In this laboratory, we study biomolecular functions in a living cell, in particular, protein functions in signal transduction pathways, using theoretical/computational chemistry. For this purpose, we aim to understand and predict protein-ligand or protein-protein binding processes in dilute solution or crowded cellular environments.
Since the processes are usually slower than the time scale currently accessible by all-atom molecular dynamics (MD), we have developed various enhanced conformational sampling methods like the Generalized-ensemble algorithms or free-energy calculation methods. We have implemented them in GENESIS (GENeralized-Ensemble SImulation System), which has been developed in collaboration with Computational Biophysics Research Team, RIKEN R-CCS and Theoretical Molecular Science Laboratory, RIKEN CPR. The enhanced sampling methods or free-energy calculation methods are useful for basic life science as well as in-silico drug discovery. We contribute to these research areas by providing GENESIS and new computational methods developed by us to the academic research scientists as well as industrial users.
(Laboratory for biomolecular function simulation)