(3rd-February-2020)
-MDGRAPE-4A, a computer dedicated for molecular simulation-
The research team of Masahiro Taiji, team leader of the Computational Molecular Design Research Team of the RIKEN Center for Biological Sciences, has been working on a computer dedicated to molecular dynamics (MD) simulation "MDGRAPE-4A ". Successful development.
The results of this research are expected to greatly expand the potential of in silico drug discovery.
MD simulation is a method of “moving” a protein in a computer by calculating the forces acting on the atoms that make up the protein and surrounding water molecules in order to analyze the protein structure that keeps changing in aqueous solution. The analysis of large proteins requires an enormous amount of time even with a general-purpose supercomputer (supercomputer), so the development of a dedicated supercomputer that performs high-speed molecular simulation has been awaited.
This time, the research team installed 512 dedicated large-scale integrated circuits (LSI) designed and developed by himself, and the MDGRAPE- 4A was developed. MDGRAPE-4A is capable of simulating a 100,000-atom system composed of proteins and water molecules by a maximum of 1.1 microseconds per day (one microsecond equals one millionth of a second). This makes it possible to analyze the interaction between proteins and drugs in aqueous solution in a sub-millisecond (~ 100 microsecond) time scale in a realistic time.
This development was reported at the "Informatics Computational Chemistry and Biology 2019 Conference" held in Tokyo (October 24). Part of the finished product will also be exhibited at the international conference "Supercomputing SC19" in Denver, USA (November 18-21, local time), and the entire system will be open to the public in RIKEN Osaka area 2019 (November 23) Publish in.
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