Cited by 428vaccines and immunoinformatics approachesImmunotherapy and Immune ResponsesMachine Learning in Bioinformatics

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IEDB-AR: immune epitope database-analysis resource in 2019

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Dhanda, Sandeep Kumar, Mahajan, Swapnil, Paul, Sinu, Yan, Zhen, Kim, Haeuk, Jespersen, Martin Closter, Jurtz, Vanessa, Andreatta, Massimo, Greenbaum, Jason A, Marcatili, Paolo, Sette, Alessandro, Nielsen, Morten, Peters, Bjoern·2019·Nucleic Acids Research

DOI 10.1093/nar/gkz452PMC PMC6602498

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Abstract

The Immune Epitope Database Analysis Resource (IEDB-AR, http://tools.iedb.org/) is a companion website to the IEDB that provides computational tools focused on the prediction and analysis of B and T cell epitopes. All of the tools are freely available through the public website and many are also available through a REST API and/or a downloadable command-line tool. A virtual machine image of the entire site is also freely available for non-commercial use and contains most of the tools on the public site. Here, we describe the tools and functionalities that are available in the IEDB-AR, focusing on the 10 new tools that have been added since the last report in the 2012 NAR webserver edition. In addition, many of the tools that were already hosted on the site in 2012 have received updates to newest versions, including NetMHC, NetMHCpan, BepiPred and DiscoTope. Overall, this IEDB-AR update provides a substantial set of updated and novel features for epitope prediction and analysis.

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The Immune Epitope Database (IEDB): 2018 update
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Authors: Dhanda, S. K., Mahajan, S., Paul, S., Yan, Z., Kim, H., Jespersen, M. C., Jurtz, V., Andreatta, M., Greenbaum, J. A., Marcatili, P., Sette, A., Nielsen, M., & Peters, B.
Affiliations: La Jolla Institute for Immunology (US)
Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
Technical University of Denmark (DK)
National University of General San Martín (AR)
Corresponding author: Peters, Bjoern
ORCID: Dhanda, Sandeep Kumar
Mahajan, Swapnil
Paul, Sinu
Jurtz, Vanessa
Andreatta, Massimo
Greenbaum, Jason A
Marcatili, Paolo
Sette, Alessandro
Nielsen, Morten
Peters, Bjoern
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2019-05-22
Volume: 47
Issue: W1
Pages: W502-W506
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gkz452
PMC: PMC6602498
OpenAlex: W2945153532
Cited by: 427
References: 35
Citations by year: 2026: 45 · 2025: 63 · 2024: 68 · 2023: 53 · 2022: 70 · 2021: 80 · 2020: 38 · 2019: 9
FWCI: 16.37
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by-nc
creativecommons.org/licenses/by-nc/4.0/ (vor)
Locations: Nucleic Acids Research (publishedVersion, cc-by-nc)
Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
PubMed Central (publishedVersion, cc-by-nc)
PubMed (publishedVersion)
Technical University of Denmark, DTU Orbit (Technical University of Denmark, DTU) (submittedVersion, other-oa)
LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, cc-by-nc-sa)
Funders: National Institutes of Health (HHSN272201200010C, 75N93019C00001)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
Life Sciences › Immunology and Microbiology › Immunology › Immunotherapy and Immune Responses
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Machine Learning in Bioinformatics
Keywords: IEDB, B-cell epitopes, T cell epitopes, epitope prediction, NetMHCpan, REST API, virtual machine image
MeSH terms: Animals, Histocompatibility Antigens, Humans, Software, Epitopes, T-Lymphocyte, Epitopes, B-Lymphocyte, Databases, Protein, Mice

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