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Hamidreza Ghafouri

@hamidrgh.bsky.social
49 followers 123 following 18 posts

PhD student @Biocomputing UP lab @University of Padova-Italy 🇮🇹 Research IDPs , Conformational ensembles🍝 Hamidrgh.github.io/hamidrgh

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Reposted by Hamidreza Ghafouri
Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 18/08/2026
Two new CALVADOS preprints Coarse-grained models for simulations of double-stranded nucleic acids for mixed protein-nucleic acid condensates doi.org/10.64898/202... MEM-CALVADOS: A Residue-Level Model for Flexible Proteins at Membrane Interfaces doi.org/10.64898/202...
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Hamidreza Ghafouri @hamidrgh.bsky.social · 20/05/2026
Day 2 started with a great talk by Andrea Sinz on the application of XL-MS for studying IDPs #ml4ngp
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Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026
Today’s talks ended by San Hadži He presented: A fuzzy-to-ordered switch in the binding mode of the disordered regulator HigA2 mediates a ratio-sensing gene circuit #ml4ngp
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Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026
IDRs in mycobacterium transcription by Lukas Zidek #ml4ngp
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Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026
Next: Achieving Predictive All-Atom Simulations of Disordered Proteins and Condensates By: Milos Ivanovic #ml4ngp
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Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026
3rd keynote speech an amazing talk by Ben Schuler: Probing the Rapid Interaction Dynamics of Charged Disordered Proteins #ml4ngp
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Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026
Another amazing talk by Sveinn Bjarnasor on Sox2 promotes chromatin accessibility via distinct mechanisms directed by intrinsically disordered regions #ml4ngp
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Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026
The 6th talk by Dirk Linke on intrinsically disordered in bacterial surface proteins #ml4ngp
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Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026
Zsuzanna Dosztanyi presented: Variant effect predictors in IDPs are systematically biased #ml4ngp
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Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026
The 2nd keynote speaker, Michael Feig, presented : peptide dynamics inside condensates of different scales #ml4ngp
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Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026
3rd talk by Juan Cortes: Generative design of idps based conditional protein language models #ml4ngp
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Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026
Key tools for using pLMs presented by Michael Heinzinger #ml4ngp
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Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026
2nd speaker: Beyond static structures: how pLMs help understanding protein flexibility #ml4ngp
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Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026
1st keynote talk by Rohit Pappu Phase transition of RNA-Binding Non-Globular Proteins #ml4ngp
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Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026
Last #ml4ngp conference has just started in Warswa-Poland
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Reposted by Hamidreza Ghafouri
Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 16/12/2025
We (@sobuelow.bsky.social & @kejohansson.bsky.social) tested AF-CALVADOS using the recently described PeptoneBench SAXS benchmark that contains SAXS data for >400 proteins with different amounts of order and disorder. The results look pretty good 😇 so we are sharing here while updating the preprint📝
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Hamidreza Ghafouri @hamidrgh.bsky.social · 07/04/2025
🚀 New Preprint Alert! We’re excited to share our latest work on a community-driven framework for determining conformational ensembles of intrinsically disordered proteins (IDPs) — now available as a preprint on arXiv! 📄 Read the full preprint here: [ arxiv.org/abs/2504.03590 ]
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Reposted by Hamidreza Ghafouri
Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 03/04/2025
Supervised training using data generated by multiplexed assays of variant effects is potentially very powerful, but is made difficult by assay- and protein-specific effects Here @tkschulze.bsky.social devised a strategy to take this into account while training models www.biorxiv.org/content/10.1...
Figure illustrating the framework for supervised learning across VAMP-seq datasets.
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Reposted by Hamidreza Ghafouri
IDPSeminars @idpseminars.bsky.social · 17/03/2025
Announcing the joint IDPSeminars / BPS IDP Subgroup Trainee Symposium Speakers! Join us on Mar 27, 12–2pm CST for 6 exciting talks focused on Intrinsically Disordered Proteins as part of #BophysicsWeek2025 with the @biophysicalsoc.bsky.social Sign up now at docs.google.com/forms/d/1L_K...
IDPSeminars/BPS IDP Subgroup symposium. March 27th 2025 at noon central time. Speakers are Ella Mozier, Sara Bologna, Borna Novak, Hamidreza Ghafouri, Ankith Sharma and Ananya Chakravarti!
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Reposted by Hamidreza Ghafouri
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 Hamidreza Ghafouri
Alex Holehouse @alexholehouse.bsky.social · 15/02/2025
The answer is yes! Come hear about STARLING this afternoon at the Biophysical Society IDP subgroup symposium! Thread to follow later today... www.biorxiv.org/content/10.1...
biorxiv.org
Accurate predictions of conformational ensembles of disordered proteins with STARLING
Intrinsically disordered proteins and regions (collectively IDRs) are found across all kingdoms of life and play critical roles in virtually every eukaryotic cellular process. In contrast to folded pr...
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