NEW BRUNSWICK/PISCATAWAY, N.J. – 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 biology."
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 molecules.
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 Protein Data Base 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 Protein Data Base. 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 avariety 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 (see: http://pdb.rutgers.edu/). For other users, the older Protein Data Base 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 (see: http://ftp.rcsb.org/).
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.
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. 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. The university encompasses 29 degree-granting schools on three regional campuses andincludes more than 100 specialized research institutes. For more information, visit http://www.rutgers.edu.
The San Diego Supercomputer Center (http://www.sdsc.edu/) is a research unit of the University of California, San Diego, and the leading-edge site of the National Partnership for Advanced Computational Infrastructure (NPACI, http://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 David Hart at SDSC, (619) 534-8314, or [email protected]
As a nonregulatory agency of the Department of Commerce's Technology Administration, NIST promotes U.S. economic growth by working with industry to develop and apply technology, measurements and standards through four partnerships: the Measurements and Standards Laboratories, the Advanced Technology Program, the Manufacturing Extension Partnership, and the Baldrige National Quality Program. Visit http://www.nist.gov/. For additional information about NIST contact Linda Joy at NIST, (301) 975-4403, or [email protected]
NOTE TO REPORTERS: Dr. Helen Berman can be reached at (732) 445-4667 or (732) 445-0103 for interviews.
The above story is based on materials provided by Rutgers, The State University Of New Jersey. Note: Materials may be edited for content and length.
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