BERTMHC is developed at NEC Lab Europe . It is a transformer model build to predict the binding and presentation of peptides by MHC class II molecules.

The server is only allowed for non-commercial research. Please read and agree the TERMS OF SERVICE bellow before using the server.

You can submit maximum 10k peptides per query. We will normalize the allele names. However, the system will return an error if unrecognized alleles are presented. Please be patient while the prediction is running. Do not repetitively submit jobs.

The "Submit" button will be deactivated once clicked. You can submit another job when the current job is finished. Only refresh the page after downloading your results. The "Submit" button will reactivate when the page reloaded. Please submit ONE job at a time! Submit new jobs when the current one is finished.

If you use this tool in research, please cite:

Jun Cheng, Kaïdre Bendjama, Karola Rittner, Brandon Malone
BERTMHC: Improved MHC-peptide class II interaction prediction with transformer and multiple instance learning BioRxiv (2020)

Please Upload The File

Example input data



NEC Laboratories Europe GmbH (hereinafter “NLE”) is offering through this website a service that consists of producing predictions starting from data provided by the user (hereinafter “the Service”).

The use of the Service is subject to the present terms, as these may be changed from time to time. Besides the present terms of service, the Terms of Use and the Data Privacy Statement found on NEC Laboratories Europe GmbH website are also applicable. If you don’t agree with any of the terms below, please do not use the Service.

These terms may be updated, revised or amended from time to time, at the sole discretion of NLE. You should periodically refer to any changes made to these terms. In continuing using the Service, it will thereafter constitute your deemed acceptance of the revised terms.

By using the Service, you accept the following conditions:

Limitation of Use

You may use the Service for non-commercial research purposes only. All right, title, and interest in and to the Service, the software, the outputs, as well as all materials provided on this website are and will remain the exclusive property of NLE. In particular, NLE shall retain all intellectual property rights as well as any other property rights, including, patents, trademarks, source codes, databases.

Your Obligations

Before submitting a file to the Service, you must ensure that you have the right to do so. You must either be the author or have obtained it with the authorization of the copyright holder. NLE cannot be held responsible in the event of non-compliance with this clause. Further, you agree not to submit any material that invades another’s privacy, is obscene, pornographic or offensive, racist, defamatory, spreads terror or torture, harms minors, promotes illegal activity, is false or misleading or violates any law or regulation.

In general, by uploading files to the Service, you represent and warrant that you own or have obtained all rights, licenses, consents, permissions, power and/or authority, necessary to use and/or upload such file and that the use does not and shall not (a) infringe or violate any intellectual property, proprietary or privacy, data protection or publicity rights of any third party; (b) violate any applicable local, state, federal and international laws, regulations and conventions; and/or (c) violate any of third party’s policies and/or terms of service.

NLE executes basic security checks on the files submitted but does not fully monitor the content of the files submitted and will not be held responsible for any damages claimed as a result of the usage of the Service against these terms.

You acknowledge that the output of the Service constitutes a new document owned by NLE and any subsisting IP rights are vested in NLE. Thus, you shall not publish the output without NLE’s prior authorization.


You may not attempt to modify, translate, reverse engineer, decompile, disassemble or otherwise create derivative works from the software used by NLE to provide the Service or binary-code part of it, or otherwise attempt to discover its underlying code, structure, implementation or algorithms.

You further may not reproduce, transmit, transfer, lend, rent, lease, distribute the Service, or incorporate it as part of another service or use it for providing services to a third party, or grant any rights therein to a third party in any form; or remove, modify or make illegible the designations regarding copyrights and other intellectual property rights of the Service.

You may not tamper with parts of the Service, interfere with, circumvent, impair or disrupt the operation, or the functionality of the Service, breach the security of the Service, identify, probe or scan any security vulnerabilities in the Service, send a virus or other destructive mechanism with the intention of crippling the Service, or misrepresent, or impersonate some other entity.


While NLE tries to ensure that the Service is error free, you agree that the use of the Service through the website is at your own risk. NLE will not be responsible for any damage to computer systems, failure to analyze, corruption of data, or any loss in data arising from accessing the Service provided on the website.

Warranties and Limitation of Liability

You will make use of the Service at your own risk.

The Service is provided on an “AS IS”, “WHERE IS” basis. NLE disclaims all implied warranties of satisfaction and fitness for particular purpose. No representation or other affirmation of fact, including but not limited to statements regarding capacity, suitability for use or performance of the Service, whether made by NLE employees or otherwise, shall be deemed to be a warranty by NLE for any purpose or give rise to any liability of NLE whatsoever.

In no event shall NLE be liable to you for any general, incidental, consequential, indirect, special or punitive damages, arising out of or relating to the Service or these terms; provided, however, that such limitation of liability shall not apply in respect of damages claimed against NLE as a result of (i) damage to body or health, (ii) or intentional or grossly negligent misconduct.


You agree to indemnify defend and hold NLE harmless from and against any and all claims, damages, costs, losses, liabilities, obligations, and expenses arising from your use of the Service, any violation by you of these terms, any violation by you of any third-party right and any claim levied against you that your submission caused damage to a third party.