Happy to share Piecing Together the History of Protein Folds From a Fragmented Evolutionary Record 🧪 It appears as part of a Special Section in @genomebiolevol.bsky.social organized by @cpuentelelievre.bsky.social @proteinmechanic.bsky.social and J. Douglas doi.org/10.1093/gbe/...

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This is a very cool ancestral reconstruction study by @krishnareddy.bsky.social et al. that I recommend reading! @rachellegaudet.bsky.social and I thought it was so interesting that we wrote a News & Views about it, check it out: rdcu.be/eCfyl

If you're an undergrad and want to intern with me, this is where you need to apply!

Structural bioinformatics is incredibly powerful on its own or when paired with theory or experiment. One of the PDB's superpowers isn’t from one structure, but comparing many to uncover folds, binding sites, and subtle conformational shifts. chemrxiv.org/engage/chemr...

This is a breakthrough for protein science🔥AFAIK this is the largest protein DB, with >100B seqs (3B clustered at 50%). New biology will come from LOGAN: new folds, topologies, etc. You can also improve your AlphaFold models by building better MSAs. Future AI models will also use LOGAN for training

🌎👩‍🔬 For 15+ years biology has accumulated petabytes (million gigabytes) of🧬DNA sequencing data🧬 from the far reaches of our planet.🦠🍄🌵 Logan now democratizes efficient access to the world’s most comprehensive genetics dataset. Free and open. doi.org/10.1101/2024...

1/13 🧵 Today, Bindcraft was published in @nature.com , one of the most famous AIs in biology for designing protein–protein interactions (PPI). In my opinion. Bindcraft represents one of the most important advances in the post–AlphaFold2 era.

Does anyone know of a recent comparison of the main structural classification schemes of proteins and guidance on when to choose one? Something like this but including ECOD and perhaps seq-based schemes like Pfam, SUPERFAMILY and CDD. Img source (2020) pubmed.ncbi.nlm.nih.gov/32302382/

In a new GBE Review, @cpuentelelievre.bsky.social @proteinmechanic.bsky.social & J. Douglas give an overview on protein structural phylogenetics, how to obtain evolutionary insights from structural data, and key applications and future directions. 🔗 doi.org/10.1093/gbe/evaf139 #genome #evolution

Hi @milot.bsky.social @martinsteinegger.bsky.social :) It appears that there is a problem with the FoldManson webserver. It does not allow load structures using accessions from PDB/UniProt/BFVD. e.g., when I tried with pdbID 1zg4, the error said "1 not found." The same occurs with any other acc.

Folddisco webserver result view update: - Added description texts for AFDB - Integrated TaxoView taxonomy visualization & filter by @sunjaelee.bsky.social - Inter-residue distance clustering by DBSCAN to explore motif diversity. 🌐 search.foldseek.com/folddisco 📄 www.biorxiv.org/content/10.1...

🦠🧍‍♀️From bacterial to human immunity. We report in @science.org the discovery of a human homolog of SIR2 antiphage proteins that participates in the TLR pathway of animal innate immunity. Co-led wt @enzopoirier.bsky.social by D. Bonhomme and @hugovaysset.bsky.social www.science.org/doi/10.1126/...

📣 New paper alert! One of the most exciting projects we've done in recent years is now out on BioRxiv: "An Asgard archaeon from a modern analog of ancient microbial mats". Glimpse into early complex life! ❄️🦠 🔬🧬 www.biorxiv.org/content/10.1.... A thread...

New pre-print from my group - project led by PhD student Michael Hoffert. We set out on a daunting mission to generate a 'periodic table' of bacterial diversity (1/6) www.biorxiv.org/content/10.1...

AlphaFold is great, but contrary to public opinion it has not completely solved the protein folding problem. Much work remains to be done. clauswilke.substack.com/p/no-alphafo...

As the community gets ready for #ACA2025, we're proud to present this interview with @gabbygrowsxtals.bsky.social Vivian Stojanoff and @xtalmaker.bsky.social on how to prepare for successful protein crystallisation experiments! 🥳🥳 youtu.be/m34RI500OFU?...

This paper is absolutely bananas and a tour de force of structural bioinformatics. Some random tidbits:

The "reproducibility crisis" in science constantly makes headlines. Repro efforts are often limited. What if you could assess reproducibility of an entire field? That's what @brunolemaitre.bsky.social et al. have done. Fly immunity is highly replicable & offers lessons for #metascience A 🧵 1/n

A paper thar took too long to finish. We show that AlphaFold3 its clearly better than AlphaFold2 (and Boltz-1 and Chai-1) to predict the structure of antibody-Antigens, but only for cases with (har to detect) similarity in the training set. www.biorxiv.org/content/10.1...

1. Kevin Gross and I just posted a new science-of-science preprint. This one explores the looming peer review crisis. As many of you know, it's becoming significantly more difficult for journal editors to find scholars willing to serve as peer reviewers for submitted manuscripts.

The Baker lab @uwproteindesign.bsky.social apparently had a lot of fun 😂 some examples of sequences used in the paper www.science.org/doi/10.1126/... DAVIDLIKESPEPTIDE DAVIDITISTIME DANIELSILVA HIALIENFRIEND

Out in @natbiotech.nature.com: Metagenome taxonomy profilers usually ignore unknown species. SingleM is an accurate profiler which doesn't, even detecting phyla with no MAGs. Profiles of 700,000 metagenomes at sandpiper.qut.edu.au. A 🧵

In our newest preprint, we discuss current explainable AI (XAI) methods. We divided the workflow of a generative decoder-only model into four information contexts for XAI: training dataset, input query, model components, and output sequence. See here: arxiv.org/abs/2506.19532 @aichemist.bsky.social

🧵 1/9 I want to share some (inconclusive) thoughts about the generalization capabilities of protein language models under this main question: ¿what does it mean IN distribution generalization and what does it mean OUT of distribution generalization in (protein) biology?

Example of the kind of extended water networks we see in high res cryo-EM maps - no denying these waters!

The team's first preprint is out! Led by ‪ ‪@vishnuprasoodanan.bsky.social‬‬ & @omaistrenko.bsky.social , we asked a question (almost) as old as microbiology: how many prokaryotic species exist on Earth? More specifically, how much diversity is "hiding" in existing metagenomic data? A 🧵.

We have written up a tutorial on how to run BindCraft, how to prepare your input PDB, how to select hotspots, and various other tips and tricks to get the most out of binder design! github.com/martinpacesa...

Excited to share our latest review on histone-mediated chromatin organization in prokaryotes and viruses! 🧬 @mpi-bio-fml.bsky.social

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

🦠 NEW VIDEO 🦠 The molecular biology of how Mycobacterium Tuberculosis evades the immune system so well. Starting with this simulation of a full outer envelope of m.TB--let's explore how the deadliest & most persistent human pathogen completely hacks our immune response. #molecularbiology

Karolinska is looking for 20 (!!) assistant professors and offering 6 year appointments with ~1M USD startup packages. ki.se/en/about-ki/...

Hope this is useful - consensus statement "Guidelines for preventing and reporting contamination in low-biomass microbiome studies" rdcu.be/er3Io

Excited to share our new paper in @cellreports.bsky.social that reshapes our understanding of chromosome organization's deep evolutionary roots! Our work dives into the origins of the machinery that structures our very genomes. 🔗: doi.org/10.1016/j.ce... #Genomics #Evolution #CellBiology #LECA

A short preprint describing the GlobDB is now on arXiv: arxiv.org/abs/2506.11896 If you find the resource useful, please also check globdb.org for info on how to cite the underlying resources and tools.

1/x New story - the structure of the Vault cap, at 2.3Å! Matching a beautiful preprint from @sjorsscheres.bsky.social, we show that the cap of the vault particle has C13 symmetry, in contrast to the 39-fold symmetry of the body. Study lead by talented postdoc @huanli00.bsky.social from my group! ⬇️

Here's a tutorial I wrote on how I design detection and cloning primers using Primer3. Hopefully it's helpful for students. 💚 binomicalabs.notion.site/PCR-Primer-D...

Out this weekend in @ismepublications.bsky.social We looked at 10,000 species to map the diversity and history of the bacterial #flagellar motor across the tree of life. Lots of (re)analysis , especially from Jamiema Sara Philip @unswbabs.bsky.social academic.oup.com/ismej/advanc...

@xrefugee13.bsky.social @ace-gtdb.bsky.social Could it be possible that in future versions of the GTDB, the representative proteins include info in the headers about the genome to which they belong? Or clustered ver. at n% SeqIdent? This would be very useful. Thanks a lot four your work :)

🚧Open PhD position!🚧 Do you think protein machines are super cool 🤖? Would you like to design them using Nobel prize-winning methods? ➡️ Apply and choose topic 12. www.ki.si/en/news/tend... Position is fully funded for four years. One week left to apply.

How it started... How it's going

New paper from the lab from Sriram Garg in my group. We introduce a general substitution matrix for structural phylogenetics. I think this is a big deal, so read on below if you think deep history is important. academic.oup.com/mbe/advance-...

Unicore is now published on GBE 🚀 Unicore rapidly identifies structural single-copy core genes from input species proteomes for phylogenetic analysis. Powered by Foldseek and ProstT5, Unicore enables linear-scale structure-based phylogeny of any given set of taxa. 🧵1/n 📃 doi.org/10.1093/gbe/evaf109

Just in time for Pride month! Celebrating our recent publication in @actacrystf.iucr.org by highlighting our rainbow of protein crystals! 🏳️‍🌈💎 Great to work with @gabbygrowsxtals.bsky.social & Vivian Stojanof on this paper! doi.org/10.1107/S205... #crystallization #crystals #structuralbiology

🚀 Excited to release BoltzDesign1! ✨ Now with LogMD-based trajectory visualization. 🔗 Demo: rcsb.ai/ff9c2b1ee8 Feedback & collabs welcome! 🙌 🔗: GitHub: github.com/yehlincho/Bo... 🔗: Colab: colab.research.google.com/github/yehli... @sokrypton.org @martinpacesa.bsky.social

Building virtual cells is a great goal in the age of AI, but it requires far more than training transformers with scRNAseq. *Scaling* as the primary strategy with hopes of emergent properties is lazy. Will the plan to fuse representations across mediocre (unimodal) foundation models work?!

Excited to unveil Boltz-2, our new model capable not only of predicting structures but also binding affinities! Boltz-2 is the first AI model to approach the performance of FEP simulations while being more than 1000x faster! All open-sourced under MIT license! A thread… 🤗🚀

Does anyone know of a page where I can explore protein families/clans in Pfam in an interactive way? InterPro does a great job, but their interactive interface is not easy to navigate when the clan is large (e.g. TIM barrels). www.ebi.ac.uk/interpro/set...

Its 2025 and two atoms STILL can exist in the same space according to AF3

Come work with me an Sarah and become a part of DDLS danaher.wd1.myworkdayjobs.com/CytivaJobsPP...