Number 1January 1999 RCSB
Published quarterly by the Research Collaboratory for Structural Bioinformatics

January 1999

9176 Released atomic coordinate entries

Molecule Type

  • 8143 proteins, peptides, and viruses
  • 381 protein/nucleic acid complexes
  • 643 nucleic acids
  • 12 carbohydrates

Experimental Technique

  • 206 theoretical modeling
  • 1452 NMR
  • 7521 diffraction and other
  • 2424 structure factor files
  • 522 NMR restraint files

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Welcome from Helen M. Berman
Welcome to the first newsletter of the Research Collaboratory for Structural Bioinformatics (RCSB) for the Protein Data Bank (PDB). As you all know, the management of the PDB has changed from Brookhaven National Laboratory (BNL) to the RCSB. [MORE...]

The Members of the RCSB
The RCSB is a non-profit consortium dedicated to improving our understanding of the function of biological systems through an understanding of 3-D biological macromolecular structure. [MORE...]

Current and Future Status of the PDB
Data Processing, Query, and Distribution. On January 27, 1999, the RCSB became responsible for the processing of all data received by the PDB. BNL will be responsible for processing the files received prior to January 27, 1999. For now, the process of depositing data will not change. Crystal structures of proteins and all NMR structures should be deposited using the either AutoDep or the PDB Deposition Form. [MORE...]

mmCIF and PDB formats in the RCSB PDB
The RCSB will continue to accept and distribute coordinates in the mmCIF and PDB formats. The PDB format released by the RCSB will be uniform, and will continue to utilize the four character PDB identifier. Internally, the RCSB uses the macromolecular Crystallographic Information File (mmCIF) format to process data. [MORE...]

RCSB PDB Meetings and Presentations
Presentations planned for 1999. Presentations September 1998 - January 1999. Discussion of the RCSB PDB held December 13, 1998, in Asilomar, CA. [MORE...]

New PDB Web Tools
SearchLite, ADIT, and Validation Server. When a user accesses the PDB through the World Wide Web there is a query and a subsequent result. This is shown on the left- and right-hand side of Figure 1, respectively. Each of these two components will evolve with every new release of the Web interface. [MORE...]

The PDB E-Mail Discussion Group
As of Febcuary 3, 1998, the PDB e-mail discussion group (the PDB listserver) will be maintained by the RCSB PDB staff. At this time all messages should be posted to the RCSB listserver and postings to the BNL listserver should cease—i.e., people should discontinue using the BNL PDB list and listserver addresses.

Linking to the PDB through your Browser
Articles in this newsletter have described the search query capabilities currently available at the RCSB PDB site and have given a glimpse of more extended capabilities that will become available in the future. However, a PDB user with a web resource may wish to build structure retrieval mechanisms into the resource web pages.

OMG Requests User Input Regarding CORBA Protocol Specification for Macromolecular Structure
On January 15, 1999, the Object Management Group (OMG), a non-profit industry consortium which oversees CORBA specifications, voted to issue a Request For Information (RFI) in the area of macromolecular structure. This is the first step in a process to create an official CORBA specification detailing internet access methods for PDB data. [MORE...]

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© 1999 RCSB