Isomorphic Labs Drug Design Engine (IsoDDE), a unified computational drug-design system Announcement: www.isomorphiclabs.com/articles/the... Report: storage.googleapis.com/isomorphicla...

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...

Here are the success rates of de novo pipelines based on which designs I could actually identify the methods for.

Loved this post from A-Alpha: aalphabio.substack.com/p/building-a.... If anything I think the IPSAE (or any other post-hoc metric) picture is even worse than they show: after optimization the fraction of false positives would (probably) be even higher than in this dataset

New preprint🚨 Imagine (re)designing a protein via inverse folding. AF2 predicts the designed sequence to a structure with pLDDT 94 & you get 1.8 Å RMSD to the input. Perfect design? What if I told u that the structure has 4 solvent-exposed Trp and 3 Pro where a Gly should be? Why to be wary🧵👇

I'm really excited to break up the holiday relaxation time with a new preprint that benchmarks AlphaFold3 (AF3)/“co-folding” methods with 2 new stringent performance tests. Thread below - but first some links: A longer take: fraserlab.com/2025/12/29/k... Preprint: www.biorxiv.org/content/10.6...

🧶🧬 We present LMi4Boltz: www.biorxiv.org/content/10.1... Boltz-2 is an excellent open source alternative to AlphaFold3. However, high VRAM use restricts modeling large complexes. Using careful memory management, we increase the Boltz-2 size limit by >60% while maintaining execution speed.