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Francesca Cuturello

@fra-cutu.bsky.social
32 followers 56 following 2 posts

Computational perspective on molecular evolution & function @areasciencepark

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Francesca Cuturello @fra-cutu.bsky.social · 10/06/2026
Excited to announce our pre-print on the detection of PPI interfaces using ESM3!!! Big thanks to the very young and talented authors www.biorxiv.org/content/10.6...
biorxiv.org
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Reposted by Francesca Cuturello
Valerio Piomponi @piompons.bsky.social · 04/09/2025
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...
pubs.acs.org
Evolutionary Constraints Guide AlphaFold2 in Predicting Alternative Conformations and Inform Rational Mutation Design
Investigating structural variability is essential for understanding protein biological functions. Although AlphaFold2 accurately predicts static structures, it fails to capture the full spectrum of f...
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Reposted by Francesca Cuturello
Valerio Piomponi @piompons.bsky.social · 07/07/2025
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...
areasciencepark.it
AI in Virology: Leveraging AI to Advance Our Understanding of Viruses - Area Science Park
Artificial intelligence is opening new perspectives in virus research, providing advanced tools to analyze viral evolution and to understand protein structure and dynamics on a large scale. To explore...
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Reposted by Francesca Cuturello
Alberto Cazzaniga @albecazzaniga.bsky.social · 03/06/2025
🔥 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.
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Bussi Lab @bussilab.org · 16/05/2025
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 🎉
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Spyros Lytras @spyroslytras.bsky.social · 16/05/2025
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...
nature.com
A protein language model for exploring viral fitness landscapes - Nature Communications
Ito et al. present CoVFit, an AI model that predicts variant fitness (transmissibility) from spike protein sequences alone. They further demonstrate its utility in forecasting viral evolution via sing...
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Reposted by Francesca Cuturello
Valerio Piomponi @piompons.bsky.social · 16/04/2025
🚨 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.
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Reposted by Francesca Cuturello
Damiano Sgarbossa @damianosg.bsky.social · 11/04/2025
📢 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
RAG-ESM logo
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Frank Noe @franknoe.bsky.social · 21/02/2025
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...
github.com
GitHub - microsoft/bioemu-benchmarks: Benchmarking code accompanying the release of `bioemu`
Benchmarking code accompanying the release of `bioemu` - microsoft/bioemu-benchmarks
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Reposted by Francesca Cuturello
Tominaga K. (tomiken) @pacyc184.bsky.social · 07/02/2025
Rapid and sensitive protein complex alignment with Foldseek-Multimer | Nature Methods www.nature.com/articles/s41592-025-…
nature.com
Rapid and sensitive protein complex alignment with Foldseek-Multimer - Nature Methods
Foldseek-Multimer offers a fast strategy for complex-to-complex alignment to quickly identify compatible sets of chain-to-chain alignments by their superpositions. It can compare billions of complex pairs in 11 h.
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Reposted by Francesca Cuturello
Diego del Alamo @delalamo.xyz · 27/01/2025
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...
Figs two and three from the paper showing a variety of fine-tuning schemes across various base models, none of which exceed PPI prediction accuracy of 0.65
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 03/08/2024
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...
biorxiv.org
Multiple Protein Structure Alignment at Scale with FoldMason
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Reposted by Francesca Cuturello
Giovanni Bussi @bussigio.bsky.social · 22/01/2025
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
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