Elucidating protein–ligand binding kinetics based on returning probability theory

K Kasahara, R Masayama, K Okita… - The Journal of Chemical …, 2023 - pubs.aip.org
The returning probability (RP) theory, a rigorous diffusion-influenced reaction theory,
enables us to analyze the binding process systematically in terms of thermodynamics and …

Amide cyclodextrin that recognises monophosphate anions in harmony with water molecules

T Nakamura, H Takayanagi, M Nakahata… - Chemical …, 2025 - pubs.rsc.org
Anion recognition in water by synthetic host molecules is a popular and challenging topic. It
has been considered difficult because the water molecules compete for the recognition …

Diffusion theory of molecular liquids in the energy representation and application to solvation dynamics

K Okita, K Kasahara, N Matubayasi - The Journal of Chemical Physics, 2022 - pubs.aip.org
The generalized Langevin equation (GLE) formalism is a useful theoretical fundament for
analyzing dynamical phenomena rigorously. Despite the systematic formulation of dynamics …

Flexible framework of computing binding free energy using the energy representation theory of solution

K Okita, Y Maruyama, K Kasahara… - The Journal of Chemical …, 2025 - pubs.aip.org
Host–guest binding plays a crucial role in the functionality of various systems, and its
efficiency is often quantified using the binding free energy, which represents the free-energy …

A methodology of quantifying membrane permeability based on returning probability theory and molecular dynamics simulation

Y Matsubara, R Okabe, R Masayama… - arXiv preprint arXiv …, 2024 - arxiv.org
We propose a theoretical approach to estimate the permeability coefficient of substrates
(permeants) for crossing membranes from donor (D) phase to acceptor (A) phase by means …

Constructing a Memory Kernel of the Returning Probability to Efficiently Describe Molecular Binding Processes

K Kasahara, R Masayama, Y Matsubara… - Chemistry …, 2022 - academic.oup.com
Returning probability theory enables us to systematically analyze host-guest binding kinetics
in terms of the thermodynamic and kinetic properties of the intermediate state existing in the …