I. Fukuda

Binding free-energy landscapes of small molecule binder and non-binder to FMN riboswitch: All-atom molecular dynamics

This study uses molecular dynamics to compare binding free-energy landscapes of two structurally similar ligands to an FMN riboswitch, revealing distinct binding pathways and orientation effects.

Fly-casting with ligand-sliding and orientational selection to support the complex formation of a GPCR and a middle-sized flexible molecule

This paper uses a computational method to simulate the binding mechanism of bosentan to hETB, identifying key steps like fly-casting and ligand-sliding.

Molecular interaction mechanism of a 14-3-3 protein with a phosphorylated peptide elucidated by enhanced conformational sampling

This paper uses enhanced conformational sampling to study the binding mechanism of a phosphorylated peptide to a 14-3-3 protein, identifying stable clusters and a phosphorylation-dependent binding process.

Temperature-Energy-space Sampling Molecular Dynamics: Deterministic, Iteration-free, and Single-replica Method utilizing Continuous Temperature System

This paper introduces a new molecular dynamics method that enhances sampling without iteration or replica systems by dynamically coupling temperature and energy variables.

Symmetric, explicit numerical integrator for molecular dynamics equations of motion with a generalized friction

The paper introduces a symmetric, explicit numerical integrator for molecular dynamics with generalized friction, showing improved accuracy and efficiency in simulations.