The DiffUSE Project wants examples where structural heterogeneity matters but cannot be encoded in PDBx/mmCIF. X-ray, cryo-EM, time-resolved, multi-map, or fragment screening data welcome. Submit yours: diffuse.science/submit/
We present sampleworks, an open, modular platform for generating and evaluating biomolecular conformational ensembles from structure predictors guided by experimental data doi.org/10.82153/jkx....
Bulk solvent fills ~half a protein crystal. Modeling this is required for a good fit to experimental data. How best to model this remains an open question. New from diffUSE: a Phenix patch to supply your own solvent map (MD, 3D-RISM, EDEN, neural nets). Read more here: thestacks.org/publications...
In a test case, swapping Phenix's flat bulk-solvent mask for an MD-derived map lowered cross-validated R-free from 0.147 to 0.109 in one 0.96 Å. Code here: github.com/jmholton/phe...
ICYMI: The latest Tortured Proteins Department episode. @stephanieaw.bsky.social
and @fraserlab.com on: NIH strategic plan comments (due 5/26), AI lab guidelines, two new cryo-EM preprints, training scientists for what's next diffuse.science/posts/TTPD-14/
Simulations can be valuable but there is a huge need for scalable experiments that probe protein dynamics- of course we're expanding our work here and there's also great work from others @hkws.bsky.social @ginaelnesr.bsky.social Basile Wicky (not on bsky) @diffuseproject.bsky.social