martinsteinegger.bsky.social - Profile | ThreadSky | a Reddit-style client for Bluesky

Structural biology is in an era of dynamics & assemblies but turning raw experimental data into atomic models at scale remains challenging. @minhuanli.bsky.social and I present ROCKET🚀: an AlphaFold augmentation that integrates crystallographic and cryoEM/ET data with room for more! 1/14.

submitted 6 days ago • 6 comments

In our latest review, we explore 12 deep-learning tools for metagenomic analysis, covering their strengths, limitations, and key applications. We hope it serves as both a resource and inspiration for new ways to analyze metagenomic data. Great work by Eli Levy Karin! 📄 doi.org/10.1093/nsr/...

submitted 9 days ago • 2 comments

Today we have published BioEmu-Benchmarks (MIT license): a code to evaluate the multi-conformation sampling benchmarks, MD free energy landscape benchmarks, and folding free energy benchmarks shown in the BioEmu-1 paper with BioEmu or your own model. Some details below 🧵 github.com/microsoft/bi...

submitted 9 days ago • 4 comments

I worked in Max-Planck Institute for seven years and loved every day of it. For anyone getting affected by the current changes, I can strongly recommend @maxplanck.de

submitted 15 days ago • 0 comments

The deadline for Poster Submissions is TODAY! Submit your abstract now: recomb.org/recomb2025/call_for_posters.html #RECOMB2025

submitted 17 days ago • 0 comments

Happy New Year! 🎉 If your 2025 resolution is to finally get your lab life together (read: #NewPIs), you’re not alone. A few people have requested I share how we use automation to survive: 1️⃣ Recruitment & Scheduling 👩‍🔬 2️⃣ Finance & Ordering 💸 3️⃣ Alerts & Emergencies 🚨 So here goes!—A 🧵... 1/n...

submitted 60 days ago • 5 comments

🚨BEWARE OF SCAMS🚨 The RECOMB 2025 team will NEVER: ❌ Ask for sensitive information (passport number, social security number, credit card information..) ❌ Ask for your signature in an email ❌ Request payment in an email If you receive a suspicious email, contact us at [email protected].

submitted 18 days ago • 0 comments

ProtT5, an encoder-decoder PLM, is much more sensitive to differences between PLA2G2 sequences than ESM C, an encoder-only PLM. Any guesses why? www.biorxiv.org/content/10.1...

submitted 19 days ago • 2 comments

Join us at SNU and gain access to leading-edge hardware: m.youtube.com/watch?v=ztth...

submitted 20 days ago • 4 comments

Excited to share a new preprint! We developed a new algorithm for POA, POASTA (pronounce it with your best Bo-ah-ston accent). It is based on the A* framework and inspired by other recent alignment algorithms such as the WFA and Astarix. www.biorxiv.org/content/10.1...

submitted 278 days ago • 1 comment

Excited to share our latest preprint evaluating AlphaFold3, Boltz-1, Chai-1 and Protenix for predicting protein-ligand interactions, featuring our newly introduced benchmark dataset 🌹Runs N’ Poses🌹! www.biorxiv.org/content/10.1... 🧵👇 (1/n)

submitted 23 days ago • 4 comments

Foldseek-Multimer is a strategy for complex-to-complex protein structure alignment to quickly perform large-scale structural comparisons between complexes. @martinsteinegger.bsky.social www.nature.com/articles/s41...

submitted 23 days ago • 0 comments

Rapid and sensitive protein complex alignment with Foldseek-Multimer | Nature Methods https://www.nature.com/articles/s41592-025-02593-7

submitted 24 days ago • 0 comments

Foldseek-Multimer—now published in @naturemethods.bsky.social—our fast multimer search tool, enables complex comparisons against the full PDB in seconds. It comes with BFMD, a collection of 300K+ predictions gathered from community projects. 📄 nature.com/articles/s41... 🌐 search.foldseek.com

submitted 25 days ago • 0 comments

🚨Registration open🚨 1st - 6th of June, me, Katie Jenike, @rayanchikhi.bsky.social and Gene Myers will run a week long workshop on k-mers for biodiversity genomics organised by @connectingscience.bsky.social at @sangerinstitute.bsky.social. Join us & get equipped to wrestle large genomic datasets!

submitted 30 days ago • 1 comment

Our paper out @Nature: CARD domains mediate anti-phage defense in bacterial gasdermin systems CARDs are essential for caspase recruitment during human inflammasome activation. We now find them in bacterial immune systems Congrats Tana Wein! Thank you Kranzusch lab! www.nature.com/articles/s41...

submitted 32 days ago • 4 comments

Try out our integration of the amazing protein structure search tool #Foldseek on #SubtiWiki (subtiwiki.uni-goettingen.de/foldseek)! Just upload a structure or use PDB/AlphaFoldDB entries to find similar structures. #IMPRS-GS #UniGoettingen #alphafold #bacillus #subtilis

submitted 34 days ago • 3 comments

join us!

submitted 35 days ago • 0 comments

Just coincidentally found GenBank Release 84.0 from 1994 in the neighboring lab. Anyone out there with an even older version?

submitted 36 days ago • 6 comments

🚨 UPCOMING DEADLINES 🚨 ⭐️Highlights: January 27, 2025 📋Posters: January 27, 2025 RECOMB-Seq: January 31 (abstracts) RECOMB-Microbiome: January 31 RECOMB-P&E: February 5 RECOMB-CG: February 7 RECOMB-CCB: February 7 (abstracts) RECOMB-Genetics: February 14 #RECOMB2025 #deadlines

submitted 38 days ago • 0 comments

🚨 Keynotes at RECOMB-seq 2025! 🚨 🌟 Alicia Oshlack – computational transcriptomics @aliciao.bsky.social 🌟 Rayan Chikhi – sequencing data structures @rayanchikhi.bsky.social 🗓️ Dates: April 24–25, 2025 📍 Seoul, South Korea recomb-seq.github.io/speakers/

submitted 38 days ago • 0 comments

Great opinion piece in the Guardian by Youngmi Kim: South Korean democracy was nearly toppled by its president. It was saved by its people. www.theguardian.com/commentisfre...

submitted 40 days ago • 1 comment

www.nature.com/articles/d41...

submitted 41 days ago • 0 comments

Foldseek 10 with 4-27x (1-8 GPUs) faster search through MMseqs2-GPU. Faster ProstT5 protein search w/o structure prediction through multi-GPU/Apple Metal, new BFVD/BFMD databases and multimer clustering (preview). 💾 github.com/steineggerla... 📄 www.biorxiv.org/content/10.1... 🐍 available in bioconda

submitted 41 days ago • 1 comment

✈️ Travel fellowships applications are open! ✈️ Application deadline ➡️ January 20 If you have an accepted or conditionally accepted paper, go to --> recomb.org/recomb2025/t... and fill out the Google form to apply 📝

submitted 43 days ago • 0 comments

The Foldseek webserver for fast protein structure searches now features a Sankey tree taxonomy visualization and filter, allowing to subset hits by clades. Developed by my talented student @sunjaelee.bsky.social. Try it out! 🌐 search.foldseek.com

submitted 44 days ago • 4 comments

📣 Call for papers in Satellite Workshops are open 📣 @recombseq.bsky.social: recomb-seq.github.io CG: recomb-cg.org Genetics: recomb.org/recomb2025/r... CCB: recomb.org/recomb-ccb20... Microbiome: recomb.org/recomb2025/r... P&E: recomb-privacy-equity.github.io #RECOMB2025 #callforpapers

submitted 45 days ago • 0 comments

📌 Registrations for #RECOMB2025 are now open! 📌 Visit recomb2025.com for details. The early registration deadline is March 15, 2025.

submitted 47 days ago • 1 comment

Finally got around to reading the FoldMason paper for structural phylogenetics. Fantastic work www.biorxiv.org/content/10.1...

submitted 49 days ago • 0 comments

Awesome paper! BioEmu from MSR: Scalable emulation of protein equilibrium ensembles with generative deep learning www.biorxiv.org/content/10.1... Looking forward to hearing more explanainers in tomorrow's reading group session on zoom at 9am PT / 12pm ET / 6pm CET: portal.valencelabs.com/logg

submitted 49 days ago • 1 comment

Super excited for my lab's first paper at @recombconf.bsky.social. See you all in South Korea!

submitted 75 days ago • 0 comments

✈️ Travel fellowships applications are now open! ✈️ If you have an accepted or conditionally accepted paper, go to --> recomb.org/recomb2025/t... and fill out the Google form to apply 📝

submitted 53 days ago • 0 comments

SNU Profs Woon Ju Song & Martin Steinegger (Biology) developed the AI-based SeekRank algorithm to discover enzymes for cancer immunotherapy. doi.org/10.1093/nar/...

submitted 54 days ago • 0 comments

FastOMA is out now in Nature Methods 🎉: nature.com/articles/s41592-024-02552-8 A new orthology inference algorithm that scales linearly and is highly accurate. FastOMA can process all >2000 eukaryotic UniProt ref proteomes <24 hours 🚀. Try it out github.com/DessimozLab/fastoma @dessimoz.bsky.social

submitted 58 days ago • 1 comment

More than 1'800 tomograms available for the community. Towards visual proteomics using our favorite organism Chlamy! Check out the preprint: www.biorxiv.org/content/10.1... Find it on EMPIAR (11830) and fully annotated on the CZI data portal: cryoetdataportal.czscience.com #TeamTomo

submitted 63 days ago • 3 comments

CAZyme3D: a database of 3D structures for carbohydrate-active enzymes https://www.biorxiv.org/content/10.1101/2024.12.27.630555v1

submitted 65 days ago • 1 comment

Unicore enables scalable and accurate phylogenetic reconstruction with structural core genes https://www.biorxiv.org/content/10.1101/2024.12.22.629535v1 🧬🖥️🧪 https://github.com/steineggerlab/unicore

submitted 68 days ago • 2 comments

Here's a year-end update from #PLINDER. It's been really great working on this project and all the other projects that it has kickstarted - the gift that keeps on giving. Happy holidays everyone! www.plinder.sh/blog/updates

submitted 68 days ago • 0 comments