Reposted by Hamidreza GhafouriKresten Lindorff-Larsen @lindorfflarsen.bsky.social · 18/08/2026Two 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... 13112
Hamidreza Ghafouri @hamidrgh.bsky.social · 20/05/2026Day 2 started with a great talk by Andrea Sinz on the application of XL-MS for studying IDPs #ml4ngp 000
Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026Today’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 000
Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026IDRs in mycobacterium transcription by Lukas Zidek #ml4ngp 000
Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026Next: Achieving Predictive All-Atom Simulations of Disordered Proteins and Condensates By: Milos Ivanovic #ml4ngp 010
Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/20263rd keynote speech an amazing talk by Ben Schuler: Probing the Rapid Interaction Dynamics of Charged Disordered Proteins #ml4ngp 010
Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026Another amazing talk by Sveinn Bjarnasor on Sox2 promotes chromatin accessibility via distinct mechanisms directed by intrinsically disordered regions #ml4ngp 000
Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026The 6th talk by Dirk Linke on intrinsically disordered in bacterial surface proteins #ml4ngp 000
Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026Zsuzanna Dosztanyi presented: Variant effect predictors in IDPs are systematically biased #ml4ngp 010
Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026The 2nd keynote speaker, Michael Feig, presented : peptide dynamics inside condensates of different scales #ml4ngp 010
Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/20263rd talk by Juan Cortes: Generative design of idps based conditional protein language models #ml4ngp 020
Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026Key tools for using pLMs presented by Michael Heinzinger #ml4ngp 000
Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/20262nd speaker: Beyond static structures: how pLMs help understanding protein flexibility #ml4ngp 000
Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/20261st keynote talk by Rohit Pappu Phase transition of RNA-Binding Non-Globular Proteins #ml4ngp 000
Hamidreza Ghafouri @hamidrgh.bsky.social · 19/05/2026Last #ml4ngp conference has just started in Warswa-Poland 030
Reposted by Hamidreza GhafouriKresten Lindorff-Larsen @lindorfflarsen.bsky.social · 16/12/2025We (@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📝 1239
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 ] 131
Reposted by Hamidreza GhafouriKresten Lindorff-Larsen @lindorfflarsen.bsky.social · 03/04/2025Supervised 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... 0276
Reposted by Hamidreza GhafouriIDPSeminars @idpseminars.bsky.social · 17/03/2025Announcing 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... 02010
Reposted by Hamidreza GhafouriFrank Noe @franknoe.bsky.social · 21/02/2025Today 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.comGitHub - microsoft/bioemu-benchmarks: Benchmarking code accompanying the release of `bioemu`Benchmarking code accompanying the release of `bioemu` - microsoft/bioemu-benchmarks 47521
Reposted by Hamidreza GhafouriAlex Holehouse @alexholehouse.bsky.social · 15/02/2025The 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.orgAccurate predictions of conformational ensembles of disordered proteins with STARLINGIntrinsically 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... 02913