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.

Website: http://openvax.github.io/mhcflurry/
GitHub: https://github.com/openvax/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

Website: https://karchinlab.org/apps/appMHCnuggets.html
GitHub: https://github.com/KarchinLab/mhcnuggets-2.0
Citation: Bhattacharya R, Sivakumar A, Tokheim C, Beleva Guthrie V, Anagnostou V, Velculescu VE, Karchin R (2017) Evaluation of machine learning methods to predict peptide binding to MHC Class I proteins. Submitted [bioRxiv preprint].
License: Apache License 2.0

Website: http://www.cbs.dtu.dk/services/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. PubMed PMID: 11983929.
License: Academic License

Website: http://www.cbs.dtu.dk/services/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

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

Website: https://blast.ncbi.nlm.nih.gov/Blast.cgi
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.