Computational Structural Biology
COMPUTATIONAL STRUCTURAL BIOLOGY RESEARCH TEAM
LEAD PI: FLORENCE TAMA
PROJECT MENTOR(S): Osamu Miyashita and Florence Tama
(COMPUTATIONAL STRUCTURAL BIOLOGY RESEARCH TEAM, RIKEN R-CCS)
Biomolecules perform many vital cellular functions, such as gene transcription, protein synthesis or regulation of cellular transport, and dysfunctions of those result in severe diseases. In order to understand diseases, the functional mechanisms of these biological complexes need to be elucidated. A crucial step in this process is the characterization of the structure and dynamics of these complexes. The research goals would be either:
- Development of computational methods to obtain atomic level description of the functional states of biological complexes through the integration of various experimental data such as high-resolution X-ray crystallography, medium resolution cryo-EM and emerging X-ray free electron lasers with computational modeling through high performance computing; OR
- Applications of integrative modeling to study a specific biological system given a new set of experimental data.
We aim to train students in cutting edge integrative modeling techniques either in terms of development or applications. Our team would gladly welcome new collaborations in the applications of our computational tools. If the participants are interested in the applications of our methods to particular biological molecules, we could establish long term collaborations to perform modeling.
As we aim to integrate via computational tools different types of experimental data, we welcome participants working with U.S. based mentors who have expertise in experimental techniques such as X-ray, EM, SAXS, FRET, AFM etc.
Participants are welcome to attend our group meetings. Participants and co-mentors will be asked to follow RIKEN rules.
REQUIRED SKILLS
- Basic knowledge of experimental techniques (diffraction, AFM, EM) and/or
- Experience (even limited) in processing experimental data.
- Experience in programming is required.
COMPUTATIONAL RESOURCES
US students and their mentors can use our resources, upon agreeing on the rules and regulations of Japanese Export Control and Act and compliance with the Foreign Exchange and Foreign Trade Act. US students will get access to:
- our local PC-clusters and GPU workstations.
- RIKEN HOKUSAI supercomputer system
- Fugaku - Note: a research agreement between RIKEN and US university would be required.