|Staff||Prof. Yutaka Ueno and Kazuhiko Fukui||Laboratory's HP|
For studying a mechanisms of molecular recognition between proteins and formation of a molecular complex with nuclear acids or chemical compounds, the molecular dynamics simulation and quantum mechanics calculations are employed. Using the statistics of molecular interactions found from exhaustive search into PDB database, a docking study will predict a candidate proteins that interact with the target molecule.
For efficient analysis with molecular dynamics and quantum chemical calculations, we involve development of parallel computing code. In addition to the grid computing system, program code are devised to take advantage of multi-core CPU architecture and other accelerator hardware, such as graphics processors.
Image processing plays an important rule in the structural analysis of molecular complex of proteins with electron microscopy: averaging images to reduce noise, and classify images in the same orientation. With incomplete set of observed data informatics based estimations are useful in the analysis.
The molecular models will be edited to fit various experimental data to probe conformation of proteins at work, the molecular mechanism of the protein function are examined. Obtained conformational change would be visualized by animating molecular models. To support these studies, the scripting language that describes the molecular conformation, interaction, and the movements with reasonable efficiency is developed.
This laboratory was started since 2000, a collaborative laboratory inviting students to study at CBRC, Computational Biology Research Center in Tokyo, a part of AIST, National Institute of Industrial Science and Technology. Graduate students from Tokyo University and Tokyo Science University also join the activities and share the seminar from researchers inside or outside the institute. There are also additional lectures of bioinformatics training course for professionals engineers organized by an consortium with industry.
Researchers at CBRC studies both biology and informatics with wide variety of their tehcniques which is open to students. Dr.Fukui, professor, recently introduced an application of the graphics processor for the molecular simulation of proteins. A prototype computing motherboard runs in his office at maximum cooling strategy, disclosing open air and healthy operating sounds. Dr.Ueno, is pioneering Lua language in Japan for writing programs for his study. Two researchers working in biological problem, but there are no boundary between biology and informatics. Those who aims to handle both biology and informatics, CBRC will offer an excellent place to study.
I came to CBRC and feel that there are a lot of discussions. Even in a tea time or a luch time. Researchers are just like professors, talking about very deep stuff. It is a point that professionals from variety of fields get togehter here.
I think a good point of CBRC is the degree of freedom. Most researchers concentrate on their research topics. On the other hand, it is not good for those with indecisions on his working target. Being here does not promise a nice study. Once the research theme is decided, and working steady here toward the goal, CBRC is a good place to study.
After my study in CBRC, I got a job at a private company trying to another research position in there. In CBRC, I was watching on many researchers and captured the feeling of professional researchers' life, that was a really good for me. I learned that researchers works not only inside a research institute, but also outside institute.