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-...

Gonzalo Parra@gonzaparra.bsky.social · 10mo ago

After months of buildup, it’s finally real! 🎉 The Evolutionary Systems Biophysics Group (ESBG) is officially alive at @bsc-cns.bsky.social . Proud to start this new adventure as a Ramon y Cajal Junior Group Leader🧬 Thanks to all who have been part of this process! tinyurl.com/4r9vf4zx

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

GPU-accelerated homology search with MMseqs2 - Nature Methods

Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...

nature.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

PDB101: Poster Prize Awarded at ISMB/ECCB 2025

PDB-101: Training, Outreach, and Education portal of RCSB PDB

pdb101.rcsb.org

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

Adaptyv Bio - Protein Optimization 103: Racing to the Top 100

What a close race this one was! In this blog post, we look at how submissions evolved throughout our latest EGFR binder design competition. We highlight the most widespread model and design choices, h...

adaptyvbio.com

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!)

Kevin K. Yang 楊凱筌@kevinkaichuang.bsky.social · 2y ago

I tried to make a bioml starter pack. DM if you want me to add or remove you? go.bsky.app/2VWBcCd

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

CATH v4.4: major expansion of CATH by experimental and predicted structural data

Abstract. CATH (https://www.cathdb.info) is a structural classification database that assigns domains to the structures in the Protein Data Bank (PDB) and

academic.oup.com

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...

UCL-led research reveals new protein map with potential to transform disease research

UCL researchers have developed The Encyclopedia of Domains (TED), a tool mapping millions of unknown protein regions, with potential for breakthroughs in drug discovery and disease research.

ucl.ac.uk