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Integrative Nutriomics and Oncology

Molecular life sciences and drug discovery based on physics and computational science

Physical research on thermal dynamics of biomolecules

All life activities are based on molecular interactions in atomic scale, which are governed by physical laws such as quantum mechanics and statistical thermodynamics. Because of recent advance in supercomputer it is getting possible to perform molecular dynamics simulations of biomolecules such as protein, DNA and RNA after building up accurate molecular models based on quantum mechanics. If the molecular dynamics simulations are accurate enough, we might predict the medical activity of new drugs by computer simulations and it will promote the computer aided drug design. Molecular interactions between water, small compounds, and large biomolecules such proteins and nucleic acids are described by molecular mechanical force field. Using high-level quantum mechanical theory we are developing more accurate unified force field than traditional ones. Using nonequilibrium Jarzynski identity we developed massively parallel computational method of binding free energy (MP-CAFEE), which made it possible to quantitatively compare the calculated binding free energies with experimental binding constants commonly measured in the drug development. We implemented efficient MP-CAFEE program to K computer, which is widely used. Recently we succeeded to improve the accuracy of DNA force field in consistent way with the protein force field. It enables highly accurate molecular dynamics simulations for the protein and DNA complex system with drug small molecules. We will continue the research to make concrete physical basis for the life science.

Quantum calculation for protein backbone
Quantum calculation for protein backbone
Nonequilibrium free energy evaluation
Nonequilibrium free energy evaluation
Dynamics of nuclear receptor on DNA
Dynamics of nuclear receptor on DNA

Member

  • Takefumi YAMASHITA
  • Specialized field:Chemical reaction theory, Molecular dynamics
 
<As of May 2020>

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