RCSB Assumes Full Responsibility for Protein Data Bank July 1 After Successful Nine-Month Transition
Joseph Blumberg, Rutgers 732-932-7084 x652, firstname.lastname@example.org
David Hart, SDSC, 858-534-8314, email@example.com
Linda Joy, NIST, 301-975-4403, firstname.lastname@example.org
EDITOR'S NOTE: Dr. Helen Berman can be reached at 732-445-4667 or
732-445-0103 for interviews during the week of June 28.
On July 1, responsibility for the Protein Data Bank (PDB) formally shifts
from Brookhaven National Laboratory to the Research Collaboratory for
Structural Bioinformatics (RCSB) a full three months ahead of schedule.
The PDB, the nonprofit international archive for biomolecular structures
used in pharmaceutical and medical research, has provided substantial
improvements in service during the past few months. Since the RCSB began
assuming responsibility for the PDB, data deposited by users has been
turned around in record time, and new tools now provide a broader range of
search and reporting options. The success of these developments has
accelerated the transition timetable.
"The PDB is an enormously important resource for biomedical research, and
it is gratifying to learn that the move from Brookhaven National Laboratory
to the RCSB has been seamless," said Dr. Stephen K. Burley, Furlaud
Professor at The Rockefeller University and Investigator in the Howard
Hughes Medical Institute. "With the advent of many new protein structures,
I anticipate that implementation of modern database technologies by the
RCSB will yield important dividends for all of molecular and cellular
The three-dimensional structures of proteins and other biological
macromolecules contained in the PDB hold significant promise for the
pharmaceutical and biotechnology industries in the search for new drugs
with few or no side effects and the effort to understand the mystery of
human disease. Medical researchers envision gaining new insights on the
causes, effects and treatment of many diseases by unlocking the
disease-fighting potential of biological macromolecules. This requires very
precise and accurate information on the atomic structure of complex
The RCSB's PDB gives researchers access to more information about
biological structures from a single source than ever before. Via the Web,
database users in academia, government and industry access archival
services and formulate complex queries that will provide reliable answers
to further their research efforts.
The RCSB is directed by Helen Berman, a professor of chemistry at Rutgers,
the State University of New Jersey, and principal investigator for the PDB
project. The RCSB brings together experts from fields ranging from
high-performance computing to bioinformatics to structural biology to fully
integrate and upgrade all aspects of the PDB. In addition to Rutgers, Phil
Bourne, senior principal scientist, leads a team at the San Diego
Supercomputer Center (SDSC), a research unit of the University of
California, San Diego; and Gary Gilliland, chief of the Biotechnology
Division, leads the RCSB team at the National Institute of Standards and
Technology (NIST) in Gaithersburg, Md.
PDB responsibilities have been divided among the institutions to take
advantage of their expertise. Rutgers processes and annotates the data
deposited; SDSC integrates the databases and distributes the information;
and NIST oversees data uniformity, evaluation and archiving. The combined
qualifications of its members have allowed the RCSB to increase the scope
of PDB services without an increase in funding.
The RCSB has improved the PDB by creating an integrated system for data
intake and data distribution. This system facilitates faster and more
accurate data processing. In turn, the more uniform data support complex
queries about macromolecular structure and provide more dependable results.
The search options available allow for both simple text and complex
searching across the database.
The RCSB is dedicated to meeting the challenges posed to the PDB by the
increasing number of structures deposited and their growing complexity, and
by the increasing size and diversity of the user community. These needs are
being met through the RCSB's dedication to rapid and reliable data
processing, its commitment to providing uniform data, and its development
of versatile query and reporting capabilities for individual structures and
across the archive.
"Our vision is for the PDB to enable scientists worldwide to gain a greater
understanding of structure-function relationships in biological systems,"
said Berman. "We have been able to make strides in this direction because
of the unique environment the RCSB offers in terms of personnel, hardware,
software and network infrastructure."
While July 1 officially marks the end of the management transition, users
have already taken advantage of the RCSB's enhancements. Depositors, who
rely upon the PDB to take their data and place it in a standardized format
accessible to all types of scientists, have had their data processed by the
RCSB since Jan. 27. New deposition tools have made submitting data to the
PDB easier and faster, and RCSB annotators have been processing the data to
completion within a few days, as compared to months previously.
The RCSB has also introduced an interface that allows depositors to create
reports from a variety of tools to aid in structure evaluation. Researchers
and students have been searching the PDB and generating specialized reports
by utilizing the new tools released by the RCSB since Feb. 3. The versatile
reporting capabilities available for individual structures and across the
PDB archive include Structure Explorer pages that highlight the features of
a structure, quickly formatted reports on general and specific geometrical
information, structure comparisons to find all similar structures, and a
variety of molecular graphics.
The end of the transition is marked by a few final changes invisible to
most users. For depositors, new deposits should now be made with the RCSB's
ADIT tool. For other users, the older PDB
Web address will be automatically redirected to the current RCSB site. RCSB
will now support the older FTP file structure so existing mirror sites will
be able to maintain operation. New mirror sites will use the improved
RCSB FTP file structure.
The PDB is supported by funds from the National Science Foundation, the
Office of Biology and Environmental Research at the Department of Energy,
and two units of the National Institutes of Health: the National Institute
of General Medical Sciences and the National Library of Medicine.
# # #
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information about SDSC, contact David Hart at SDSC,
(619) 534-8314, or .
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RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics: Rutgers and UCSD/SDSC
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National Science Foundation, the
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