RCSB to assume responsibility for the Protein Data Bank ahead of schedule
FOR IMMEDIATE RELEASE
Rutgers: Christine Zardecki
SDSC: David Hart
NIST: Linda Joy
NEW BRUNSWICK/PISCATAWAY, N.J. -- The timetable for the transition of the
Protein Data Bank (PDB) from Brookhaven National Laboratory (BNL) to the
Research Collaboratory for Structural Bioinformatics (RCSB) has been
accelerated. The RCSB will assume full responsibility for the NSF-funded
PDB on July 1, 1999 - a full three months ahead of schedule.
This progress is possible because all aspects of the project involving the
RCSB, from deposition of structural data, through query and distribution,
to long term archival and clean up of original data have proceeded smoothly
and because of the cooperation of the RCSB and BNL staff.
For structural data deposition, 300 files were processed by RCSB prior to
the changeover of data processing responsibilities on January 27, 1999.
Since then all files - 283 in all - have been processed using the ADIT
system developed by the RCSB. Virtually all files were fully processed,
reviewed by the depositors and put into final format within two weeks of
submission. As a result, it has been possible to abandon the need for
release of not-fully-processed files (Layer 1) in favor of higher quality
Query and distribution of the data are available at the RCSB Web site
(http://www.rcsb.org) and ftp archive (ftp://ftp.rcsb.org). Virtually all
PDB files designated for immediate distribution have been released within
two weeks of submission with the majority of files released within one
week. Both users and mirrors can access data from these sites. Phase I of
the Web query interface (SearchLite) provides convenient search and
analysis capabilities for one or more structures. Phases II and III, which
incorporate advanced query options, will appear in the coming months.
Mirror sites of the primary archive are currently available at Rutgers and
NIST; sites in Europe and Asia are planned.
Of the data in the PDB prior to the changeover of responsibilities, 2,300
entries have been reprocessed and put into the latest PDB format.
Consultations with the NMR community are ongoing to ensure better ways to
represent those data in the PDB.
Because of the success of these developments, the final date of the
transition is June 30, 1999. At that point the RCSB will have
responsibility for all PDB operations formerly carried out by BNL. It is
planned that after this date all access to the old BNL Web site will be
automatically redirected to the RCSB Web site.
The revised timeline for structure deposition -
* Now: At RCSB, the AutoDep Input Tool (ADIT), a new and improved
deposition system, is in the final phases of beta testing. AutoDep, the
original system developed by BNL, continues to be offered by BNL and the
European Bioinformatics Institute (EBI).
* April 15: Both AutoDep and ADIT will be available.
The revised timeline for query and distribution -
* Now: At RCSB, SearchLite is available for keyword-based searches. All
data are accessible via the Web and ftp.
* May: Advanced query and analysis available.
Up-to-date transition news can be found at
The members of the RCSB have been in collaboration with the EBI since its
inception. EBI has been accepting depositions and forwarding the data for
further processing to the US. It is likely that at some time in 1999 the
EBI will commence full processing of biological macromolecular structure
data. RCSB welcomes the advent of such an endeavor and expects to continue
to collaborate technically with this, and any other international group, to
help ensure full data exchange.
The RCSB's 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.
The RCSB is a consortium consisting of Rutgers University, San Diego
Supercomputer Center, and The National Institute of Standards and
Technology. 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 http://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
(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 Ann Redelfs at SDSC, (619) 534-5032,
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The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
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The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.