Martin Steinegger 🇺🇦
@martinsteinegger.bsky.social
Developing data intensive computational methods • PI @ Seoul National University 🇰🇷 • #FirstGen • he/him • Hauptschüler
Pinned
Folddisco finds similar (dis)continuous 3D motifs in large protein structure databases. Its efficient index enables fast uncharacterized active site annotation, protein conformational state analysis and PPI interface comparison. 1/9🧶🧬
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
📄 www.biorxiv.org/content/10.1...
🌐 search.foldseek.com/folddisco
Reposted by Martin Steinegger 🇺🇦
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. 🇫🇷
Slight change to my office window view from Tokyo Tower🗼 to the Tour Eiffel. 🇫🇷
November 15, 2025 at 6:42 AM
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. 🇫🇷
Slight change to my office window view from Tokyo Tower🗼 to the Tour Eiffel. 🇫🇷
Reposted by Martin Steinegger 🇺🇦
📖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...
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...
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...
www.nature.com
November 12, 2025 at 5:55 PM
📖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...
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...
Reposted by Martin Steinegger 🇺🇦
🚨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...
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...
November 6, 2025 at 5:26 PM
🚨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...
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...
Reposted by Martin Steinegger 🇺🇦
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.
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.
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 ...
www.ebi.ac.uk
November 4, 2025 at 9:58 AM
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.
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.
Reposted by Martin Steinegger 🇺🇦
Reposted by Martin Steinegger 🇺🇦
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
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...
doi.org
October 30, 2025 at 12:16 PM
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
Reposted by Martin Steinegger 🇺🇦
#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)
Feb 15 - 18, 2026
Brisbane, Australia
Register here: biosig.lab.uq.edu.au/strphy26/reg...
(in-person only)
October 30, 2025 at 12:55 AM
#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)
Feb 15 - 18, 2026
Brisbane, Australia
Register here: biosig.lab.uq.edu.au/strphy26/reg...
(in-person only)
Reposted by Martin Steinegger 🇺🇦
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
@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
October 30, 2025 at 3:21 AM
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
@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
Reposted by Martin Steinegger 🇺🇦
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👇
October 28, 2025 at 6:30 PM
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👇
Reposted by Martin Steinegger 🇺🇦
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
October 28, 2025 at 5:58 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Martin Steinegger 🇺🇦
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...
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
github.com
October 28, 2025 at 9:30 AM
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...
Reposted by Martin Steinegger 🇺🇦
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
October 27, 2025 at 5:02 AM
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
Chris Sanders is now in bsky. Welcome!
Great scientific public service with participation of the EVfold team. @sandercbio (Chris Sander) now active on bluesky.
October 24, 2025 at 3:14 AM
Chris Sanders is now in bsky. Welcome!
Reposted by Martin Steinegger 🇺🇦
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/🧵
October 23, 2025 at 1:08 PM
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/🧵
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
🌐 evedesign.bio
October 22, 2025 at 2:30 PM
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
🌐 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...
📄 academic.oup.com/bioinformati...
October 16, 2025 at 1:01 PM
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...
📄 academic.oup.com/bioinformati...
Reposted by Martin Steinegger 🇺🇦
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...
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...
October 16, 2025 at 7:29 AM
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...
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...
Reposted by Martin Steinegger 🇺🇦
Easy and interactive taxonomic profiling with Metabuli App academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/steineggerla...
October 14, 2025 at 5:55 PM
Easy and interactive taxonomic profiling with Metabuli App academic.oup.com/bioinformati... 🧬🖥️🧪 github.com/steineggerla...
Reposted by Martin Steinegger 🇺🇦
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 🧵👇
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 🧵👇
October 9, 2025 at 12:03 PM
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 🧵👇
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 🧵👇
Reposted by Martin Steinegger 🇺🇦
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!
This saves some clicking around. Neat!
October 7, 2025 at 2:54 PM
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!
This saves some clicking around. Neat!
Reposted by Martin Steinegger 🇺🇦
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.
🚀 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.
We’re renewing our collaboration with Google DeepMind!
We'll keep developing the AlphaFold Database to support protein science worldwide 🎉
To mark the moment we’ve synchronised the database with UniProtKB release 2025_03.
www.ebi.ac.uk/about/news/t...
🖥️🧬 #AlphaFold
@pdbeurope.bsky.social
We'll keep developing the AlphaFold Database to support protein science worldwide 🎉
To mark the moment we’ve synchronised the database with UniProtKB release 2025_03.
www.ebi.ac.uk/about/news/t...
🖥️🧬 #AlphaFold
@pdbeurope.bsky.social
October 7, 2025 at 2:33 PM
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.
🚀 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.
Reposted by Martin Steinegger 🇺🇦
#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!
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!
September 26, 2025 at 3:03 PM
#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!
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!
Reposted by Martin Steinegger 🇺🇦
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
www.biorxiv.org/content/10.1...
(1/n)
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
📄 www.nature.com/articles/s41...
💿 mmseqs.com
GPU-accelerated homology search with MMseqs2 - Nature Methods
Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...
www.nature.com
September 21, 2025 at 8:06 AM
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
📄 www.nature.com/articles/s41...
💿 mmseqs.com
Reposted by Martin Steinegger 🇺🇦
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...
www.nature.com/articles/s41...
GPU-accelerated homology search with MMseqs2 - Nature Methods
Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...
www.nature.com
September 18, 2025 at 8:09 PM
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...
www.nature.com/articles/s41...