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 🇺🇦
Amazing summary of our recent ProteinTTT paper youtube.com/shorts/XWueh...
【論文簡単解説】One protein is all you need簡単解説💨 #shorts #vtuber準備中 #澪乃ゆい
YouTube video by Miono Yui ch. | 澪乃ゆい
youtube.com
January 3, 2026 at 1:25 PM
Amazing summary of our recent ProteinTTT paper youtube.com/shorts/XWueh...
Reposted by Martin Steinegger 🇺🇦
Looking to start your lab in generative biology / AI?
Come join us at the @sangerinstitute.bsky.social
Sanger is core-funded so you can generate data at scale to train the next generation of models and understanding. Design/Engineering/Chemistry/Proteins/Pathways!
pls RT
tinyurl.com/GenGenFaculty
Come join us at the @sangerinstitute.bsky.social
Sanger is core-funded so you can generate data at scale to train the next generation of models and understanding. Design/Engineering/Chemistry/Proteins/Pathways!
pls RT
tinyurl.com/GenGenFaculty
Group Leader - Generative Biology and AI
Do you want to help us improve human health and understand life on Earth? Make your mark by shaping the future to enable or deliver life-changing science to solve some of humanity’s greatest challenge...
tinyurl.com
January 1, 2026 at 12:08 PM
Looking to start your lab in generative biology / AI?
Come join us at the @sangerinstitute.bsky.social
Sanger is core-funded so you can generate data at scale to train the next generation of models and understanding. Design/Engineering/Chemistry/Proteins/Pathways!
pls RT
tinyurl.com/GenGenFaculty
Come join us at the @sangerinstitute.bsky.social
Sanger is core-funded so you can generate data at scale to train the next generation of models and understanding. Design/Engineering/Chemistry/Proteins/Pathways!
pls RT
tinyurl.com/GenGenFaculty
Got three emails on Dec 24th, 25th, and Saturday the 27th asking me to review a manuscript… only to be removed as reviewer today. When I complained, the response was: “Our offices are closed December 24-January 1.”
Thank you @plos.org Computational Biology.
Thank you @plos.org Computational Biology.
December 30, 2025 at 2:02 PM
Got three emails on Dec 24th, 25th, and Saturday the 27th asking me to review a manuscript… only to be removed as reviewer today. When I complained, the response was: “Our offices are closed December 24-January 1.”
Thank you @plos.org Computational Biology.
Thank you @plos.org Computational Biology.
Reposted by Martin Steinegger 🇺🇦
"..based on a common wavefront design that can be adapted to support a variety of dynamic programming algorithms: local, global, and semi-global alignment of genomic and protein sequences with a variety of commonly used scoring schemes" from
@martinsteinegger.bsky.social andco
@martinsteinegger.bsky.social andco
Accelign: a GPU-based Library for Accelerating Pairwise Sequence Alignment https://www.biorxiv.org/content/10.64898/2025.12.17.694868v1
December 20, 2025 at 11:05 AM
"..based on a common wavefront design that can be adapted to support a variety of dynamic programming algorithms: local, global, and semi-global alignment of genomic and protein sequences with a variety of commonly used scoring schemes" from
@martinsteinegger.bsky.social andco
@martinsteinegger.bsky.social andco
Reposted by Martin Steinegger 🇺🇦
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🧵👇
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🧵👇
December 16, 2025 at 3:15 PM
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🧵👇
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🧵👇
Reposted by Martin Steinegger 🇺🇦
💾 Prokka 1.15.6 is released!
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
Release Heading into the sunset · tseemann/prokka
The future
This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwen...
github.com
December 15, 2025 at 9:09 PM
💾 Prokka 1.15.6 is released!
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics
github.com/tseemann/pro...
Reposted by Martin Steinegger 🇺🇦
Congratulations, Julia Mahamid!
Julia Mahamid receives the @dfg.de Leibniz Prize for her work on structural cell biology!
#LeibnizPreis
Julia Mahamid receives the @dfg.de Leibniz Prize for her work on structural cell biology!
#LeibnizPreis
Und hier sind sie – die 10 Preisträger*innen des Gottfried Wilhelm #LeibnizPreis' 2026 – ausgezeichnet für ihre exzellenten Forschungsarbeiten und Errungenschaften in der Wissenschaft! 🏆👏
Die Verleihung der Preise feiern wir am 18. März in Berlin.
Einzelheiten & Kurzprofile: sohub.io/1uv1
Die Verleihung der Preise feiern wir am 18. März in Berlin.
Einzelheiten & Kurzprofile: sohub.io/1uv1
December 11, 2025 at 10:12 AM
Congratulations, Julia Mahamid!
Julia Mahamid receives the @dfg.de Leibniz Prize for her work on structural cell biology!
#LeibnizPreis
Julia Mahamid receives the @dfg.de Leibniz Prize for her work on structural cell biology!
#LeibnizPreis
Reposted by Martin Steinegger 🇺🇦
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
Fresh from bioRxiv our latest work introducing The Embedded Alphabet (TEA), a powerful new representation for protein sequences obtained by discretising ESM2 embeddings into 20 characters.
Pre-print: www.biorxiv.org/content/10.1...
🧵👇(1/n)
Pre-print: www.biorxiv.org/content/10.1...
🧵👇(1/n)
Rewriting protein alphabets with language models
Detecting remote homology with speed and sensitivity is crucial for tasks like function annotation and structure prediction. We introduce a novel approach using contrastive learning to convert protein...
www.biorxiv.org
December 1, 2025 at 10:58 AM
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
Reposted by Martin Steinegger 🇺🇦
Fresh from bioRxiv our latest work introducing The Embedded Alphabet (TEA), a powerful new representation for protein sequences obtained by discretising ESM2 embeddings into 20 characters.
Pre-print: www.biorxiv.org/content/10.1...
🧵👇(1/n)
Pre-print: www.biorxiv.org/content/10.1...
🧵👇(1/n)
Rewriting protein alphabets with language models
Detecting remote homology with speed and sensitivity is crucial for tasks like function annotation and structure prediction. We introduce a novel approach using contrastive learning to convert protein...
www.biorxiv.org
December 1, 2025 at 10:28 AM
Fresh from bioRxiv our latest work introducing The Embedded Alphabet (TEA), a powerful new representation for protein sequences obtained by discretising ESM2 embeddings into 20 characters.
Pre-print: www.biorxiv.org/content/10.1...
🧵👇(1/n)
Pre-print: www.biorxiv.org/content/10.1...
🧵👇(1/n)
Reposted by Martin Steinegger 🇺🇦
Reliable Identification of Homodimers Using AlphaFold https://www.biorxiv.org/content/10.1101/2025.11.27.691011v1
November 28, 2025 at 2:46 AM
Reliable Identification of Homodimers Using AlphaFold https://www.biorxiv.org/content/10.1101/2025.11.27.691011v1
Reposted by Martin Steinegger 🇺🇦
mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing https://www.biorxiv.org/content/10.1101/2025.11.24.690271v1
November 27, 2025 at 5:46 PM
mim: A lightweight auxiliary index to enable fast, parallel, gzipped FASTQ parsing https://www.biorxiv.org/content/10.1101/2025.11.24.690271v1
Reposted by Martin Steinegger 🇺🇦
LoL-align: sensitive and fast probabilistic protein structure alignment https://www.biorxiv.org/content/10.1101/2025.11.24.690091v1
November 26, 2025 at 2:46 AM
LoL-align: sensitive and fast probabilistic protein structure alignment https://www.biorxiv.org/content/10.1101/2025.11.24.690091v1
Reposted by Martin Steinegger 🇺🇦
From Sameer Velankar & colleagues in @narjournal.bsky.social #NARDatabaseIssue | #AlphaFold #Protein #Structure #Database 2025: a redesigned interface and updated structural coverage | #Bioinformatics #Proteomics #OpenScience #AFDB 🧪🔓 CC/ @ebi.embl.org
⬇️
academic.oup.com/nar/advance-...
⬇️
academic.oup.com/nar/advance-...
AlphaFold Protein Structure Database 2025: a redesigned interface and updated structural coverage
Abstract. The AlphaFold Protein Structure Database (AFDB; https://alphafold.ebi.ac.uk), developed by EMBL–EBI and Google DeepMind, provides open access to
academic.oup.com
November 24, 2025 at 12:56 AM
From Sameer Velankar & colleagues in @narjournal.bsky.social #NARDatabaseIssue | #AlphaFold #Protein #Structure #Database 2025: a redesigned interface and updated structural coverage | #Bioinformatics #Proteomics #OpenScience #AFDB 🧪🔓 CC/ @ebi.embl.org
⬇️
academic.oup.com/nar/advance-...
⬇️
academic.oup.com/nar/advance-...
I knew early on I wanted to work with computers, but because of dyslexia I ended up in a lower-tier German school. The career office said a tech job wasn’t realistic. I ignored that, took a convoluted path into university, discovered bioinformatics, got hooked on algorithms&proteins, and became a PI
November 24, 2025 at 2:42 AM
I knew early on I wanted to work with computers, but because of dyslexia I ended up in a lower-tier German school. The career office said a tech job wasn’t realistic. I ignored that, took a convoluted path into university, discovered bioinformatics, got hooked on algorithms&proteins, and became a PI
Reposted by Martin Steinegger 🇺🇦
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
November 19, 2025 at 9:16 PM
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
Reposted by Martin Steinegger 🇺🇦
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)
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
November 19, 2025 at 8:15 AM
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)
py2dmol.solab.org
Integration with AlphaFoldDB (will auto fetch results). Drag and drop results from AF3-server or ColabFold for interactive experience! (1/4)
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👇