Another exciting opportunity, this time as a colleague at Duke! Join as tenure track assistant prof. in Cell Bio & let’s work on closing the gap between in-silico and in-vivo: www.nature.com/naturecareer... Important: application closes Nov 1st!!!

Another opening: Senior Multiscale Biology Applied Research Scientist! nvidia.eightfold.ai/careers/job/... Are fascinated by fundamental data modalities across biology like RNA-seq, mass spec & want to build computational tools that harnessing data to build intelligence? Come: join the team!

Are you passionate about leading collaborative, fast moving, applied bioinformatics research projects that help the entire community move forward? Apply to work in my team at NVIDIA: nvidia.eightfold.ai/careers/job/...

Great talk by @machine.learning.bio at the 5th Virtual @chembiotalks.bsky.social. He talked about the use of #MachineLearning and #BigData to address biological questions. Cool insights into both predicting functions and designing proteins ieeexplore.ieee.org/document/947... arxiv.org/abs/2503.00710

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...

Looking forward to hearing about the potential of machine learning for #Biology and #DrugDiscovery from an industry perspective. Register for the Virtual @chembiotalks.bsky.social to hear the perspective of Chris Dallago (@machine.learning.bio) from Nvidia. #ChemBio #Chemsky #ML #MachineLearning

(1/5) Venoms are a vast, largely untapped library of bioactive molecules—and our new paper in @natcomms.nature.com ‬ @natprot.nature.com reveals just how powerful they can be. 🐍⚡️

Excited to have participated in the 2025 Symposium on Generative AI in Molecule Discovery in beautiful Munich, along with amazing scientists and colleagues @machine.learning.bio, Francesca Grisoni, ‪@ewaszczurek.bsky.social‬‬, @fabiantheis.bsky.social and more... 🔬🤖 events.hifis.net/event/2015/

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

With contributions from fantastic colleagues @martinsteinegger.bsky.social , @mikeinouye.bsky.social, @jlistgarten.bsky.social , @ideasbyjin.bsky.social, @michael-heinzinger.bsky.social, and many more, the first CSHL volume on ML for Protein Science and Engineering is out: lnkd.in/dQdgGPpp

The final program is now online for the 5th Virtual @chembiotalks.bsky.social: web.cvent.com/event/60e9f3... Looking forward to talks by Sarah O'Connor, Chengqi Yi, @machine.learning.bio, @cathleenzeymer.bsky.social, @kellychibale.bsky.social, Jennifer Prescher and @craigmcrews.bsky.social.

@michael-heinzinger.bsky.social and I are seeking talented postdocs to support for the Marie Skłodowska-Curie Fellowship! Join our international AI+biology team, collaborate on protein design, and access top labs in the US & EU. Interested? Apply by July 15! Details: machine.learning.bio/news/msca

Save the date for the Helmholtz Munich AI for Health Symposium 2025, devoted to the topic of Generative AI in Molecule Discovery! July 4, 2025 Helmholtz Munich Campus in Neuherberg, Germany What now? Register and submit abstracts (deadline May 2, 2025!) events.hifis.net/event/2015/r...

📢📢 "Proteina: Scaling Flow-based Protein Structure Generative Models" #ICLR2025 (Oral Presentation) 🔥 Project page: research.nvidia.com/labs/genair/... 📜 Paper: arxiv.org/abs/2503.00710 🛠️ Code and weights: github.com/NVIDIA-Digit... 🧵Details in thread... (1/n)

🔸Proteina is a fantastic collaboration with wonderful colleagues at NVIDIA: 🔥 Tomas Geffner*, @kdidi.bsky.social*, Zuobai Zhang*, Danny Reidenbach, Zhonglin Cao, @jyim.bsky.social , Mario Geiger, @machine.learning.bio, Emine Kucukbenli, @arashv.bsky.social, @karstenkreis.bsky.social* 🔥 (10/n)

Big time

Two major life updates: - I'm moving to Senior Applied Research Scientist in Digital Biology at NVIDIA (Jan '25) - I'm starting a new lab at Duke as Visiting Assistant Prof (early '25) Both roles focus on tackling hard problems in biological machine learning through collaborative research. Long 🧵

After a busy CASP/CAPRI year we resume our rolling CAPRI rounds, announcing the 1st target of 2025. It consists of an antibody-glycan complex. The glycan is heptyl α-D-mannopyranoside. Registration for this target is now open. pdbe.org/capri

We've a postdoc opening for our lab at the Broad: Cambridge MA! Must have experience in toxicology + data science Work on the wonderful OASIS dataset we are producing... Cell Painting, transcriptomics, proteomics in various liver cell and tissue models! broad.io/mlcbpostdoc

CDC just confirmed the first severe case of #H5N1 in the US in a patient in Louisiana. This virus seems to be the same genotype D1.1 that is spreading in birds at the moment (so not the cattle genotype B3.13) that severely sickened the teenager in Canada.

Protein language models excel at generating functional yet remarkably diverse artificial sequences. They however fail to naturally sample rare datapoints, like very high activities. In our new preprint, we show that RL can solve this without the need for additional data: arxiv.org/abs/2412.12979

Starting the new BSC IA factory. Financed by Europe, Spanish & Catalan governments + contributions from Portugal, Turkey, Romania New HPC and AI resources at the service of companies (hospitals included) With Juan Cruz Sec Estado Núria Montserrat Consellera Mateo Valero Dir @bsc-cns.bsky.social

We trained a model to co-generate protein sequence and structure by working in the ESMFold latent space, which encodes both. PLAID only requires sequences for training but generates all-atom structures! Really proud of @amyxlu.bsky.social 's effort leading this project end-to-end!

AF3 BEST METHOD followed by cluspro but also some conversion errors

Assessors’ conclusions of the 3D category (individual protein chains) of #CASP16 🧪

I've seen cases where the AF2 model is correct and the experimental structure has artifacts (e.g. AF2 model has disulfide bonds for surface receptor and PDB does not bc it was in reducing conditions). I've seen AF2 capture conformational states not in PDB but later validated by cryoEM.

Major differences are also observed when using these models as training data. Hsu et al found that inverse folding methods trained on 10^4 to 10^5 experimental structures outperformed those trained on 10^7 alphafold models (table shows perplexities, lower is better). doi.org/10.1101/2022...

By now it’s clear that alphafold models don’t always work for e.g., small molecule docking. In one study, no difference was observed between success w/ docking into pockets of DL-generated models and those of homology models, despite major improvements in RMSD of the former. doi.org/10.7554/elif...

#CASP16 results are in! Template-based VFold seems to be lead method for nucleic acid structure prediction! AlphaFold2 and 3 still seem to be best methods for protein monomer and complex prediction.

#CASP16 program is posted (so you can guess the "winners". Congratulations to Yang and Kihara who seems to have done well in RNA+Proteins. Also congratulations to AF3-server (i.e. me) who was selected to talk (i.e. most people did worse than the server). predictioncenter.org/casp16/doc/C... .

Chai-1, the open source AF3 clone, is now available with an Apache 2 license github.com/chaidiscover...

Wow! 🤩 This may be the most carefully documented dataset on @polarishq.bsky.social. Great work by @roman-bushuiev.bsky.social! Do I have any #MassSpec researchers in my 🦋 network yet? I would love to hear what you think! github.com/polaris-hub/... #mass #spectrometry #dataset #benchmark

MMseqs2 Release 16 Highlights: GPU-accelerated search📄, ORF or new 6-frame translated search modes, contig taxonomy always keeps the longest ORF, bug fixes (reduced memory and higher sensitivity) and relicensed as MIT 📄 biorxiv.org/content/10.1... 💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶

Please consider spending a few moments of your day supporting our resource by providing your feedback to our team! The things we learn from the user survey is essential for our continued success! 🖥️🧬

Our data resources underpin life science research and scientists worldwide use them on a regular basis: 🌍 101 million requests to our data resource websites on an average day 💻 36 million unique IP addresses annually Which of our resources have you used recently? 👀 www.ebi.ac.uk/about/our-im...

If you are a PhD student and like protein disorder (or want to learn more), Birthe Kragelund @bbkrage.bsky.social and Kristian Strømgaard are organizing a PhD course on How IDPs work 🧶🧬🧪 Note the cost if you are not at a Danish university. Details: phdcourses.ku.dk/DetailKursus...

The best hope we at NVIDIA have to help dent progress in machine learning biology is to enable everyone to do it as efficiently as possible. We released BioNeMo Framework open-source to share our learnings with the community, and learn from everyone here about what we need to build for you to scale

Yeah, yeah, I know... but: gotta make that investment 4y ago pay off at some point, thanks 🦋 for allowing custom domains 😇 Promise I'll only post and re-post (machine) learning bio posts! Except for this one. Starting with the next,.. Oh and an announcement in December. 🤫

GPUs are *fast* at aligning protein sequences (and profiles!). 178x faster than JackHMMER! In ColabFold, 23x faster end-to-end compared to AlphaFold2 reaching the same accuracy! You get immediate speedups for all methods leveraging MSAs, from DCA, to PoET, and even AlphaFold3!