Another day, another paper describing an ML method for generating conformational ensembles without comparison to any experimental data 😩
20.01.2026 07:45
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Another day, another paper describing an ML method for generating conformational ensembles without comparison to any experimental data 😩
My time in @martinsteinegger.bsky.social's group is ending, but I’m staying in Korea to build a lab at Sungkyunkwan University School of Medicine. If you or someone you know is interested in molecular machine learning and open-source bioinformatics, please reach out. I am hiring!
mirdita.org
Don't fret if you weren't in the room this week when @ginaelnesr.bsky.social gave her stellar seminar because you can check out the recording 👇
youtu.be/I-utRMS84E8
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
We can't wait until Wednesday, November 19th 2025 to arrive because we have @ginaelnesr.bsky.social from @possuhuanglab.bsky.social speaking at 7pm EST in Room 6055, Longwood Center, @danafarber.bsky.social
"Learning millisecond protein dynamics from what is missing in NMR spectra"
bpdmc.org
MLSB is coming to Copenhagen, DK 🎉
Submission is under the same portal, just simply indicate your location preference(s).
... each independent simulation is 500 ns long, almost certainly too short to sample the sorts of large-scale functionally relevant conformational changes that ML methods should be learning from, which means I must once again repost this excerpt from Janson et al
Not sure how many scientists here have tried Claude Code or similar command line coding assistants. I had a complicated family property tax problem that was best solved by a brute force Monte Carlo simulation approach, so I spent a few days coding up and analyzing a model with Claude Code.
I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!
Uncancelled! 🥳
The MLSB workshop will be in San Diego, CA (co-located with NeurIPS) this year for its 6th edition in December 🧬🔬
Stay tuned @workshopmlsb.bsky.social as we share details about the stellar lineup of speakers, the official call for papers, and other announcements!🌟
is this how small molecules bind?? 😼
molecular cat-formations
Enzyme design! Benchmark data! Wet-lab validation! Expression & activity assays!! ✨
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
Seems it has happened in the past. Some examples are MLCB and MHLC, which were once conference workshops and after being rejected, they spun out into separate conferences.
ugh we thought so too 😪 currently looking into alternative solutions!
Noooo😭
This was the BEST workshop at NeurIPS!!
Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
Unfortunately, the MLSB Workshop @ NeurIPS (@workshopmlsb.bsky.social) was rejected this year.
Feedback from the deciding committee indicates it was a coin flip decision, with 283 proposals & a number related to “computational biology”
More on the future of MLSB soon…
Speak up to prevent a major loss for the field. CASP, which helped shaping structural biology including AlphaFold is on the verge of shutting down. NIH funding has lapsed, UC Davis support ends and the core team is being let go. Painfully shortsighted.
Exclusive: An international scientific competition widely credited with spurring the development of artificial intelligence for biology appears to be on its deathbed. scim.ag/44ukS90
The dependence of the amino acid backbone conformation on the translated synonymous codon is not statistically significant
doi.org/10.1073/pnas...
[Following: Codon-specific Ramachandran plots show amino acid backbone conformation depends on identity of the translated codon doi.org/10.1038/s414...
philosophy at its finest
Oh well in that case, I guess this sequence is purification ready, with an SA spacer nicely placed for a TEV-tag insertion
Ran some sequence design with LigandMPNN and it... designed a protein with an (almost) His-tag 🤔
someone said we need a meme
"De novo prediction of protein structural dynamics"
I'll be presenting an overview of the field tomorrow at a workshop. Link to a PDF copy of the presentation: delalamo.xyz/assets/post_...
