Rutgers, UC San Diego and NIST win grant to manage Protein Data Bank
FOR IMMEDIATE RELEASE
TO THE POINT: Rutgers, UC San Diego and NIST win grant to manage
Protein Data Bank
NEW BRUNSWICK/PISCATAWAY, N.J. - The Research Collaboratory for Structural
Bioinformatics (RCSB; http://www.rcsb.org/), a consortium composed of Rutgers,
the State University of New Jersey; the University of California at San Diego;
and the National Institute of Standards and Technology (NIST), has received a
$10 million, five-year award from the National Science Foundation (NSF), the
Department of Energy (DOE), and two units of the National Institutes Of
Health: the National Institute Of General Medical Sciences (NIGMS) and the
National Library Of Medicine (NLM). The award will enable the RCSB to operate
and significantly extend the capabilities of the Protein Data Bank (PDB), a
critical tool for unlocking the secrets of biological systems in
pharmaceutical and medical research.
The RCSB's Protein Data Bank, in addition to being a repository of
data, will now provide mechanisms for researchers to understand
biological function through investigation of sequence and molecular
structure. Previously maintained by Brookhaven National Laboratory,
the PDB's change in management will be transparent and seamless as it
moves to the RCSB with the addition of new capabilities for searching
and for improving the consistency and content of existing and future
depositions.
"The RCSB proposal was evaluated using a standard merit review procedure which
included a site visit and advisory panel" said Gerald Selzer, Program Director
in the NSF Division of Biological Infrastructure. "Experts in x-ray
crystallography, other areas of structural and computational biology, computer
science, and database technology were asked to participate in the evaluation
of the proposal."
"The funding decision was reached on the basis of the comments of these
experts," Selzer continued. "Reviewers and agency staff alike were impressed
with the technical merit of the plans for operating the database, with the
detailed scheme for management across the three participating sites, and the
depth of technical and managerial expertise that the RCSB will bring to this
important task."
The transfer of the Protein Data Bank from Brookhaven to the RCSB
will result in several improvements, including a higher, faster
throughput; a greater number of query capabilities, including more
complex and more accurate queries; a uniform archive; a dynamic
cross-link to other databases; and the availability of structure
validation and structure and sequence neighboring. The RCSB Protein
Data Bank will be scalable and will provide rapid and reliable data
processing. Validation reports will be available to depositors.
RCSB has already developed tools, demonstrated on the group's Web
site, that allow biologists to perform queries that search several
databases at the same time.
The PDB data will be stored and mirrored at all three RCSB sites.
The three institutions have divided their responsibilities according
to their expertise in data deposition and processing, database query
and integration, and database uniformity. The PDB will also be
mirrored at key sites worldwide, notably in Europe and the Pacific
Rim.
The experience of the RCSB members in structure data processing
and analysis covers data validation, data modeling, database
development, query languages and visualization tool development. The
group has developed and currently maintains 11 publicly available
structural biology databases. This combined expertise lays the
foundation for the future.
Principal investigator Helen Berman, a Rutgers professor of
chemistry, was part of the original team that developed the Protein
Data Bank at Brookhaven in 1971. She is responsible for the
development of the Nucleic Acid Database (NDB) at Rutgers, which
assembles and distributes structural information about nucleic acids
and contains an atlas, an archive and a sophisticated search engine
to access the data. She has drawn upon her experience in developing
that database to help design the new capabilities of the PDB.
"Our vision is that the PDB will enable scientists worldwide to gain
a greater understanding of structure-function relationships in
biological systems," Berman said. "We are capable of doing this
because of the unique infrastructure the RCSB offers in terms of
personnel, hardware, software and network infrastructure."
At the San Diego Supercomputer Center (SDSC) at UCSD, principal
scientist Phil Bourne leads a group of scientists in a Biological
Data Representation and Query initiative. The group has developed
locally a number of databases containing derived data on protein
structures and maintains a mirror site of Berman's NDB. Recent work
produced a database of structure comparisons for the more than 8,000
structures in the PDB.
The NIST effort will be led by Gary L. Gilliland, chief of the
Biotechnology Division in NIST's Chemical Science and Technology
Laboratory. He has maintained an active research program in protein
crystallography for more than 20 years. Also, he played a key role in
establishing the Center for Advanced Research in Biotechnology
(CARB), a joint effort of NIST and the University of Maryland
Biotechnology Institute, where he served as the Associate Director
until 1996. NIST will establish data uniformity of the old and new
structures in order to improve the accessibility and reliability of
queries.
The PDB effort will also take advantage of computational
infrastructure development by the National Partnership for Advanced
Computational Infrastructure (NPACI), led by UCSD and SDSC and in
which all three RCSB sites participate.
The three-dimensional structures of proteins and other biological
macromolecules are helping to unlock the secrets of how biological
systems work. They hold significant promise for the pharmaceutical
and biotechnology industries in the search for effective new drugs
with few or no side effects and the effort to understand the mystery
of human disease.
Medical researchers also envision gaining new insights on the
causes, effects and treatment of many diseases by understanding the
biological macromolecule structure and function. Very precise and
accurate information on the atomic structure of complex biological
macromolecules is needed to unlock their disease-fighting potential.
The RCSB's Protein Data Bank will give researchers access from a
single source to more information about biological structures than
ever before. Via the World Wide Web, database users in academia,
government and industry will be able to access archival services and
formulate complex queries that will provide reliable answers to
further their research efforts.
# # #
Rutgers, the State University of New Jersey, is a member of the
Association of American Universities, the 62 leading research
universities in North America, distinguished for both teaching and
generating new knowledge. It is the only university to have grown in
designation from a colonial college to a land-grant college to a
major public research institution. Currently, Rutgers ranks among
America's top 10 public universities in the number of national
academy memberships held by its faculty, with a total of 38. Today,
Rutgers encompasses 29 degree-granting schools on three regional
campuses and includes more than 100 specialized research institutes.
For more information, visit www.rutgers.edu.
The San Diego Supercomputer Center (SDSC) is a research unit of the
University of California, San Diego, and the leading-edge site of the
National Partnership for Advanced Computational Infrastructure
(www.npaci.edu). SDSC is sponsored by the National Science
Foundation through NPACI and by other federal agencies, the State
and University of California and private organizations. For
additional information about SDSC, contact Ann Redelfs at SDSC,
(619) 534-5032, [email protected].
As a nonregulatory agency of the Commerce Department's Technology
Administration, NIST promotes U.S. economic growth by working with
industry to develop and apply technology, measurements and standards.
