Our study is now published on JCIM🎉 We expanded and refined the preprint thanks to the insightful feedback from reviewers! paper: pubs.acs.org/doi/10.1021/... code: github.com/RitAreaScien...

Workshop not to be missed at Area Science Park (Trieste) on the 9th of September. Special Guests: David Robertson (UK), @grovearmada.bsky.social (UK), Emanuele Andreano (IT) www.areasciencepark.it/en/events/ai...

🔥 Two PhD positions open @UniTrieste funded by @AreaSciencePark! 🔥 Join the Laboratory of Data Engineering to advance research in AI and its scientific applications. We’re looking for motivated students ready to dive into interdisciplinary research in deep learning and AI.

Our integrative approach using #MD and #cryoEM data to construct structural ensembles of #RNA just published on @natcomms.bsky.social doi.org/10.1038/s414... Lead by Elisa Posani, with @magistratolab.bsky.social @bonomimax.bsky.social @pjanos.bsky.social @navtejtoor.bsky.social and Daniel Haack 🎉

The CoVFit paper is now published @natcomms.nature.com !! Exciting work led by Jumpei Ito really showing the potential of pLMs for genotype-2-phenotype predictions!! www.nature.com/articles/s41...

🚨 New paper! By combining protein language models, clustering, and DCA, we reveal how MSA subclusters drive AF2 predictions toward alternative conformations, and how statistics from the clustered sequences can inform deisgn of mutations that shift conformer populations.

📢 Our new preprint is out on bioRxiv! We introduce RAG-ESM, a retrieval-augmented framework that improves pretrained protein language models like ESM2 by making them homology-aware with minimal additional training costs. 🔗 doi.org/10.1101/2025... 💻 github.com/Bitbol-Lab/r... 1/7

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...

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

PPI prediction accuracy doesn't appear to ever exceed ~0.65 when using embeddings from sequence-only protein language models, regardless of model size or fine-tuning scheme www.biorxiv.org/content/10.1...

FoldMason progressively aligns thousands of protein structures in seconds, enabling remote MSA for distant phylogeny. Highlights: structural flexible MSA, LDDT conservation score, friendly webserver 💾 github.com/steineggerla... 🌐 search.foldseek.com/foldmason 📄 www.biorxiv.org/content/10.1...

Nice day at Area Science Park! It was beautiful to see what previous students of our group are doing @fra-cutu.bsky.social @piompons.bsky.social