 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.

AB - 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.

U2 - 10.1002/jmr.815

DO - 10.1002/jmr.815

M3 - Journal article

C2 - 17205610

VL - 20

SP - 75

EP - 82

JO - Journal of Molecular Recognition

JF - Journal of Molecular Recognition

SN - 0952-3499

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ER -