.. _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

  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
__________

- GitHub: https://github.com/KarchinLab/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 <https://pubmed.ncbi.nlm.nih.gov/31871119/>`_

- License: `JHU Academic Software License Agreement <https://github.com/KarchinLab/mhcnuggets/blob/master/LICENSE>`_

BigMHC
______

- GitHub: https://github.com/KarchinLab/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 <https://pubmed.ncbi.nlm.nih.gov/37829001/>`_

- License: `BigMHC Academic License <https://github.com/KarchinLab/bigmhc/blob/master/LICENSE>`_

DeepImmuno
__________

- Website: https://deepimmuno.research.cchmc.org/
- GitHub: https://github.com/frankligy/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 <https://pubmed.ncbi.nlm.nih.gov/34009266/>`_

- License: `MIT License <https://github.com/frankligy/DeepImmuno/blob/main/LICENSE>`_

NetChop
_______

- 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.

  doi: https://doi.org/10.1007/s00251-005-0781-7

  PubMed PMID: `15744535 <https://www.ncbi.nlm.nih.gov/pubmed/15744535>`_.

- License: `Academic License
  <http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netchop>`_

NetMHCstabpan
_____________

- 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 <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.