Life activities are based on the atomic interaction and molecular reactions within the lives, whose behaviors are ruled by the physical principles such as quantum mechanics and thermo-dynamic statistics. Molecular force field well describes the room temperature behaviors of bio molecules such as water, small molecules, proteins, nucleic acids. We developed FUJI force field for accurate and unified descriptions of bio molecule taking advantage of high level quantum molecular orbital calculations. Since the simulation should be checked by quantitative comparison with experiments, we developed the binding free energy calculation method of MP-CAFEE utilizing Jarzynski equality in nonequibrium thermodynamic statics to compare with binding constants commonly measured in the drug development. In the collaboration with Professor Lindahl at the Stockholm University, we developed *SIMD kernels of GROMACS molecular dynamics suite, which are highly optimized and doubly speed up the K computer performance.
  The project target proteins were decided after careful investigations, IT company members engaged in the fragment based de novo design of drugs, University researchers performed MP- CAFEE on the K computer, and pharmaceutical companies performed synthesis and assay of the designed compounds. We performed about 300 MP-CAFEE calculations for the cancer target protein and the most promising compounds are now under investigational new drug enabling study (animal test).

Open Up Special Talk : Approach to the four Themes during the past five years and its achievements

  Theme 1  Simulations of biomolecules in cellular environments
  Theme 2  Simulation applicable to drug design
  Theme 3  Hierarchical integrated simulation for predictive medicine
  Theme 4  Large-scale analysis of life data