News Archive

RCSB To Assume Responsibility for the Protein Data Bank Ahead of Schedule

Published 03/19/1999

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 data.

Query and distribution of the data are available at the RCSB Web site ( and ftp archive ( 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

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 ( 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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