T. Ekimoto

Molecular dynamics unveils multiple-site binding of inhibitors with reduced activity on the surface of dihydrofolate reductase

This study uses molecular dynamics to analyze inhibitor binding to DHFR, showing that reduced activity correlates with multiple-bound states on the protein surface.

Binding and unbinding pathways of peptide substrate on SARS-CoV-2 3CL protease

This study investigates the binding and unbinding pathways of an eight-residue peptide to SARS-CoV-2 3CL protease using weighted ensemble simulations, revealing the sequential formation of hydrogen bonds during the binding process.

Allosteric regulation of 3CL protease of SARS-CoV-2 and SARS-CoV observed in the crystal structure ensemble

The paper analyzes the structural dynamics of SARS-CoV-2 and SARS-CoV 3CLpro using crystal structures to understand allosteric regulation and ligand binding effects.

Moving toward generalizable NZ-1 labeling for 3D structure determination with optimized epitope tag insertion

The paper improves epitope tag insertion for 3D structure determination by using PA14 tags, which reduce structural changes in targets compared to PA12 tags.