M. Ikeguchi

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.

gr Predictor: a Deep-Learning Model for Predicting the Hydration Structures around Proteins

This paper introduces a deep-learning model that rapidly predicts protein hydration structures, achieving high accuracy and speed compared to traditional methods.

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.

The molecular basis of ubiquitin-specific protease 8 autoinhibition by the WW-like domain

This study identifies an autoinhibitory WW-like domain in USP8 that regulates its enzyme activity and links its release to Cushings disease.

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.

Energetics and Conformational Pathways of Functional Rotation in the Multidrug Transporter AcrB

This study calculates the minimum free energy pathway of functional rotation in AcrB, linking it to proton translocation and drug transport at the atomic level.