Hosted by Adaptyv Bio, in partnership with

Protein Design Competition

Round 2

In this competition, you can continue testing your skills as a protein designer by leveraging data from Round 1 to design a binding protein to the extracellular domain of EGFR. The top 200 designs will be experimentally validated in Adaptyv Bio’s automated wet lab with all results being open-sourced.

ROUND 1 DATA

Round 1 finished with 700+ designs submitted and 200 of them being tested through Adaptyv Bio’s lab. Use the newly generated data to inform your designs ahead of your submission for Round 2. Same target, more data, better proteins?

Round 1

Competition structure

Submission process

Every protein designer can submit up to 10 designs.

Designs must adhere to the following criteria:

• Only natural amino acids
NEW: Max 250 amino acids in length
• Single chain
• At least 10 amino acid edit distance from published sequences

Evaluation criteria

NEW: Designs will be ranked based on the average of 3 computational metrics:

1. AlphaFold2 PAE_interaction
2. AlphaFold2 ipTM
3. ESM2 log likelihood

The complete methodology is described here.

The top 100 designs will be selected for experimental testing.

100 additional designs will be chosen for their novelty, creativity in the design process or other interesting factors.

Lab evaluation

Selected designs will be tested in our Affinity Characterization workflow which includes protein expression and a high-quality kinetics assay to determine the binding affinity of the protein to the target.

NEW: In this round we will also conduct a neutralization assay against EGF to assess whether your designed protein can block its interaction with the receptor. This assay will test how effectively a molecule inhibits ligand-receptor binding and ensure your binder targets the correct site on EGFR for optimal neutralization.

You can find more information in our RFdiffusion case study

Timeline

Submission deadline: November 4, 2024 at 11:59 pm PT.

Results announcement: December 4, 2024

Prizes

In partnership with the AIDrugX Workshop at NeurIPS 2024, the top 3 designers will be given a presentation slot to describe their design approach. In addition, the top 5 designers with the best binding affinity (= lowest KD value) will receive 10 free assays each to run at Adaptyv Bio for their own protein design campaigns. Top 10 designers will additionally receive an Adaptyv Bio & Polaris Merch Pack.

Make a submission

🚧 Submissions are now closed

The final virtual leaderboard will be available in the next few hours. We're working hard to process all the remaining designs. Thanks for your patience!

Want to receive updates?

VIRTUAL LEADERBOARD

Best designs based on PAE_interaction, ipTM and ESM2 log likelihood*

Rank

Designer

PAE

ipTM

PLL

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*We are using the rank average of 3 computational metrics:

1. AlphaFold2 PAE_interaction
2. AlphaFold2 ipTM
3. ESM2 log likelihood

The complete methodology is described here.

The top 100 designs will be selected for experimental testing.

Want to get started designing proteins? Check out some protein design tools