David Andrew Case

The paper introduces NEF, a standard for NMR data exchange, and demonstrates its application in structure determination, metabolomics, and ligand screening.

FoldaVirus generates icosahedral virus capsid models using AlphaFold predictions and structural knowledge, validated by energy minimization and distance metrics.

The paper provides a library of 37,000 minimized small molecule geometries for use in macromolecular refinement and molecular dynamics simulations.

This paper evaluates blind predictions of dynamic water and ion ensembles around RNA using cryo-EM densities from CASP16, finding that molecular dynamics approaches perform best.

Two Tetrahymena ribozyme cryo-EM maps (2.2 and 2.3 Å) reveal cross-validated ordered waters and Mg2+ ions, plus reproducible diffuse solvent density resembling molecular dynamics water networks.

The paper integrates the Amber force field into Phenix for crystallographic refinement, improving model quality through better stereochemistry, fewer clashes, and better hydrogen bonds.