_machine

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

Mapping the yeast atructural interactome with AlphaFold3: an open call for collaboration We are excited to announce the early-stage release of our S. cerevisiae  structural interactome mapping project. Using AlphaFold3 (AF3), w...

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...

Low resolution cryo-EM map that looks like Cuban's skull

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

GitHub - bytedance/Protenix: Toward High-Accuracy Open-Source Biomolecular Structure Prediction. Toward High-Accuracy Open-Source Biomolecular Structure Prediction. - bytedance/Protenix

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

Multiple protein structure alignment at scale with FoldMason Protein structure is conserved beyond sequence, making multiple structural alignment (MSTA) essential for analyzing distantly related proteins. Computational prediction methods have vastly extended ou...

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)

YouTube video by Serizawa Fumino(CV Ito Kanae) - Topic Happy New Nya

はっぴぃにゅうにゃあ
www.youtube.com/watch?v=W-o9...

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.

Reliable Identification of Homodimers Using AlphaFold https://www.biorxiv.org/content/10.1101/2025.11.27.691011v1