@judewells.bsky.social
PhD student University College London: machine learning for protein design and structure-based drug discovery
Reposted
🚀 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-...
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-...
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
Thanks to all who have been part of this process!
tinyurl.com/4r9vf4zx
October 2, 2025 at 8:12 AM
🚀 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-...
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-...
Reposted
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
📄 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...
www.nature.com
September 21, 2025 at 8:06 AM
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
📄 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.
September 18, 2025 at 10:33 AM
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.
Reposted
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!
August 6, 2025 at 12:33 PM
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!
Reposted
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
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
August 22, 2025 at 3:09 PM
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
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
January 9, 2025 at 1:21 AM
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)?
December 14, 2024 at 1:31 PM
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
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...
www.adaptyvbio.com
December 6, 2024 at 8:53 AM
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
www.adaptyvbio.com/blog/po103
Reposted
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!)
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!)
Anybody have a bioml starter pack?
November 18, 2024 at 5:09 PM
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!)
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!)
Reposted
A new version of CATH, v4.4, is out! 🎉
Here’s a link to the manuscript in NAR.
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
November 20, 2024 at 12:52 PM
A new version of CATH, v4.4, is out! 🎉
Here’s a link to the manuscript in NAR.
Here’s a link to the manuscript in NAR.
Reposted
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!
November 17, 2024 at 4:20 PM
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...
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.
www.ucl.ac.uk
November 18, 2024 at 11:38 AM
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...
www.ucl.ac.uk/computer-sci...