Francesca Cuturello
@fra-cutu.bsky.social
Computational perspective on molecular evolution & function @areasciencepark
Reposted by Francesca Cuturello
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...
We expanded and refined the preprint thanks to the insightful feedback from reviewers!
paper: pubs.acs.org/doi/10.1021/...
code: github.com/RitAreaScien...
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...
pubs.acs.org
September 4, 2025 at 7:49 AM
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...
We expanded and refined the preprint thanks to the insightful feedback from reviewers!
paper: pubs.acs.org/doi/10.1021/...
code: github.com/RitAreaScien...
Reposted by Francesca Cuturello
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...
Special Guests: David Robertson (UK), @grovearmada.bsky.social (UK), Emanuele Andreano (IT)
www.areasciencepark.it/en/events/ai...
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...
www.areasciencepark.it
July 7, 2025 at 3:33 PM
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...
Special Guests: David Robertson (UK), @grovearmada.bsky.social (UK), Emanuele Andreano (IT)
www.areasciencepark.it/en/events/ai...
Reposted by Francesca Cuturello
🔥 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.
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.
June 3, 2025 at 1:31 PM
🔥 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.
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.
Reposted by Francesca Cuturello
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 🎉
May 16, 2025 at 9:16 AM
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 🎉
Reposted by Francesca Cuturello
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...
www.nature.com/articles/s41...
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...
www.nature.com
May 16, 2025 at 4:01 PM
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...
www.nature.com/articles/s41...
Reposted by Francesca Cuturello
🚨 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.
Evolutionary constraints guide AlphaFold2 prediction of alternative conformations and inform rational mutation design [new]
AlphaFold2: Protein conf. via evolution. Coevolution stabilizes.
AlphaFold2: Protein conf. via evolution. Coevolution stabilizes.
April 16, 2025 at 2:35 PM
🚨 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.
Reposted by Francesca Cuturello
📢 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
🔗 doi.org/10.1101/2025...
💻 github.com/Bitbol-Lab/r...
1/7
April 11, 2025 at 2:47 PM
📢 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
🔗 doi.org/10.1101/2025...
💻 github.com/Bitbol-Lab/r...
1/7
Reposted by Francesca Cuturello
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/microsoft/bi...
GitHub - microsoft/bioemu-benchmarks: Benchmarking code accompanying the release of `bioemu`
Benchmarking code accompanying the release of `bioemu` - microsoft/bioemu-benchmarks
github.com
February 21, 2025 at 3:49 PM
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/microsoft/bi...
Reposted by Francesca Cuturello
Rapid and sensitive protein complex alignment with Foldseek-Multimer | Nature Methods https://www.nature.com/articles/s41592-025-02593-7
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.
www.nature.com
February 7, 2025 at 2:43 AM
Rapid and sensitive protein complex alignment with Foldseek-Multimer | Nature Methods https://www.nature.com/articles/s41592-025-02593-7
Reposted by Francesca Cuturello
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...
January 27, 2025 at 4:56 PM
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...
Reposted by Francesca Cuturello
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...
💾 github.com/steineggerla...
🌐 search.foldseek.com/foldmason
📄 www.biorxiv.org/content/10.1...
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
www.biorxiv.org
August 3, 2024 at 7:37 AM
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...
💾 github.com/steineggerla...
🌐 search.foldseek.com/foldmason
📄 www.biorxiv.org/content/10.1...
Reposted by Francesca Cuturello
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
Our research presented today at AreaSciencePark! @bussigio.bsky.social will discuss our recent results in enhanced sampling of #RNA Mg interactions, integration of #cryoEM data, and refinement of force fields for modified nucleotides. www.areasciencepark.it/en/scientifi...
RNA dynamics from combining molecular simulations and experimental data - Area Science Park
Abstract: RNA molecules play a fundamental role in biology, and their function is often tightly connected to their dynamics. Molecular dynamics (MD) simulations can be used to reconstruct RNA dynamics. However, MD simulations suffer from poor accuracy due to incorrect force field parametrizations and poor precision due to slow sampling. In the group, we develop […]
www.areasciencepark.it
January 22, 2025 at 4:35 PM
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