(31th-January-2020)
However, in the molecular dynamics method, tens of thousands of atoms that make up the causative molecule are moved one by one, so that the calculation amount is extremely large. For this reason, when running on a normal computer, it is necessary to reduce the amount of calculation by devising a group of several atoms as if it were one atom and calculating. In the body, the causative molecule is surrounded by water, but when calculating the water molecule, the amount of calculation increases, so there is also a problem that it is difficult to incorporate the water molecule.
"Kyo" has achieved not only cutting-edge results but also practical results
K computer was able to perform molecular dynamics calculations on all atoms, including the surrounding water molecules, in addition to the causal molecules and compounds. Calculating how about 10 types of compounds bind to 5 types of proteins (causal molecules of disease), and predicting which one binds the most strongly, the correct answer rate was over 50%. On the other hand, with the conventional docking method, the correct answer rate was about 5%. This result indicates that the most suitable lead compound can be predicted by the molecular dynamics method if abundant calculations are performed on a supercomputer with high computational power. In other words, it was demonstrated that molecular dynamics optimization could be used in the pharmaceutical field in the future.
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