Kei-ichi Okazaki

This paper improves AlphaFold3's ability to predict protein conformations by introducing a repulsive bias in its diffusion model, enabling better capture of ligand-induced structural changes.

This study uses AlphaFold and Markov state modeling to analyze the conformational dynamics of Na+-NQR, revealing how redox state and Na+ binding regulate Na+ translocation.

This study uses CG-MD simulations to show that dynamin's GDP state induces conformational changes leading to membrane constriction.

This study identifies five conformational states of Na+-NQR in Vibrio cholerae using mutants and inhibitors, revealing that 2Fe-2S reduction drives Na+ translocation through structural rearrangements.

This paper uses molecular dynamics simulations to show how rotation direction affects IF1's binding to ATP synthase, revealing atomic mechanisms for IF1 ejection and inhibition.