A dataset of 40 million protein families and an autoregressive model of protein families. Great to see other protein Atlases popping up after Dayhoff!! @judewells.bsky.social @dmmiller597.bsky.social www.biorxiv.org/content/10.6...

Built by CATH, TÜM and NVIDIA, ProFam-1 is our new open-source protein family language model (pfLM) designed to generate functional protein variants and predict fitness using in-context example sequences.

Ok let’s go @adaptyv.bio binder design competition: this time designing proteins to neutralise the Nipah virus. Lots of great de novo ML binder design tools out there now, but this year I’m submitting an entry from TEAM HUMAN, seeing if pure rational design can win against the machines.

🚀 As first official act, we are hiring! 🎓 We’re looking for a PhD student to work at the interface of computational biophysics, machine learning & human mutations. 📌 FPI fellowship, 4 years fully funded! More information here: www.bsc.es/join-us/job-...

MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n 📄 www.nature.com/articles/s41... 💿 mmseqs.com

It was lovely to speak at the CATH 30 symposium, celebrating 30 years of the @cathgene3d.bsky.social protein structure classification database. I was presenting recent work on our new generative protein-family language model: preprint coming soon.

I also truly appreciated the chance to meet my future colleagues @nbordin.bsky.social, David Miller, Vaishali Waman, @judewells.bsky.social and Ian Sillitoe. I am thrilled to be joining your team soon!

Poster Prize Awarded at ISMB/ECCB 2025 Congratulations to Jude Wells for Design in voxel space, decode in smiles space: Plixer generates drug-like molecules for protein pockets

Thanks to everyone who came and talked with me about my poster at #PSB2025 : computational methods for predicting which mutations will cause drug inefficacy via protein-drug binding disruption

Does anyone know if Rosetta Interface Analyzer from @rosettacommons.bsky.social is the best method within the Rosetta framework for estimating binding affinity between antibodies and antigens? (Including ddG of mutations)?

Great blog post from AdaptyvBio summarising submissions for round 2 of the protein design competition: including a few interesting methods I had never heard of. Results will be released tomorrow: www.adaptyvbio.com/blog/po103

Two BioML starter packs now: Pack 1: go.bsky.app/2VWBcCd Pack 2: go.bsky.app/Bw84Hmc DM if you want to be included (or nominate people who should be!)

A new version of CATH, v4.4, is out! 🎉 Here’s a link to the manuscript in NAR.

Thrilled to announce Boltz-1, the first open-source and commercially available model to achieve AlphaFold3-level accuracy on biomolecular structure prediction! An exciting collaboration with Jeremy, Saro, and an amazing team at MIT and Genesis Therapeutics. A thread!

Our recent work TED: The Encyclopedia of Domains showcased by UCL: 365 million domain like structures identified in the AlphaFold DB, 194 million with proposed assignments to CATH superfamilies, plus a catalogue of domain-domain interactions. www.ucl.ac.uk/computer-sci...