RCSBPDB Newsletter
Number 4Winter 1999 RCSB
Published quarterly by the Research Collaboratory for Structural Bioinformatics

December 21, 1999

11,317 Released atomic coordinate entries

Molecule Type

  • 10044 proteins, peptides, and viruses
  • 487 protein/nucleic acid complexes
  • 768 nucleic acids
  • 18 carbohydrates

Experimental Technique

  • 9263 diffraction and other
  • 3277 structure factor files
  • 1800 NMR
  • 681 NMR restraint files
  • 254 theoretical modeling

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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