GPU-accelerated MMseqs2 offers tremendous speedup for homology retrieval, protein structure prediction with ColabFold, and protein structure search with Foldseek. @martinsteinegger.bsky.social @milot.bsky.social @machine.learning.bio

www.nature.com/articles/s41...

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

AtomWorks is out! Building upon @biotite_python, we built a toolkit for all things biomolecules and trained RF3 with it. All open-source, test it via `pip install atomworks`!

AtomWorks: github.com/RosettaCommo...
RF3: github.com/RosettaCommo...
Paper: tinyurl.com/y2w4z65b

1/6

RosettaFold 3 is here! 🧬🚀

AtomWorks (the foundational data pipeline powering it) is perhaps the really most exciting part of this release!

Congratulations @simonmathis.bsky.social and team!!! ❤️

bioRxiv preprint: www.biorxiv.org/content/10.1...

(1/7)
Training biomolecular foundation models shouldn't be so hard. And open-source structure prediction is important. So today we're releasing two software packages: AtomWorks and RosettaFold3 (RF3)

[https://www.biorxiv.org/content/10.1101/2025.08.14.670328v2](www.biorxiv.org/content/10.1...)

Very excited about our latest all-atom generative model proteina, check out the project page (research.nvidia.com/labs/genair/...) and stay tuned for the code release soon!

Excited to present my first paper officially as a PhD student now as an ICLR Oral this week! Super fun work with the GenAIR team at NVIDIA.

Talk: Fr 10:54 - 11:06 (Oral Session 3B, Garnet 213-215)
Poster: Fr 15:00-17:30 (Hall 3 + Hall 2B #5)

Come by the poster/reach out to chat

Such a fun project to work on with a stellar team! Stay tuned for other things to come here, and see you all in Singapore!

Yet another story of issues with benchmarks and evaluations in ML4bio + a much stronger and fair benchmark #bioMLeval

Have a look at our shiny new benchmark for motif-scaffolding in computational protein design! New (and harder) tasks, including a reproducible evaluation pipeline

This!

Also well put in this editorial in PLOS Comp Biol:
Putting benchmarks in their rightful place: The heart of computational biology
doi.org/10.1371/jour...

Our paper on computational design of chemically induced protein interactions is out in @natureportfolio.bsky.social. Big thanks to all co-authors, especially Anthony Marchand, Stephen Buckley and Bruno Correia!

t.co/vtYlhi8aQm

After two years, our paper on generative models for structure-based drug design is finally out in @natcomputsci.bsky.social

www.nature.com/articles/s43...

Thanks Jascha 🫶

We’re working hard to create sustainable funding mechanisms for open source scientific tooling - understanding the challenge landscape is a key first step!

Love PyMOL Remote, one of these tools that does one thing and does it well!

This should go chiral

MSAs go brrr with MMseqs2-GPU! Super fun project, happy to work with and learn from a stellar team of engineers and scientists. Try it out and stay tuned!

📄 Preprint: www.biorxiv.org/content/10.1...
💾 Code: mmseqs.com
🗞️ Blog: developer.nvidia.com/blog/boost-a...