PDB COMMUNITY FOCUS: HARUKI NAKAMURA, PDBJ
Haruki Nakamura is the Director of the Protein Data Bank Japan (PDBj) in Osaka, Japan, and one of the founding members of the wwPDB. Born in Tokyo, Japan, he received his Doctor of Science degree in physics
at the Faculty of Science, University of Tokyo. His doctoral research
resulted in a thesis titled 'Dielectric studies of the biological
polyelectrolytes by Fourier-synthesized- pseudorandom-noise-dielectric
He began his post-graduate career as a Research Associate at the
Department of Applied Physics Faculty of Engineering at the University
of Tokyo. As a Visiting Researcher at the Astbury Department of
Biophysics at Leeds University, Haruki studied molecular graphics in
the laboratory of Professor A. C. T. North. He has also been a guest
professor at a number of prestigious universities. In 1987, he became
the Director of Second Department, Protein Engineering Research
Institute (PERI) at Osaka, studying molecular modeling, design and
analysis, and in 1996, he was named Research Director, Department of
Bioinformatics, Biomolecular Engineering Research Institute (BERI) - a
successive institute of PERI.
In addition to being the director of PDBj, Haruki is currently a
Professor in the Laboratory of Protein Informatics, at the Research
Center for Structural and Functional Proteomics, Institute for Protein
Research, Osaka University.
Throughout his career his research interests have included biophysical
studies of protein architecture, electrostatic properties and
enzymatic functions, protein modeling, protein design, computational
chemistry, and structural bioinformatics.
Q:How did you come to be involved with the PDBj, and how has your own
research influenced your vision for the PDBj?
A: The Institute of Protein Research (IPR) at Osaka University has
collaborated with the PDB since its foundation in the 1970s. However,
up until five years ago, the collaboration had been very limited due
to little governmental support. What I first did after moving to IPR
was to emphasize the importance of the life science databases and
bioinformatics technology, and to persuade the university and the
government that IPR should contribute to the PDB database much more
than before. Fortunately, my proposal to develop these areas -- to
curate, edit, and distribute structural data, develop a new XML format
with an XML-based browser, develop several secondary databases, and
start a mirror site of BMRB -- was approved by our Japanese
government, to accompany the structural genomics project in Japan. In
order to promote all these activities, we founded a new organization
called PDBj. The PDBj activity is not pure research, but provides many
services to scientists, students, and general citizens all over the
world; in particular, we have some responsibility for the Asian and
Oceania regions. However, as a service provider, our knowledge areas
now cover a much wider field: Crystallography, NMR, Informatics,
Graphics, Web technology, and so on. In particular, our experience
developing the canonical PDBML in collaboration with the RCSB PDB has
increased our skills in XML and GRID computing. Development of our
secondary databases provided a good opportunity to learn about
integrating computational chemistry and information science.
Q:What are your long-term goals for PDBj, especially in light of the
rapid changes taking place in structural biology?
A: With more protein and DNA structures being determined rapidly,
every data curation and editing procedure should be automated as much
as possible without sacrificing data quality. The raw experimental
data should also be stored and distributed from the PDB. Thus, one of our
long-term goals for the future is to establish a stable data
management system as a sustainable system that will not require much
manual effort or large financial support. This may be realized with
the rapid development of data grid technology, in which the
distributed data yielded by structural biologists may be gathered and
integrated based on the grid architecture through the
Internet. Otherwise, database services may not be sustainable in
society. The introduction of XML for description and validation of PDB
data is the very first step to this goal.
Q:What is the nature of your interactions with the RCSB PDB and with
EBI-MSD and what effect, if any, does the formation of the wwPDB have
on these interactions?
A: When we started PDBj, the collaborations with RCSB PDB and with
EBI-MSD were essential, because PDBj is the newest entry in this
field. Therefore, the PDBj members have frequently visited both RCSB
PDB and EBI-MSD, and we have also invited people from RCSB PDB and
EBI-MSD, for example, when we organized international workshops at
IPR, Osaka University. The foundation of wwPDB should make these
collaborations much tighter than before. I am looking forward to
attending the first annual meeting of wwPDB this year.
Q:Do you think that the wwPDB will be effective in providing for the
long-term stability of the PDB archives?
A: Sure. Structural genomics projects and most structural biology
research rely upon financial support from the governments of
individual countries. The data management should thus be made by
several different countries collaborating with each other. Foundation
of the wwPDB is one of the essential points to make PDB a sustainable
Q:The amount of biological structure data is increasing almost
exponentially. From your experience, what do you see as the overall
future for databases that have to deal with this explosion of data?
A: As mentioned previously, a stable data management system in the
future should not require much manual effort or very huge financial
support to be a sustainable system. Introducing a new procedure is
inevitable, in which every data curation and editing procedure can be
automated without losing any data quality. Development of PDBML for
description and validation of PDB data is the very first step to this
goal. In the near future, the processes and workflows procedures
should be described using the standard ML technology. For that goal,
more collaboration with computer scientists is necessary.