So far, sophisticated protein structure prediction methods have emerged. However, they are primarily limited to folded proteins and do not offer comprehensive insights into equilibrium properties. In this research, I aim to develop a generative model capable of producing an equilibrium ensemble of proteins. This project is supported by JST ACT-X.
We proposed the constant-force steered molecular dynamics simulation to estimate unbiased dissociation rate.
The input structures and topologies are provided 👉 github.
Our review paper for non-equilibrium molecular dynamics simulation 👉 Iida, S. & Tomoshi, K. Free energy and kinetic rate calculation via non-equilibrium molecular simulation: application to biomolecules.
We have found unique side-chain fluctuations of cryptic binding sites via molecular dynamics simulations.
Source code to analyse the fluctuations 👉 github
We have explored the structural ensemble of an intrinsically disordered region, p53 C-terminal domain, via a generalised ensemble molecular dynamics simulation. We have identified various binding modes on a target protein.
Our papers 👇
We have investigated monomeric and dimeric states of the SARS-CoV-2 main protease, identifying water molecules that can be crucial to keep the dyad configuration.