Biography

Research Interests

We investigate thermodynamic characters of proteins and nuclear acids(DNA, RNA) by performing large-scale molecular dynamics simulations on high performance computers. We developed the massively parallel computation method of an absolute binding free energy of protein and ligand based on the nonequilibrium equality of free energy between thermodynamic states. Molecular mechanical models were examined in comparison with ab initio molecular orbital calculations. Traditional force field models of the protein backbone did not agreed with highly accurate molecular orbital calculations so that we developed new force field parameters to agree with the ab initio results. These methods are applied for computer aided drug design.