.. _tools:

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 <10.1093/nar/gky1006>`_. [Epub ahead
  of print] PubMed PMID: `30357391 <https://www.ncbi.nlm.nih.gov/pubmed/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 <http://tools.iedb.org/mhci/download/>`_
  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/
- 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 <https://doi.org/10.1016/j.cels.2018.05.014>`_.
  PubMed PMID: `29960884 <https://www.ncbi.nlm.nih.gov/pubmed/29960884>`_.
- License: `Apache License 2.0 <https://github.com/openvax/mhcflurry/blob/master/LICENSE>`_

MHCnuggets
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- 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
  <https://www.biorxiv.org/content/early/2017/07/27/154757>`_].
- License: `Apache License 2.0 <https://github.com/KarchinLab/mhcnuggets-2.0/blob/master/LICENSE>`_

NetChop
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- 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 <https://www.ncbi.nlm.nih.gov/pubmed/11983929>`_.
- License: `Academic License
  <http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netchop>`_

NetMHCstabpan
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- 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 <https://doi.org/10.4049/jimmunol.1600582>`_.
  PubMed PMID: `27402703 <https://www.ncbi.nlm.nih.gov/pubmed/27402703>`_.
- License: `Academic License
  <http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCstabpan>`_

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 <https://www.biorxiv.org/content/10.1101/142919v2>`_.
- License: `Apache License 2.0 <https://github.com/openvax/vaxrank/blob/master/LICENSE>`_

BLAST
_____

- Website: https://blast.ncbi.nlm.nih.gov/Blast.cgi
- Citations: `Link <https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=References>`_
- 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.