Status of PDB WWW Mirrors

RCSB PDB Mirrors

In addition to the existing RCSB mirrors at Rutgers and NIST, over the past few months the RCSB PDB has been working to establish a world-wide set of mirrors. Our immediate focus is to establish a relatively small number of mirror sites at strategic locations around the globe.

The first set of www mirrors will include sites in Brazil (Universidade Federal de Minas Gerais), Singapore (BioInformatics Centre, NUS), United Kingdom (Cambridge Crystallographic Data Center) and Japan (Institute for Protein Research, Osaka University). Most of these sites are now partially or fully established and are in the final stages of testing before their web site addresses are made accessible to the PDB user community. Notification to the community as to when these sites are publicly available will be made on the PDB web site and PDB discussion list.

Our current expectation is that it will not be necessary to provide as many RCSB PDB WWW mirrors as BNL PDB WWW mirrors in order to achieve good PDB access in all parts of the world. The situation will be evaluated once this first tier of mirrors is fully established and operating in a routine manner.

BNL PDB Mirrors

Prior to the shutdown of Brookhaven National Laboratory on June 30, 1999, all the official BNL PDB mirror sites were notified that the RCSB would provide the means for them to continue their key activities as (a) repositories of the PDB entries and (b) providers of query capability.

To facilitate the continuation of these services, these sites were provided with information on accessing the RCSB maintained copy of the FTP archive (ftp://bnlarchive.rcsb.org/) with the same structure as BNL's PDB FTP archive. Access to this archive allows these sites to continue to update their structure entries with only minimal changes to their mirroring scripts. In addition, these sites were provided with a static Web page to launch the 3DB/PDBLite and to link to RCSB resources.

The RCSB's intention in this process was to provide the BNL PDB's mirrors with a simple path, requiring minimal ongoing effort to continued operation.

Of the 17 official BNL PDB web site mirrors, 11 sites changed their PDB home pages to the page supplied by the RCSB, and most of these sites have been updating their structure holdings on a weekly basis. All but two of these sites (the two US mirrors) have continued to offer the 3DB/PDBLite query capability from this Web page.

The PDB mirrors that have changed their Web sites from the BNL to the RCSB-created page are:

Argentina

  • University of San Luis, http://pdb.unsl.edu.ar/, Australia
  • ANGIS, http://molmod.angis.org.au/pdb/
  • The Walter and Eliza Hall Institute of Medical Research, Melbourne
    http://pdb.wehi.edu.au:8181/pdb/, France
  • Institut de Genetique Humaine, Montpellier, http://pdb.igh.cnrs.fr/

India

  • Bioinformatics Centre, University of Pune, http://202.41.70.33/

Israel

  • Weizmann Institute of Science, Rehovot, http://pdb.weizmann.ac.il/

Taiwan

  • National Tsing Hua University, HsinCh http://pdb.life.nthu.edu.tw/

United Kingdom

  • Cambridge Crystallographic Data Centre, Cambridge, http://pdb.ccdc.cam.ac.uk/
    EMBL Outstation
  • European Bioinformatics Institute, Hinxton http://www2.ebi.ac.uk/pdb/

United States

  • Bio Molecular Engineering Research Center, Boston University, Massachusetts, http://www.pdb.bu.edu/
  • North Carolina Supercomputing Center, Research Triangle Park, North Carolina, http://pdb.ncsc.org/

It should be emphasized that although these sites are offering a valuable service, they are not RCSB PDB mirrors. The RCSB's only role in their operation is to provide access to the data that they need to continue. The level of performance of these sites may vary and is outside the RCSB's control. For example, Eric Martz lists a smaller subset of sites at http://www.umass.edu/microbio/rasmol/pdblite.htm that appear to be maintaining a fully functional PDBLite.