Challenge — BioML Society

The BioML Challenge 2024: Bits to Binders, organized by the University of Texas at Austin BioML Society, is a 5-week competition helping to advance the field of protein design with modern AI tools. This year's challenge is to design a protein sequence that can effectively bind a to-be-announced cancer antigen target. Teams from academic institutions, research labs, and industry are encouraged to enter. Each team will submit their designed protein sequences to be synthesized and tested by LEAH Laboratories using their pooled CAR-T screening platform. Winners will be chosen based on how well their predicted designs bind to the antigen target, signal through a CAR, and activate a CAR-T cell proliferation and killing response.

The design stage has ended, thank you for participating! We have begun the testing stage for 12K proteins and are expecting results in early 2025. Stay tuned!

Nature feature on the Bits to Binders competition

Event Format

Teams will design the antigen binding domain of a Chimeric Antigen Receptor (CAR) that will engage to a to-be-announced cancer antigen target. The goal is that the antigen binders will activate a CAR-T cell killing and proliferation response, resulting in a quantifiable increase in the designed antigen binders that function while the designed antigen binders that don't will do nothing. Binder designs will be constrained to 80 amino acids (a function of DNA synthesis limitations) with the rest of the CAR (both CD28z and 41-BBz) remaining constant between designs.

The challenge kicks off with a one-day remote event on Saturday August 24th at 11am CST. This kickoff will consist of an announcement of the binding target, overview of design constraints and supporting data, presentations by community partners, and a tutorial for a baseline design workflow. Breakout rooms will then be provided for teams to work together and receive technical support.

Following the kickoff, teams will have approximately 5 weeks to submit their designs (dates below). Teams are encouraged to use existing tools and develop creative methods at each stage of the design process: design, optimization, and downselection. Each team will submit their protein sequences for synthesis and testing alongside a GitHub repository with their code and a brief writeup of their methods.

Testing and Evaluation

Submitted sequences will be synthesized as DNA and the corresponding proteins experimentally evaluated using LEAH Laboratories’ CAR-T platform. The evaluation will take several months, with the winners announced at a future event. Winners will be scored based on how well their predicted antigen binders activate CAR-T cells in a pooled competition assay against antigen-positive cancer cells.

The top three teams will be invited to present their methods and receive a trophy for their work. Following the challenge, a manuscript will be compiled outlining the design approaches, winning sequences, and lessons learned. The dataset of CAR-T measurements obtained by LEAH Laboratories will be released to the community. As such, all methods and protein sequences must be open sourced.

Awards and Scientific Dissemination

Participant Agreement

By participating in this competition, competitors agree to the following terms:

Intellectual Property: No intellectual property (IP) rights will be claimed on the designed sequences. All designed sequences must be released to the public domain. The organizers and sponsors will not be claiming intellectual property rights to the designed sequences nor will they be commercializing them.
Open Source and Public Availability Requirement:
- All datasets, models, methods, and code developed or used during the competition should be made open source whenever possible.
- In cases where open sourcing is not feasible (like AlphaFold3 or ESM-3), competitors must ensure that the models and methods are well-documented and made publicly available. This includes providing comprehensive documentation and access to the models to allow for public use and verification.
- Update (8/17/24): We discourage teams from using closed-source and license-restrictive models such as AlphaFold3 and ESM-3. However, we cannot police this given the number of submissions we are dealing with, so by submitting your designs you agree that the burden of responsibility for all software used rests upon you, the submitting party, and not the organizers or sponsors.

Further, the participant represents that they have the right to use any software, models, tools or data that they have used or will use to produce any entry in the competition. Participant also represents that Participant (i) has not filed a patent application or submitted an invention disclosure to Participant’s employer or institution for the purpose of a patent application being filed, and (ii) is not aware of any invention disclosure or patent application, that attempts to protect or cover the sequence, sequences, molecule or molecules, or any method of using them, that Participant has submitted or will submit as an entry in the competition. Participant further represents that Participant will not in the future file such an application or submit such an invention disclosure to an employer or institution.

Ethical Disclaimer

This competition is intended solely for educational and research purposes. All participants are advised to ensure that their designs comply with relevant ethical guidelines and regulatory standards, and the organizers disclaim any responsibility for misuse of the resulting protein binders or described methods.