The Computational Molecular Design Group aims to simulate biomolecular interactions and to design effective molecular regulators using large-scale computer simulations. X-ray crystallography and NMR studies provide a large number of 3D structures of biomolecules, and advances in molecular detection technologies have greatly improved our understandings of intracellular molecular behaviors. To connect molecular behavior with molecular structure and to predict molecular functions, however, require large scale, atomic level molecular simulations. We are therefore focusing on molecular dynamics (MD) and quantum chemistry simulations to study this relationship in large biomolecules. Through collaboration with groups inside and outside BDR, we are designing novel compounds for various target biomolecules by utilizing our computational techniques. Furthermore, by developing exclusive high-performance computers, we aim to achieve unprecedented long-term MD simulations.
- Understanding thermodynamic and physicochemical properties of the interaction of biopolymers with their regulators and hydration water
- Theoretical study on binding and enzymatic reactions of protein/DNA-regulator complexes
- Designing new peptides for protein target binding
- Development of MDGRAPE-4A, a special purpose computer for MD simulations.