Tools Used By pVACtools¶
IEDB (Immune Epitope Database)¶
Website: https://www.iedb.org
Citation: Vita R, Mahajan S, Overton JA, Dhanda SK, Martini S, Cantrell JR, Wheeler DK, Sette A, Peters B. The Immune Epitope Database (IEDB): 2018 update. Nucleic Acids Res. 2018 Oct 24.
doi: 10.1093/nar/gky1006. [Epub ahead of print]
PubMed PMID: 30357391.
License: Non-Profit OSL 3.0
By using the IEDB software, you are consenting to be bound by and become a “Licensee” for the use of IEDB tools and are consenting to the terms and conditions of the Non-Profit Open Software License (“Non-Profit OSL”) version 3.0.
Please read these two license agreements here before proceeding. If you do not agree to all of the terms of these two agreements, you must not install or use the product. Companies (for-profit entities) interested in downloading the command-line versions of the IEDB tools or running the entire analysis resource locally, should contact IEDB (license@iedb.org) for details on licensing options.
MHCflurry¶
Website: http://openvax.github.io/mhcflurry/
Citation: T. J. O’Donnell, A. Rubinsteyn, M. Bonsack, A. B. Riemer, U. Laserson, and J. Hammerbacher, “MHCflurry: Open-Source Class I MHC Binding Affinity Prediction,” Cell Systems, 2018.
doi: https://doi.org/10.1016/j.cels.2018.05.014
PubMed PMID: 29960884.
License: Apache License 2.0
MHCnuggets¶
Citation: Shao XM, Bhattacharya R, Huang J, Sivakumar IKA, Tokheim C, Zheng L, Hirsch D, Kaminow B, Omdahl A, Bonsack M, Riemer AB, Velculescu VE, Anagnostou V, Pagel KA, Karchin R. High-Throughput Prediction of MHC Class I and II Neoantigens with MHCnuggets. Cancer Immunol Res. 2020 Mar;8(3):396-408.
doi: https://doi.org/10.1158/2326-6066.CIR-19-0464
PubMed PMID: 31871119
BigMHC¶
Citation: Albert BA, Yang Y, Shao XM, Singh D, Smit KN, Anagnostou V, Karchin R. Deep neural networks predict class I major histocompatibility complex epitope presentation and transfer learn neoepitope immunogenicity. Nat Mach Intell. 2023 Aug;5(8):861-872.
doi: https://doi.org/10.1038/s42256-023-00694-6
PMID: 37829001
License: BigMHC Academic License
DeepImmuno¶
Citation: Li G, Iyer B, Prasath VBS, Ni Y, Salomonis N. DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity. Brief Bioinform. 2021 Nov 5;22(6):bbab160.
doi: https://doi.org/10.1093/bib/bbab160
PubMed PMID: 34009266
License: MIT License
NetChop¶
Citation: The role of the proteasome in generating cytotoxic T cell epitopes: Insights obtained from improved predictions of proteasomal cleavage. M. Nielsen, C. Lundegaard, O. Lund, and C. Kesmir. Immunogenetics., 57(1-2):33-41, 2005.
doi: https://doi.org/10.1007/s00251-005-0781-7
PubMed PMID: 15744535.
License: Academic License
NetMHCstabpan¶
Citation: Pan-specific prediction of peptide-MHC-I complex stability; a correlate of T cell immunogenicity. Michael Rasmussen, Emilio Fenoy, Mikkel Harndahl, Anne Bregnballe Kristensen, Ida Kallehauge Nielsen, Morten Nielsen, Soren Buus. J Immunol. 2016 Aug 15;197(4):1517-24.
doi: https://doi.org/10.4049/jimmunol.1600582
PubMed PMID: 27402703.
License: Academic License
Vaxrank¶
Website: https://github.com/openvax/vaxrank
Citation: Rubinsteyn, A., Hodes, I., Kodysh, J., & Hammerbacher, J. (2017). Vaxrank: a computational tool for designing personalized cancer vaccines. bioRxiv, 142919.
License: Apache License 2.0
BLAST¶
Citations: Link
License: This software/database is a “United States Government Work” under the terms of the United States Copyright Act. It was written as part of the author’s official duties as a United States Government employee and thus cannot be copyrighted. This software/database is freely available to the public for use. The National Library of Medicine and the U.S. Government have not placed any restriction on its use or reproduction.