New post: blog.escalante.bio/teaching-gen.... You can massively improve in silico metrics for BoltzGen using standard post-training techniques (with a structure model as your reward function). If this holds up (no wetlab testing yet!) you could get binders in seconds rather than hours...
なお、進捗🥺
New paper from former PhD student @tkschulze.bsky.social on supervised learning of protein variant effects across large-scale mutagenesis datasets
MAVE/DMS experiments provide large amounts of data for benchmarking variant effect predictors, but may be difficult to use in supervised learning. 1/5
We have started a project trying to predic the interactions/structures of all yeast protein pairs using an AlphaFold pooling approach. We are making the current dataset open and we welcome collaborations.
www.evocellnet.com/2026/03/mapp...
When you still haven't solved the orientation bias of your protein sample #CryoEM
Results from an impressive world-wide binder design competition.
悔しいから午後はナイトレインの練習すっか
くやC
Protenix v1.0 is out with some very impressive performance numbers (exceeding AF3 performance on protein-protein complexes)
Naturally I had to add this to mosaic. Here's a VHH designed using `protenix_base_20250630_v1.0.0`. Example notebook here: github.com/escalante-bi...
まあ複数人だといける気もしなくもない
FoldMason is out now in @science.org. It generates accurate multiple structure alignments for thousands of protein structures in seconds. Great work by Cameron L. M. Gilchrist and @milot.bsky.social.
📄 www.science.org/doi/10.1126/...
🌐 search.foldseek.com/foldmason
💾 github.com/steineggerla...
Potential fork of PPIFlow with a more permissive license is very exciting: github.com/Mingchenchen...
Highly recommend their paper: results are super impressive and it's *not* an AF3 clone
Here are the success rates of de novo pipelines based on which designs I could actually identify the methods for.
Huge congratulations @nboyd.bsky.social with Mosaic that absolutely killed in the competition! 𝑩𝒊𝒏𝒅𝑪𝒓𝒂𝒇𝒕2 did also pretty well with the second highest hit rate in the competition!
proteinbase.com/collections/...
New Preprint!! We show that binding entropy can be quantitatively predicted from crystallographic ensemble models, accounting for both protein conformational entropy and solvent entropy! www.biorxiv.org/content/10.6...
映えな照明買ったよ🥺 (Switch 2の側に置いてる)
こちらが~4万円したSteiffコラボのカービィちゃんです (持ったときの密度がすごい)
タルトタタンを食べました☺️
Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...
Boltz関係が面白い動きしましたねえ
Check our new preprint smoothing rugged Cryo-EM landscapes: shorturl.at/gYs9U
We tackle practical hurdles of Optimal Transport (OT) loss—differentiability, cost & noise sensitivity—make it a feasible inference workhorse.
W/ G. Woollard, D. Herreros, @pilarcossio.bsky.social, K. Dao Duc 🧵👇 (1/9)
AmberTools 25 is now available on Homebrew🎉
brew install brewsci/bio/ambertools
Our review on Integrative modelling of biomolecular dynamics 💃 is now live at COSB
We discuss approaches to integrate computational methods with time-dependent & time-resolved experiments to study protein dynamics
With @dariagusew.bsky.social & Carl G. Henning Hansen
doi.org/10.1016/j.sb...
『エルデンリング ナイトレイン』の新DLCでは「毒沼」とうとう実装へ。“いつの間にか誰かが入れた”毒沼
automaton-media.com/articles/new...
Papier-mâché Suica Penguin, the Japanese railway character—made like a matryoshka doll 🐧
Been excited about this one for a while! What would you do with a new alphabet and the wealth of protein sequence bioinformatics at your disposal? We're also around at #EMBOComp3D Heidelberg and MLSB Copenhagen this week to discuss
Swapped my silent linear switches to regular linears for my home setup, and upgraded the keycaps to a PBS profile while I was at it. 🫐🫐🫐
People say de novo antibody design lets you target any epitope, but I doubt it. Antibody topology can’t cover all protein surfaces, and PDB-trained methods narrow that space even more.
