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📝
We also outline key challenges in the field—such as force field accuracy, efficient sampling, and environmental dependency—and call for collaborative benchmarking and standardized protocols.
Kudos to all co-authors and contributors who made this work possible!
Our framework is built around three pillars:
🔹Experimental techniques
🔹 Computational ensemble generation
🔹 Ensemble validation
🍝 Disordered proteins are central to many biological processes, but their dynamic nature makes structural characterization a major challenge. Here, we present a modular framework that bridges experimental methods with computational tools, like molecular dynamics, knowledge-based sampling, and ML.
🚀 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 ]
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...
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!
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...
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...
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...