June 30, 1999, was the day that the address http://www.rcsb.org/ became the single home of the Protein Data Bank. All queries to the old BNL-PDB are being redirected to the new site. This final step marked the end of the transition period that began in October 1998, for the RCSB to assume responsibility for the PDB. During this time, features of the RCSB-PDB were introduced as the BNL-PDB was phased out. The ultimate goal of the transition period was to make these changes as seamless as possible.
What did this entail? It meant introducing a new deposition tool while not abruptly discontinuing the older one. The AutoDep Input Tool (ADIT: http://pdb.rutgers.edu/adit/) was introduced by the RCSB in April and has been extensively utilized. AutoDep was kept online at BNL and EBI, with the data deposited after January 26, 1999, successfully processed to completion by the RCSB staff. To ensure that depositors were not adversely affected by the BNL closing, the RCSB ported a version of AutoDep and the current BNL AutoDep sessions to its site.
The transition also meant coordinating with the BNL team, who continued to process structures in the queue as of January 26, 1999. Every Monday, the two sets of structures and updated status information were combined and sent to SDSC for distribution.
At SDSC, the distribution team uploaded the data into the database and into two FTP servers. Again, the RCSB team has attempted to minimize the disruption to the community. The original BNL-style FTP archive is maintained at ftp://bnlarchive.rcsb.org/ and a new and simpler RCSB-style ftp archive is available at ftp://ftp.rcsb.org/.
The past few months have also found the RCSB staff cataloging the PDB paper files and magnetic media that have been stored at BNL since 1971. These data have been moved to NIST where the master archive is maintained.
Most importantly, the transition period was a time for the RCSB to tell the community what we were doing via e-mail lists, newsletters, meetings, and workshops. Our goal was to eliminate any possible surprises and to keep open the lines of communication. To this end, we have changed the PDB network address so that all PDB traffic is sent to the RCSB.
None of this could have been accomplished without the dedication of the project teams and the institutional support at the RCSB sites -Rutgers, SDSC, and NIST. We are indebted to the countless conversations and e-mails from the members of the community offering suggestions, advice, and questions. We are especially appreciative of the efforts of our beta testers, the PDB Advisory Board, Herb and Frances Bernstein, and the dedicated efforts of the agencies that fund the PDB: the NSF, NIH, and DOE. Finally, the transition would not have been complete without the BNL group under the direction of Joel Sussman, who worked until the last day to make sure the PDB would endure as the single archive of macromolecular structures. Special thanks also go to Regina Shea and John McCarthy for their contributions.
We look forward to working with you in the years to come, and will welcome your input to help maintain the integrity of the resource and to make it a vital and enabling technology for biology.
The RCSB Project Leaders
Helen M. Berman
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.