MHC-II Download

MHC-II binding dataset - Download

This MHC class II binding affinity dataset consists of 44, 541 experimentally measured binging affinities covering 26 alleric variants.
Two sets of randomly splitted 5-fold cross validation data are provided: the entire dataset ("ALL") and the similarity reduced dataset ("SR").

To download the dataset in tar.gz format:

Prediction scores for MHC-II binding dataset - Download

The prediction scores for the six implemented algorithms based on above dataset can be download here. The scores were generate via 5-fold cross validation based on two sets of data: the entire dataset ("ALL") and the similarity reduced dataset "SR".

To download the scores in tar.gz format:

Combinatorial peptide scanning library scoring matrices - Download

This file contains the scoring matrices for sixteen MHC class II alleles developed from the combinatorial peptide scanning library data.

To download the dataset in tar.gz format:

MHC-II binding predictions - Download

The MHC_II binding tool contains a collection of following peptide binding prediction methods for Major Histocompatibility Complex (MHC) class II molecules.The collection is a mixture of pythons scripts and linux 32-bit environment specific binaries.

combinatorial library
smm_align
tepitope
Consensus
NetMHCIIpan

License Agreements
By downloading the standalone tool, you are consenting to be bound by and become a party as the "Licensee" for the use of NetMHC 3.0".
Also you are consenting the terms and conditions of the Non-Profit Open Software License ("Non-Profit OSL") version 3.0
Please read folowing two agreements before proceeding. If you do not agree to all of the terms of these two agreements, you must not click the download button, not install the product nor use the product, and you do not become a LICENSEE under these agreements.

ACADEMIC SOFTWARE LICENSE AGREEMENT FOR END-USERS AT PUBLICLY FUNDED
ACADEMIC, EDUCATION OR RESEARCH INSTITUTIONS FOR THE USE OF NetMHC 3.0
By downloading the Software you are consenting to be bound by and become
a party to this agreement as the "Licensee". If you do not agree to all
of the terms of this agreement, you must not click the Acceptance
button, not install the product nor use the product, and you do not
become a LICENSEE under this agreement.

If you are not a member of a publicly funded Academic and/or Education
and/or Research Institution you must obtain a commercial license, please
send mail to (software@cbs.dtu.dk). This software license agreement is
entered into by and between Center for Biological Sequence Analysis,
Technical University of Denmark (hereinafter "CBS") and the "LICENSEE".
WHEREAS CBS has the right to license all copyrights and other property
rights in the Licensed Software identified as NetMHC 3.0 and developed
by CBS and CBS desires to license the Software so that it becomes
available for public use and benefit.
WHEREAS LICENSEE is a public funded Academic and/or Education and/or
Research Institution.
WHEREAS LICENSEE desires to acquire a free non-exclusive license to use
the Software for internal research purposes only.
NOW, THEREFORE, in consideration of the mutual promises and covenants
contained herein, the parties agree as follows:

1. Definitions
"Licensed Software" means the specific version NetMHC 3.0 pursuant
to this Agreement. Any opinion, findings, conclusions or recommendations
expressed in the Licensed Software are those of the authors and do not
necessarily reflect the views of CBS.

2. License
Subject to the terms and conditions of this Agreement a non-exclusive,
non-transferable License to use and copy the Licensed Software is made
available free of charge for the LICENSEE which is a non-profit
educational, academic and/or research institution. The License is only
granted for personal and internal use in research only at one Site,
where a Site is defined as a set of contiguous buildings in one
location. The software will be used at only one location of LICENSEE.
This license does not entitle Licensee to receive from CBS copies of the
Licensed software on disks, tapes or CD's, hard-copy documentation,
technical support, telephone assistance, or enhancements or updates to
the Licensed Software.
The user and any research assistants, co-workers or other workers who
may use the Software agree to not give the program to third parties or
grant licenses on software, which include the Software, alone or
integrated into other software, to third parties. Modification of the
source code is prohibited without the prior written consent of CBS.

3. Ownership
Except as expressly licensed in this Agreement, CBS shall retain title
to the Licensed Software, and any upgrades and modifications created by
CBS.

4. Consideration
In consideration for the license rights granted by CBS, LICENSEE will
obtain this academic license free of charge.

5. Copies
LICENSEE shall have the right to make copies of the Licensed Software
for internal use at the Site and for back-up purposes under this
Agreement, but agrees that all such copies shall contain the copyright
notices and all other reasonable and appropriate proprietary markings or
confidential legends that appear on the Licensed Software provided
hereunder.

6. Support
CBS shall have no obligation to offer support services to LICENSEE, and
nothing contained herein shall be interpreted as to require CBS to
provide maintenance, installation services, version updates, debugging,
consultation or end-user support of any kind.

7. Software Protection
LICENSEE acknowledges that the Licensed Software is proprietary to CBS.
The software code shall be treated as trade secrets and confidential
information of CBS, and LICENSEE agrees to use best efforts to hold the
same in confidence. LICENSEE's obligation for confidentiality shall not
extend to any information which is or becomes generally available to the
public, is already known to or subsequently disclosed by third parties
to LICENSEE and at its free disposal, or is independently developed by
LICENSEE or its affiliates without the use of the confidential
information disclosed by CBS, or is required by law or legal process.
Except as other wise expressly permitted in this Agreement, Licensee my
not (i) modify or create any derivative works of the Licensed Software
or documentation, including customization, translation or localization;
(ii) decompile, disassemble, reverse engineer, or otherwise attempt to
derive the source code for the Product; (iii) redistribute, encumber,
sell, rent, lease, sublicense, or otherwise transfer rights to the
Licensed Software; (iv) remove or alter any trademark, logo, copyright
or other proprietary notices, legends, symbols or labels in the Product;
or (v) publish any results of benchmark tests run on the Product to a
third party without CBS's prior written consent.

8. Representations of CBS to LICENSEE
CBS represents to LICENSEE that (i) CBS has the right to grant the
License and to enter into this agreement, (ii) that, to the best of
CBS's knowledge, the Licensed software does not infringe any patent,
copyright or trade secrets of any third party, provided however that
such representation and warranty shall not apply to any addition to, or
modifications or adaptation of, the Licensed Software made by LICENSEE
and (iii) CBS undertakes to use best efforts to cooperate with and
assist LICENSEE, at LICENSEE's expense, in defending itself against any
action based on the alleged infringement of any third party patent,
copyright or trade secret rights resulting from or relating to the use
or licensing of the Licensed Software by LICENSEE.

9. Indemnity and Disclaimer of Warranties
Except as expressly set forth in this agreement, CBS makes no
representations or warranties, express or implied.
The product is provided free of charge, and, therefore, on an "as is"
basis, without warranty of any kind, express or implied, including
without limitation the warranties that it is free of defects, virus
free, able to operate on an uninterrupted basis, merchantable, fit for a
particular purpose or non-interfering. The entire risk as to the quality
and performance of the Licensed Software is borne by LICENSEE.
By way of example, but not limitation, CBS makes no representations or
warranties of merchantability or fitness for any particular application
or, except as set forth in paragraph 8, that the use of the Software
will not infringe any patents, copyrights or trademarks or other rights
of third parties. The entire risk as to the quality and performance of
the product is borne by LICENSEE. CBS shall not be liable for any
liability or damages with respect to any claim by LICENSEE or any third
party on account of, or arising from the license or use of the Software.
Should the Licensed Software prove defective in any respect, LICENSEE
and not LICENSOR or it's affiliates should assume the entire cost of any
service and repair. This disclaimer of warranty constitutes an essential
part of this agreement. No use of the licensed product is authorized
hereunder except under this disclaimer.
In no event will LICENSOR or its affiliates be liable for any indirect,
special, incidental or consequential damages arising out of the use of
or inability to use the product, including, without limitation, damages
for lost profits, loss of goodwill, work stoppage, computer failure or
malfunction, or any and all other commercial damages or losses, even if
advised of the possibility thereof, and regardless of the legal or
equitable theory (contract, tort or otherwise) upon which the claim is
based.

10. Promotional Advertising & References
LICENSEE may not use the name of the Licensed Software in its
promotional advertising, product literature, and other similar
promotional materials to be disseminated to the public or any portion
thereof. LICENSEE agrees not to identify CBS in any promotional
advertising or other promotional materials to be disseminated to the
public, or any portion thereof without CBS's prior written consent.
LICENSEE agrees that any reference to the software for crystallographic
computations will cite one or more publications as set forth in the
manual and in agreement with common scientific practice. CBS shall not
use LICENSEE's name in publicity or advertising involving this Agreement
or otherwise without LICENSEE's prior written consent which may be
withheld at LICENSEE's sole discretion.

11. Term
This Agreement and the license rights granted herein shall become
effective as of the date this Agreement is executed by both parties and
shall be perpetual unless terminated in accordance with this Section.
CBS may terminate this Agreement at any time.
Either party may terminate this Agreement at any time effective upon the
other party's breach of any agreement, covenant, or representation made
in this Agreement, such breach remaining uncorrected sixty (60) days
after written notice thereof.
LICENSEE shall have the right, at any time, to terminate this Agreement
without cause by written notice to CBS specifying the date of
termination.
Upon termination, LICENSEE shall destroy all full and partial copies of
the Licensed Software.

12. Governing Law
This Agreement shall be construed in accordance with the laws of
Denmark.

13. General
The parties agree that this Agreement is the complete and exclusive
agreement among the parties and supersedes all proposals and prior
agreements whether written or oral, and all other communications among
the parties relating to the subject matter of this Agreement. This
Agreement cannot be modified except in writing and signed by both
parties. Failure by either party at any time to enforce any of the
provisions of this Agreement shall not constitute a waiver by such party
of such provision nor in any way affect the validity of this Agreement.
The invalidity of singular provisions does not affect the validity of
the entire understanding. The parties are obligated, however, to replace
the invalid provisions by a regulation which comes closest to the
economic intent of the invalid provision. The same shall apply mutatis
mutandis in case of a gap.
IN WITNESS WHEREOF, the LICENSEE hereto have caused this Agreement to be
duly executed on the date of the download of the software and by
accepting the license conditions by pressing the Acceptance button.

This Non-Profit Open Software License ("Non-Profit OSL") version 3.0 (the "Licen
se") applies to any original work of authorship (the "Original Work") whose owne
r (the "Licensor") has placed the following licensing notice adjacent to the cop
yright notice for the Original Work:

Licensed under the Non-Profit Open Software License version 3.0

1) Grant of Copyright License. Licensor grants You a worldwide, royalty-free, no
n-exclusive, sublicensable license, for the duration of the copyright, to do the
following:

a) to reproduce the Original Work in copies, either alone or as part of a collec
tive work;

b) to translate, adapt, alter, transform, modify, or arrange the Original Work,
thereby creating derivative works ("Derivative Works") based upon the Original W
ork;

c) to distribute or communicate copies of the Original Work and Derivative Works
to the public, with the proviso that copies of Original Work or Derivative Work
s that You distribute or communicate shall be licensed under this Non-Profit Ope
n Software License or as provided in section 17(d);

d) to perform the Original Work publicly; and

e) to display the Original Work publicly.

2) Grant of Patent License. Licensor grants You a worldwide, royalty-free, non-e
xclusive, sublicensable license, under patent claims owned or controlled by the
Licensor that are embodied in the Original Work as furnished by the Licensor, fo
r the duration of the patents, to make, use, sell, offer for sale, have made, an
d import the Original Work and Derivative Works.

3) Grant of Source Code License. The term "Source Code" means the preferred form
of the Original Work for making modifications to it and all available documenta
tion describing how to modify the Original Work. Licensor agrees to provide a ma
chine-readable copy of the Source Code of the Original Work along with each copy
of the Original Work that Licensor distributes. Licensor reserves the right to
satisfy this obligation by placing a machine-readable copy of the Source Code in
an information repository reasonably calculated to permit inexpensive and conve
nient access by You for as long as Licensor continues to distribute the Original
Work.

4) Exclusions From License Grant. Neither the names of Licensor, nor the names o
f any contributors to the Original Work, nor any of their trademarks or service
marks, may be used to endorse or promote products derived from this Original Wor
k without express prior permission of the Licensor. Except as expressly stated h
erein, nothing in this License grants any license to Licensor's trademarks, copy
rights, patents, trade secrets or any other intellectual property. No patent lic
ense is granted to make, use, sell, offer for sale, have made, or import embodim
ents of any patent claims other than the licensed claims defined in Section 2. N
o license is granted to the trademarks of Licensor even if such marks are includ
ed in the Original Work. Nothing in this License shall be interpreted to prohibi
t Licensor from licensing under terms different from this License any Original W
ork that Licensor otherwise would have a right to license.

5) External Deployment. The term "External Deployment" means the use, distributi
on, or communication of the Original Work or Derivative Works in any way such th
at the Original Work or Derivative Works may be used by anyone other than You, w
hether those works are distributed or communicated to those persons or made avai
lable as an application intended for use over a network. As an express condition
for the grants of license hereunder, You must treat any External Deployment by
You of the Original Work or a Derivative Work as a distribution under section 1(
c).

6) Attribution Rights. You must retain, in the Source Code of any Derivative Wor
ks that You create, all copyright, patent, or trademark notices from the Source
Code of the Original Work, as well as any notices of licensing and any descripti
ve text identified therein as an "Attribution Notice." You must cause the Source
Code for any Derivative Works that You create to carry a prominent Attribution
Notice reasonably calculated to inform recipients that You have modified the Ori
ginal Work.

7) Warranty of Provenance and Disclaimer of Warranty. The Original Work is provi
ded under this License on an "AS IS" BASIS and WITHOUT WARRANTY, either express
or implied, including, without limitation, the warranties of non-infringement, m
erchantability or fitness for a particular purpose. THE ENTIRE RISK AS TO THE QU
ALITY OF THE ORIGINAL WORK IS WITH YOU. This DISCLAIMER OF WARRANTY constitutes
an essential part of this License. No license to the Original Work is granted by
this License except under this disclaimer.

8) Limitation of Liability. Under no circumstances and under no legal theory, wh
ether in tort (including negligence), contract, or otherwise, shall the Licensor
be liable to anyone for any direct, indirect, special, incidental, or consequen
tial damages of any character arising as a result of this License or the use of
the Original Work including, without limitation, damages for loss of goodwill, w
ork stoppage, computer failure or malfunction, or any and all other commercial d
amages or losses. This limitation of liability shall not apply to the extent app
licable law prohibits such limitation.

9) Acceptance and Termination. If, at any time, You expressly assented to this L
icense, that assent indicates your clear and irrevocable acceptance of this Lice
nse and all of its terms and conditions. If You distribute or communicate copies
of the Original Work or a Derivative Work, You must make a reasonable effort un
der the circumstances to obtain the express assent of recipients to the terms of
this License. This License conditions your rights to undertake the activities l
isted in Section 1, including your right to create Derivative Works based upon t
he Original Work, and doing so without honoring these terms and conditions is pr
ohibited by copyright law and international treaty. Nothing in this License is i
ntended to affect copyright exceptions and limitations (including "fair use" or
"fair dealing"). This License shall terminate immediately and You may no longer
exercise any of the rights granted to You by this License upon your failure to h
onor the conditions in Section 1(c).

10) Termination for Patent Action. This License shall terminate automatically an
d You may no longer exercise any of the rights granted to You by this License as
of the date You commence an action, including a cross-claim or counterclaim, ag
ainst Licensor or any licensee alleging that the Original Work infringes a paten
t. This termination provision shall not apply for an action alleging patent infr
ingement by combinations of the Original Work with other software or hardware.

11) Jurisdiction, Venue and Governing Law. Any action or suit relating to this L
icense may be brought only in the courts of a jurisdiction wherein the Licensor
resides or in which Licensor conducts its primary business, and under the laws o
f that jurisdiction excluding its conflict-of-law provisions. The application of
the United Nations Convention on Contracts for the International Sale of Goods
is expressly excluded. Any use of the Original Work outside the scope of this Li
cense or after its termination shall be subject to the requirements and penaltie
s of copyright or patent law in the appropriate jurisdiction. This section shall
survive the termination of this License.

12) Attorneys' Fees. In any action to enforce the terms of this License or seeki
ng damages relating thereto, the prevailing party shall be entitled to recover i
ts costs and expenses, including, without limitation, reasonable attorneys' fees
and costs incurred in connection with such action, including any appeal of such
action. This section shall survive the termination of this License.

13) Miscellaneous. If any provision of this License is held to be unenforceable,
such provision shall be reformed only to the extent necessary to make it enforc
eable.

14) Definition of "You" in This License. "You" throughout this License, whether
in upper or lower case, means an individual or a legal entity exercising rights
under, and complying with all of the terms of, this License. For legal entities,
"You" includes any entity that controls, is controlled by, or is under common c
ontrol with you. For purposes of this definition, "control" means (i) the power,
direct or indirect, to cause the direction or management of such entity, whethe
r by contract or otherwise, or (ii) ownership of fifty percent (50%) or more of
the outstanding shares, or (iii) beneficial ownership of such entity.

15) Right to Use. You may use the Original Work in all ways not otherwise restri
cted or conditioned by this License or by law, and Licensor promises not to inte
rfere with or be responsible for such uses by You.

16) Modification of This License. This License is Copyright © 2005 Lawrence Ros
en. Permission is granted to copy, distribute, or communicate this License witho
ut modification. Nothing in this License permits You to modify this License as a
pplied to the Original Work or to Derivative Works. However, You may modify the
text of this License and copy, distribute or communicate your modified version (
the "Modified License") and apply it to other original works of authorship subje
ct to the following conditions: (i) You may not indicate in any way that your Mo
dified License is the "Open Software License" or "OSL" and you may not use those
names in the name of your Modified License; (ii) You must replace the notice sp
ecified in the first paragraph above with the notice "Licensed under <insert
your license name here>" or with a notice of your own that is not confusingly 
similar to the notice in this License; and (iii) You may not claim that your original
works are open source software unless your Modified License has been approved b
y Open Source Initiative (OSI) and You comply with its license review and certif
ication process.

17) Non-Profit Amendment. The name of this amended version of the Open Software
License ("OSL 3.0") is "Non-Profit Open Software License 3.0". The original OSL
3.0 license has been amended as follows:

(a) Licensor represents and declares that it is a not-for-profit organization th
at derives no revenue whatsoever from the distribution of the Original Work or D
erivative Works thereof, or from support or services relating thereto.

(b) The first sentence of Section 7 ["Warranty of Provenance"] of OSL 3.0 has be
en stricken. For Original Works licensed under this Non-Profit OSL 3.0, LICENSOR
OFFERS NO WARRANTIES WHATSOEVER.

(c) In the first sentence of Section 8 ["Limitation of Liability"] of this Non-P
rofit OSL 3.0, the list of damages for which LIABILITY IS LIMITED now includes "
direct" damages.

(d) The proviso in Section 1(c) of this License now refers to this "Non-Profit O
pen Software License" rather than the "Open Software License". You may distribut
e or communicate the Original Work or Derivative Works thereof under this Non-Pr
ofit OSL 3.0 license only if You make the representation and declaration in para
graph (a) of this Section 17. Otherwise, You shall distribute or communicate the
Original Work or Derivative Works thereof only under the OSL 3.0 license and Yo
u shall publish clear licensing notices so stating. Also by way of clarification
, this License does not authorize You to distribute or communicate works under t
his Non-Profit OSL 3.0 if You received them under the original OSL 3.0 license.

(e) Original Works licensed under this license shall reference "Non-Profit OSL 3
.0" in licensing notices to distinguish them from works licensed under the origi
nal OSL 3.0 license.

To download the tools in tar.gz format:
To return to the main page:
For previous versions, please click here.

IEDB Tools Downloads

Complete Download: IEDB Analysis Resource Virtual Machine Image

For users that would like to run the entire analysis resource locally, a virtual machine image file is available with a paid commercial license. The image is kept in sync with the current version of the IEDB Analysis Resource and is updated on a six month cycle. Please contact us for details on licensing options.

Standalone Downloads

Many of the tools hosted on the IEDB-AR are available as command-line tools. They are freely available to academic users through an open source license. Please contact us to inquire about a commercial license or if you have any questions in general. For a complete list of standalone tools, including previous versions, please click here.

Linear B cell epitope predictor
This allows for scoring of amino acid residues using the 6 scale-based methods of the linear B cell epitope prediction tool.

Linear B cell epitope predictor

MHC class I & II epitope predictors
For users with batch processing needs, the MHC class I and II binding prediction tools are available as standalone scripts for download. These command line tools are kept in sync with the web tools and should therefore produce the same results as clicking through the web interface.

ElliPro
This will produce the same output as the web version of the tool but does not include the initial template finding functionality. It accepts either a PDB ID or a path to a PDB file as input. Usage instructions are printed by calling the program without any parameters.

ElliPro

Class I Immunogenicity
This tool uses amino acid properties as well as their position within the peptide to predict the immunogenicity of a peptide MHC (pMHC) complex.

Class I Immunogenicity

Proteasomal Cleavage Prediction
The distributions 'IEDB_NetChop-1.0.tar.gz' contains methods for NetChop, NetCTL and NetCTLpan.
NetChop is a predictor of proteasomal processing based upon a neural network. NetCTL is a predictor of T cell epitopes along a protein sequence. It also employs a neural network architecture. NetCTLpan is an update to the original NetCTL server that allows for prediction of CTL epitope with restriction to any MHC molecules of known protein sequence.

Proteasomal Cleavage Prediction

Population Coverage
This tool calculates the fraction of individuals predicted to respond to a given epitope set on the basis of HLA genotypic frequencies and on the basis of MHC binding and/or T cell restriction data. HLA allele genotypic frequencies were obtained from Allele Frequency database.

Population Coverage