Adaptyv Bio

💡 Protein Design Competition Update Assays are in progress for all 400 protein designs! Given that we doubled the number of designs to be validated and our current high demand, we will be moving the release date by a couple of days to Saturday December 7. Teaser: There are more binders than last time. Stay tuned! 👀

We love open-source protein engineering tools! 🧬 Check out how No Labs has integrated the Adaptyv API to connect their protein design workflow to our wet lab ⬇️ https://lnkd.in/eCcUbBBm Want to use our API for your protein engineering workflows? -> Request access here https://lnkd.in/eUy9fj4W

🌐 Introducing the Adaptyv Bio API Imagine if you could let your AI agent design novel proteins, autonomously test them in our wet lab and then improve itself based on the results We’re excited to release beta access for integrating our lab API with your protein design tools. Our API allows you to programmatically create experimental campaigns, get experiment updates and query lab results. By abstracting away the complexity of the wet lab we’re enabling thousands of protein design teams to get easier access to experimental data to validate their protein designs. From the smallest techbio to the largest pharma company - we’re making experimental data generation easier than ever before to allow you to engineer better proteins! Request access: https://lnkd.in/eUy9fj4W

🚀 Protein Design Competition: Design phase completed -> Wet lab validation started We’ve received well over 1000 protein designs by 130 amazing proteins designers for the 2nd round of our competition. With so many people enthusiastic about designing novel proteins and so many interesting submissions, we decided to double the number of proteins that we will test in the lab! So instead of just 200 proteins we will experimentally characterize 400 novel proteins in our lab and open-source all the results. Here’s how we selected them: - Top 100 designs according to the computational selection metric - For the other 300, we picked between 1 and 5 designs per protein designer, depending on the quality and novelty of their design process descriptions That means that every participant that wrote at least some description of their design process will have at least one of their proteins validated in the lab! 🎉 Find out which designs got selected here: https://lnkd.in/ebQfjMnm Want to see the full leaderboard? -> https://lnkd.in/eZv2tpiB Big thanks to Twist Bioscience for giving us a discount for the DNA synthesis to make this happen! 🧬 And big thanks again to Modal for sponsoring the compute for the competition 💻

🚨 Less than 10 hours till submissions close for the Protein Design Competition 🚨 The official deadline is 11:59 pm PST - make sure to upload your designs before if you want them to be selected for experimental characterization in our lab! After the submissions close, we will run one large scale job to compute the computational metrics for all proteins submitted since the last leaderboard refresh. This might take up to 24 hours or more as we've received already >500 designs in the last 24 hours alone and we expect a few hundred more in the coming hours till the submission deadline. Then we will publish the final virtual leaderboard and select the protein designs that will be characterized in the lab! You can find all up-to-date information here: https://lnkd.in/evZChbY5 For questions, please email us at competitions@adaptyvbio.com Good luck! 💪

More and more submissions are rolling in for Round 2 of the Protein Design Competition! 💪 Our virtual leaderboard is refreshing every 24h and we just published the scripts we're running to compute the evaluation metrics. This way you can check your protein designs by yourself and improve them before submitting! You can also submit more than once but we will only count the last 10 designs for the leaderboard! The submission deadline is November 4 at 11:59 PM PT -- good luck everyone! Github repo for computational metrics: https://lnkd.in/egaAebTU

👑 Leaderboard for Protein Design Competition Round 2 is now live! Andrejs Tucs from U Tokyo takes the top spots! With only 10 more days to go, can someone beat him? Leaderboard refresh every 24h; submission deadline Nov 4 at midnight! Go upload your protein designs at design.adaptyvbio.com

⏳ 2 weeks left to submit your designs to the Protein Design Competition Round 2! We're excited to partner with Modal to make it easier for you to run your protein design pipeline.  Get cloud compute that you can use to make your submission -> https://lnkd.in/evZChbY5

🏆🔬 Protein Optimization 102: Lessons from the protein design competition Curious about the strategies behind the winning designs in the protein design competition Round 1? Our latest blog post dives into the different approaches used, and how the top method stood out from the rest. We’ve also provided practical insights and a guide to help you navigate the best design strategies for your own projects. Check it out here: https://lnkd.in/guJYknG6

📊 Selection Criteria for Protein Design Competition Round 2 Based on the observations from Round 1 of the competition and feedback from the community, we’ve decided to use the rank average of 3 computational metrics to select which designs to validate in our lab: 1. AlphaFold2 PAE_interaction 2. AlphaFold2 ipTM 3. ESM2 log likelihood First, we kept PAE_interaction as a local interface confidence metric. We added ipTM as a global metric to improve hit rates, based on Martin Pacesa's suggestion in the recent BindCraft pre-print. Lastly, we chose the ESM2 log likelihood to bias the score towards designs with higher expression potential, given its ease of use and the positive correlation with expression observed in Round 1, as highlighted by Nikhil Haas. While this might favor more “natural” designs, we think it's a good trade-off to select designs that are more likely to express. Thanks to everyone who contributed to the discussion 🙌