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Message From the PDB
PDB News
Citing the PDB
A journal reference is now available for
citing the PDB:
H.M.Berman, J.Westbrook, Z.Feng, G.Gilliland, T.N.Bhat, H.Weissig, I.N.Shindyalov, P.E.Bourne,
The Protein Data Bank, Nucleic Acids Research, 28 pp. 235-242 (2000)
Availability of PDB Services December 31, 1999, through January 3, 2000
The PDB has taken all reasonable precautions to ensure the
software and hardware supporting our operations are Y2K compliant. [MORE...]
PDB Newsletter - Final Advisory
Based on feedback from the
September 1, 1999, Advisory Notice, the PDB plans to discontinue the printed Newsletter starting with the 4th quarter issue for 1999.
The Newsletter will continue to be available from the Web site in HTML format and a text version will continue to be emailed to those
people subscribed to the Newsletter list. A printed Annual Report will summarize the past year's events. Final comments on this
change were mailed to info@rcsb.org up to December 15, 1999.
PDB at the Biophysical Society Annual Meeting
The PDB will have an exhibition booth at the Biophysical Society 2000 Meeting in New Orleans, LA from
February 13-15. Please stop by and say hello!
New Building for the Rutgers University PDB Team
The PDB team at Rutgers University has moved into a newly renovated building located on Rutgers University's
Busch Campus. [MORE...]
One-Year Anniversary of RCSB PDB Grant Award
One year has passed since the Research Collaboratory for Structural Bioinformatics (RCSB) was awarded the grant to manage the
Protein Data Bank (PDB). We are pleased to report that our initial goals have been met, and in many cases surpassed, with the help
and support of the PDB community. [MORE...]
Data Deposition, Processing and Uniformity
Data Deposition and Processing Summary
From January 27, 1999 - December 1, 1999, 1994 structures were deposited with the RCSB. On average,
these structures are processed and returned to the author in less than ten days. [MORE...]
Data Uniformity
The Data
Uniformity project, whose goal is to make the archive as consistent and error-free as possible, is being accomplished by using two
methods: "file by file" and "batch." [MORE...]
Completion of Layer 1 Entry Processing
Starting next week and continuing until the end of the year, the fully processed versions of the PDB
Entries currently classified as "Layer 1" will be released. [MORE...]
Processing of Backlog Structures Completed
Processing of the backlog structures inherited at the time of the PDB transition has been completed by the RCSB.
These 458 structures arrived at the RCSB PDB in various stages of processing on July 1, 1999.
[MORE...]
PDB Format Changes Implemented
Starting November 30, all
files released by the PDB will reflect the changes listed below. A full description and explanation is available in the summary of
comments on PDB Change Advisory Notice that was announced on October 13, 1999. [MORE...]
Data Distribution and Query
Data Distribution
Data in the form of PDB files continue to be distributed once per week and become available no later than 1:00 am PST each
Wednesday. [MORE...]
New CD-ROM of PDB Holdings Now Available
Issue 90 of the PDB CD-ROM Sets, which includes PDB structures deposited before October 1, 1999, is now
available for on-line orders. In addition to ordering Issue 90, you can place orders for the four issues of 2000. The CD-ROM sets
are provided at no charge. Issue 91 will be available by February 2000. With Issue 90, all the NMR Constraint files have been added
to the CD-ROMs; the PDB Newsletter is also included in both text and PDF format.
PDB Opens Beta Test Site
The PDB has opened a beta test site in order to present new developments to the user community for evaluation before they appear
on the other public PDB sites. All PDB users are invited to participate in testing the new features that appear on this site.
[MORE...]
New RCSB PDB Mirrors in Japan and Singapore
RCSB
PDB mirrors at Osaka University, Japan and
the National University of Singapore, Singapore are now available. These two new mirror
sites and the other RCSB PDB mirrors are listed here.
European RCSB PDB Mirror Site Established
A mirror of the RCSB PDB Web site is now available from the
Cambridge Crystallographic Data Center in the United Kingdom. Information about this new
site and the other RCSB PDB mirror sites is available here.
Redirection of Traffic from the BNL PDB Site
Since
the shutdown of the BNL PDB site on June 30, 1999, any user attempting to access the BNL PDB Web or FTP addresses has been
automatically redirected to the appropriate RCSB PDB address. Although we will endeavor to keep this redirection in place as long
as possible, this matter is not entirely under our control and there is a possibility that it may cease in the near future. We
strongly recommend that all users of the PDB update any links in web documents, software and personal bookmarks at this time so as
to avoid the possibility of a discontinuity in service.
Recent Additions to the PDB Web Site
Documentation and information provided on the PDB Web site is constantly evolving in response to user requests and questions
received through the PDB help service. Significant recent additions to the Web site are the provision of data on the
growth of the PDB, the
education page, and the list of new
features to try on the beta test site.
New Visualization Applications on the PDB Web Site
The First Glance and
Protein Explorer applications, initially provided on the
PDB beta site, have now been added to the production Web sites. Both of these
applications are implemented as View Structure options on the Structure Explorer pages and make use of
Chemscape Chime. A description of these new applications is
available here.
Outreach Activities
Two Workshops on Structural Genomics
The PDB actively participated in two workshops held at Argonne National
Laboratory in November. These workshops brought together researchers who are actively working in the fields of bioinformatics,
high-throughput cloning, expression and purification, protein crystallization, protein structure determination and validation,
protein structure prediction, and databases. [MORE...]
New Web Site for Synchrotron Users
A new Web site is in place to
put at researchers' fingertips detailed information on US synchrotron beamlines for macromolecular crystallography. The National
Institutes of Health Division of Research Resources (NCRR) has funded the National Biomedical Computation Resource (NBCR), centered
at the San Diego Supercomputer Center, to develop a Web site for BioSync, the Structural Biology Synchrotron Users Organization.
[MORE...]
Hand-Held Models of Proteins
The opportunity exists for the
PDB, thanks to the National Science Foundation sponsored TeleManufacturing Facility at the San Diego Supercomputer Center directed
by Mike Bailey, to produce and distribute free approximately six solid models of proteins each week. The sturdy models produced
on a rapid prototyping device are approximately 4-6 inches3 and show good surface detail.
[MORE...]
RFP for CORBA Standard for Biological Macromolecular Structure Data
For the past several months RCSB has been active in the Object Management Group (OMG), the non-profit organization responsible
for the Common Object Request Broker Architecture (CORBA). [MORE...]
RCSB Staff & Statement of Support
© 1999 RCSB
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Winter 1999 