The Align Foundation

📢 Data Release Tuesday: Align TEV Protease Dataset 📊 We’re expanding the The Align Foundation data ecosystem again with ~30,000 high-quality GROQ-seq data points capturing TEV protease sequence–function relationships at scale.

TEV protease is a cornerstone tool in biotechnology, known for its high substrate specificity, and this dataset provides a rich resource for enzyme engineering and ML-driven protein design.

📢 Data Release Tuesday: Align TEV Protease Dataset 📊 We’re expanding the The Align Foundation data ecosystem again with ~30,000 high-quality GROQ-seq data points capturing TEV protease sequence–function relationships at scale.

📢 Public Data Release: Align T7 RNA Polymerase Dataset. 📊The data keeps coming at Align! We’re excited to release our T7 RNA polymerase dataset, adding ~35,000 unique GROQ-seq data points to the growing Align data ecosystem, capturing sequence–function relationships across variants at scale.

🚀 Public Data Release: GROQ-seq Transcription Factor Dataset We’re excited to announce the public release of The Align Foundation's first GROQ-seq dataset, one of the largest high-resolution transcription factor datasets of its kind.

This is the result of a fantastic collaboration with David Ross's Lab at NIST, @doelsnitz.bsky.social at @harvard.edu and the DAMP Lab. We’re thrilled to make the data publicly accessible to support the broader research community.

🚀 Public Data Release: GROQ-seq Transcription Factor Dataset We’re excited to announce the public release of The Align Foundation's first GROQ-seq dataset, one of the largest high-resolution transcription factor datasets of its kind.

📊 100,000+ data points measuring transcription factor–DNA interactions across three regulators (LacI, RamR, VanR).

Align and Google DeepMind are partnering to build AI-ready datasets & evaluations for the future of predictive #AMR biology. Researchers worldwide can submit concepts through March 31 with roadmapping workshops coming to North America + APAC this spring. 🔗 docs.google.com/forms/d/e/1F...

In partnership with @pioneerlabs.bsky.social, we’re proposing Tesseract: a large-scale, open microbial phenomics dataset to functionally annotate microbial genomes at scale. 🧬🤖 ✅5M diverse genes x 50 host strains × 100 conditions 🔗 Read the proposal:https://zenodo.org/records/17990299

1/5 To ensure the highest impact and participation, we are adjusting the timeline of the Protein Engineering Tournament. The Tournament will now begin on December 1st, 2025.

4/5 The new timeline is as follows: -Registration deadline: Nov. 14th 2025 Predictive phase: -Zero-shot track: Dec. 1st 2025 to Jan. 16th 2026 -Supervised track: Jan. 26th to Feb. 20th 2026 Generative phase: -Round-1: Mar. 9th to Apr. 3rd 2026 -Round-2: Jul. 20th to Aug. 14th 2026

1/5 To ensure the highest impact and participation, we are adjusting the timeline of the Protein Engineering Tournament. The Tournament will now begin on December 1st, 2025.

2/5 This additional time will allow us to: •Complete the generation of a high-quality training dataset 🧬🧪 •Secure the best sponsorships to expand access to the Tournament 🖥️💪 •Register more participants 👥🚀

📣 Evolutionary Scale is supporting the 2025 Protein Engineering Tournament! Teams get sponsored ESM inference through @evolutionaryscale.bsky.social's API (Forge), bringing frontier protein AI models into the competition. Level playing field, real experiments, open results. Register now 👇

1/4 We just published the 1st-year update on GROQ-seq: an open access, high-throughput experimental platform capable of testing hundreds of thousands of protein variants per run, running @ NIST and the DAMP Lab. Here’s what we built, learned, and what’s next: #GROQseq #syntheticbiology

3/4 GROQ-seq is designed for reproducibility. Standardized assays + distributed data collection = a foundation for robust, ML-ready protein function data. Next: scale up function types, refine ML pipelines, expand access.

1/4 We just published the 1st-year update on GROQ-seq: an open access, high-throughput experimental platform capable of testing hundreds of thousands of protein variants per run, running @ NIST and the DAMP Lab. Here’s what we built, learned, and what’s next: #GROQseq #syntheticbiology

1/4 🚀 Announcing the 2025 Protein Engineering Tournament. This year’s challenge: design PETase enzymes, which degrade the type of plastic in bottles. Can AI-guided protein design help solve the climate crisis? Let’s find out! ⬇️ #AIforBiology #ClimateTech #ProteinEngineering #OpenScience

4/4 🏆 Why join?: • $30K in cash prizes • Free DNA synthesis + wet lab testing • Leaderboard visibility • Publication in a special issue of Proteins • Sponsored conference presentations

1/4 🚀 Announcing the 2025 Protein Engineering Tournament. This year’s challenge: design PETase enzymes, which degrade the type of plastic in bottles. Can AI-guided protein design help solve the climate crisis? Let’s find out! ⬇️ #AIforBiology #ClimateTech #ProteinEngineering #OpenScience

2/4 This is a *lab-validated* benchmark competition for real protein function. The winner will be determined by experiment. We’ll test: 🔥 Enzymatic activity at high temperatures 🧬 Protein expression Results go straight to the leaderboard. 🔗 Register by Oct. 17: bit.ly/Tournament25

🚨 Align × ATCC are partnering to build the world’s largest public microbial phenotyping dataset. ✅ 1K strains ✅ 1K conditions ✅ 1M reproducible experiments ✅ Open access This experimental platform will use high-throughput automation, linked to ATCC’s authenticated genomes.

🧬 Growth + morphology data across diverse conditions 🔗 Linked to genome references with robust metadata 📊 Built for ML training, benchmarking, reproducibility 🙌 Thx to Jensen Lab for their foundational work that helped enable this platform. Lean more here: alignbio.org/datasets-mic...

Measuring precise enzyme kinetics (like kcat and Km) is key to understanding enzyme function. But these measurements are most often conducted in singleplex in vitro assays - expensive and tough to scale. 1/7 🧵👇

6/7 🧵Read the full, peer-reviewed proposal here—work is already underway! zenodo.org/records/1527...

Measuring precise enzyme kinetics (like kcat and Km) is key to understanding enzyme function. But these measurements are most often conducted in singleplex in vitro assays - expensive and tough to scale. 1/7 🧵👇

4/7 🧵This builds on her previous work with the metabolic enzyme dihydrofolate reductase (DHFR) in @eLife, showing how growth rates can map enzyme activities inside cells: elifesciences.org/articles/53476

Measuring precise enzyme kinetics (like kcat and Km) is key to understanding enzyme function. But these measurements are most often conducted in singleplex in vitro assays - expensive and tough to scale. 1/7 🧵👇

2/7 🧵👇 Plus, enzymes behave differently inside cells than in test tubes. To truly engineer enzymes for real-world applications, we need measurements in the cellular context.