Example of molecular dynamics simulation performed at "K"

(1st-February-2020)

Example of molecular dynamics simulation performed at "K" (Image courtesy of Prof. Yasushi Okuno, Kyoto University)

We calculated how a compound (yellow) binds to an enzyme called CDK2 (one of the causative molecules of cancer) (originally a movie). Spreading around the enzyme are water molecules.

“K” has more practical results. When the operation of the K computer began, the consortium of more than 20 pharmaceutical companies aimed at promoting drug design using the K computer throughout the pharmaceutical industry.This consortium has 631 proteins and 30 million compounds. Conducted a virtual screening (more than 18.9 billion pairs) and distributed the calculation results to member companies.

This virtual screening uses not the docking method but the pattern recognition technology used when automatically recognizing a face with a digital camera, and the calculation time for "K computer" is 5 when converted using all 80,000 nodes. Since the type of protein is selected after hearing the wishes of the member companies, it is likely to be widely used as basic data for drug design.

Part of the results of the virtual screening performed at "K computer" (Image courtesy of Prof. Yasushi Okuno, Kyoto University)

The result of examining the binding of 388 proteins (a kind of enzyme) called kinases to 500 compounds. The red places indicate that they combine. On the right is a plot of the results obtained in the experiment. The predictions on the left are in good agreement with the experimental results. The prediction indicates whether combinations that have not been tested are also combined.

`` Fugaku '' aiming for unprecedented drug development

In "Fugaku", more "long time"

Aiming to perform child dynamics simulation on a “large scale” (subtask C of priority issue (1), development of drug discovery big data integration system). Some pharmaceutical companies are also conducting their own molecular dynamics simulations at K computer, but at Fujitake, applications and interfaces are being arranged to make them easier to use, and more pharmaceutical companies are using them. It is a plan.