H. van den Bedem

Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM

This paper introduces enhanced qFit software for building multiconformer models from structural biology data, improving accuracy and usability.

Discovery of a cryptic pocket in the AI-predicted structure of PPM1D phosphatase explains the binding site and potency of its allosteric inhibitors

The paper shows that using dynamic simulations with an AlphaFold structure improves the prediction of allosteric inhibitor binding to PPM1D compared to static structures.

Ligand binding remodels protein side chain conformational heterogeneity

The paper measures conformational heterogeneity of protein side chains in ligand-bound and unbound states and finds that ligand binding increases flexibility in distant residues and correlates with inhibitor properties.

Reproducibility of protein X-ray diffuse scattering and potential utility for modeling atomic displacement parameters

qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps

qFit 3 automates multiconformer modeling of dynamic proteins from X-ray and cryo-EM data, offering improved efficiency and accessibility.

Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis

This study uses mix-and-inject XFEL crystallography to observe conformational changes in isocyanide hydratase during catalysis, showing how cysteine modification affects enzyme dynamics and function.

Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

This study compares serial X-ray crystallography and MicroED for determining structures from small macromolecular crystals, highlighting their strengths and challenges.

Molecular recognition of M1-linked ubiquitin chains by native and phosphorylated UBAN domains

This study investigates how phosphorylation affects UBAN domain binding to M1-linked ubiquitin chains, revealing structural and functional differences among related proteins.

qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps

qFit-ligand identifies unmodeled ligand conformations in crystal structures, revealing 29% of drug-like molecules exhibit conformational heterogeneity that could improve drug design.