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judewells.bsky.social

@judewells.bsky.social
621 followers 803 following 18 posts

Encode AI for Science Fellow (Pillar VC / Imperial College London) Protein Design, PhD in machine learning for structural biology at UCL

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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 07/01/2026
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...
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CATH-Gene3D @cathgene3d.bsky.social · 22/12/2025
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.
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judewells.bsky.social @judewells.bsky.social · 01/12/2025
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.
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Gonzalo Parra @gonzaparra.bsky.social · 02/10/2025
🚀 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-...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 21/09/2025
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
nature.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...
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judewells.bsky.social @judewells.bsky.social · 18/09/2025
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.
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Dr Javier Sánchez Utgés @javierutges.bsky.social · 06/08/2025
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!
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RCSB Protein Data Bank @rcsbpdb.bsky.social · 22/08/2025
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.rcsb.org
PDB101: Poster Prize Awarded at ISMB/ECCB 2025
PDB-101: Training, Outreach, and Education portal of RCSB PDB
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judewells.bsky.social @judewells.bsky.social · 09/01/2025
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
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judewells.bsky.social @judewells.bsky.social · 14/12/2024
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)?
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judewells.bsky.social @judewells.bsky.social · 06/12/2024
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
adaptyvbio.com
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...
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Kevin K. Yang 楊凱筌 @kevinkaichuang.bsky.social · 18/11/2024
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!)
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CATH-Gene3D @cathgene3d.bsky.social · 20/11/2024
A new version of CATH, v4.4, is out! 🎉 Here’s a link to the manuscript in NAR.
academic.oup.com
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
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Gabriele Corso @gcorso.bsky.social · 17/11/2024
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!
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judewells.bsky.social @judewells.bsky.social · 18/11/2024
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.ac.uk
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.
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