Martin Steinegger 🇺🇦

New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!

A few py2Dmol updates 🧬

py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)

Congratulations 🍾🎊🎉

Guess the news is officially out! Extremely excited to announce that I will be starting my own laboratory at Institut Pasteur @pasteur.fr this coming spring!

Slight change to my office window view from Tokyo Tower🗼 to the Tour Eiffel. 🇫🇷

Evolutionary characterization of antiviral SAMD9/9L across kingdoms supports ancient convergence and lineage-specific adaptations - Nature Ecology & Evolution A search for analogues of the human SAMD9/9L antiviral genes identifies convergent evolution of this gene family in the bacterial and animal kingdoms, with species-specific and recent genomic signatur...

📖Latest from the lab:
Evo. characterization #antiviral #SAMD9/9L across #kingdoms🚶‍♀️🦍🦠🧫🖥️: ancient #convergence + #adaptations @natecoevo.nature.com

Led by amazing Alexandre Legrand +major contributions by Rémi Demeure & Amandine Chantharath @ciri-lyon.bsky.social 1/n

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

🚨New preprint out!
We present a foundational genomic resource of human gut microbiome viruses. It delivers high-quality, deeply curated data spanning taxonomy, predicted hosts, structures, and functions, providing a reference for gut virome research. (1/8)
www.biorxiv.org/content/10.1...

Changes to UniProt proteomes UniProt, the data resource for protein sequence and function information, is making major changes to its proteomes resource and to the UniProt Knowledgebase. UniProt has developed a new workflow that ...

UniProt is changing its reference proteomes resource.

Reference proteomes will remain in UniProtKB, while others will move to UniParc.

Read more about these changes:
www.ebi.ac.uk/about/news/u...

🧬 🖥️

Uniprot is a collaboration between EMBL-EBI, @sib.swiss & the Protein Information Resource.

🚀 Looking for talented PhD students!
Join us in 🇸🇬 Singapore for 1-2 years to push the frontiers of AI for Genomics.
Work on:
🧬 Cancer genome reconstruction
🧫 Cancer genome & cell foundation models
💊 RNA drug & mRNA therapeutic design

#AI #Genomics #PhD
1/5

Antiviral Defence is a Conserved Function of Diverse DNA Glycosylases Bacteria are frequently attacked by viruses, known as phages, and rely on diverse defence systems like restriction endonucleases and CRISPR-Cas to survive. While phages can evade these defences by cov...

Excited to share: DNA glycosylases are diverse antiviral effectors. They recognize phage base modifications and initiate genome destruction. A structure‑guided approach made the scope of this discovery possible! 🧪 #phagesky doi.org/10.1101/2025... #phage #microbiology

#APSPM2026 is open to anyone curious about combining protein structure and evolution. Learn where to start in our workshops and discover how structure meets phylogenetics.

Feb 15 - 18, 2026
Brisbane, Australia
Register here: biosig.lab.uq.edu.au/strphy26/reg...
(in-person only)

Cryo-EM maps and atomic models of the biotin-containing 3-methylcrotonyl-CoA carboxylase (MCC) complex and long-chain acyl-CoA carboxylase (LCC) complex

New lab preprint!
@zestytoast.bsky.social tagged a scarce mycobacterial protein in M. smegmatis with TwinStep but got… something? @kjamali.bsky.social's ModelAngelo built models & @martinsteinegger.bsky.social's FoldSeek IDed them as the biotin-containing MCC & LCC complexes
🧵
tinyurl.com/ukny4ptz

OpenFold3-preview (OF3p) is out: a sneak peek of our AF3-based structure prediction model. Our aim for OF3 is full AF3-parity for every modality. We now believe we have a clear path towards this goal and are releasing OF3p to enable building in the OF3 ecosystem. More👇

Predicting protein complexes in biosynthetic gene clusters Biosynthetic gene clusters (BGCs) are contiguous genomic regions that encode diverse, non-homologous proteins required for the production of specific natural products. Their genetic diversity underlie...

Our new preprint is out. Our group performed a comprehensive protein–protein complex prediction within 2,437 biosynthetic gene clusters. We predicted a total of 487,828 complexes for known BGCs, identifying 15,438 heteromeric interactions with an ipTM ≥ 0.6. (2/3)
www.biorxiv.org/content/10.1...

GitHub - aqlaboratory/openfold-3: OpenFold3: A fully open source biomolecular structure prediction model based on AlphaFold3 OpenFold3: A fully open source biomolecular structure prediction model based on AlphaFold3 - aqlaboratory/openfold-3

Looks like OpenFold3 has been formally released in a public "preview". Not quite on parity with AlphaFold3 on a few benchmarks shown, in particular for antibody interactions. All info on the github link. I am sure we will hear more about this from the developers github.com/aqlaboratory...

We can’t wait to welcome you to sunny Brisbane. Home to world-class research and a vibrant scientific community. Join us at the University of Queensland for #APSPM2026 to discuss how protein structure and evolution come together #StrPhy26

Oh :O I am sorry!

Chris Sanders is now in bsky. Welcome!

We train machine learning models on millions of proteins. But when it comes to making predictions, do we need them to understand all proteins at once? Often, we need an accurate model for the specific protein we are studying or designing. We address this with ProteinTTT arxiv.org/abs/2411.02109 1/🧵

Great work by @deboramarks.bsky.social @thomashopf.bsky.social Simon d'Oelsnitz, Chris Sander, Artem Gazizov,
@sunjaelee.bsky.social @milot.bsky.social, Sergio Garcia Busto, Jake Reardon

End-to-end protein design in the browser through evedesign. Generate and interactively explore designs in 2D/3D and export them as codon-optimized DNA. The underlying open source framework (released soon) is build to easily add new methods, more on that soon.
🌐 evedesign.bio

Our Metabuli taxonomic classifier is now available as an app compatible with Windows, Linux, and macOS. It features an interactive visualization developed by @sunjaelee.bsky.social, along with improvements to Metabuli by @jbeom.bsky.social.
📄 academic.oup.com/bioinformati...

Easy and interactive taxonomic profiling with Metabuli App.
It integrates database curation, read QC, taxonomic profiling, and visualization right on your desktop.
No command line, server, or internet required.
Now published in Bioinformatics! 🧵1/5
doi.org/10.1093/bioi...
github.com/steineggerla...

Easy and interactive taxonomic profiling with Metabuli App academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/steineggerla...

xcrun xctrace record -t "Time Profiler" --output 'profile.trace' --launch -- /path/to/program arg1 arg2
open -a Instruments profile.traceI

Great. Looking forward to hearing more about it!

Which mutations rewire function of regulatory DNA?

Excited to share SEAM: Systematic Explanation of Attribtuion-based Mechanisms. SEAM is an explainable AI method that dissects cis-regulatory mechanisms learned by seq2fun genomic deep learning models.

Led by @EESetiz

1/N 🧵👇

You can get MSAs directly from AlphaFold DB now (alphafold.ebi.ac.uk). I also missed the FoldSeek implementation, which lets you search for structurally similar proteins direktly.

This saves some clicking around. Neat!

AFDB v6 is already available in Foldseek!

🚀 search.foldseek.com

foldseek databases Alphafold/UniProt50 afdb50 tmp
foldseek easy-search query.cif afdb50 res.m8 tmp --cluster-search 0/1 (Reps only / all 241M)

Thanks @ebi.embl.org and DeepMind for working with us to make it available to everyone.

Looking very much forward to it!

#RECOMB2026 will be in Thessaloniki, Greece on May 26-29, 2026. Satellites on May 24-25. Save the date!

Το συνέδριο #RECOMB2026 θα πραγματοποιηθεί στη Θεσσαλονίκη, στις 26-29 Μαΐου 2026. Οι δορυφορικές εκδηλώσεις θα διεξαχθούν στις 24-25 Μαΐου 2026. Σημειώστε την ημερομηνία!