RCSB logoPDB Newsletter
Number 2April 1999 -- RCSB
Published quarterly by the Research Collaboratory for Structural Bioinformatics

April 1999

9631 Released atomic coordinate entries

Molecule Type

  • 8551 proteins, peptides, and viruses
  • 403 protein/nucleic acid complexes
  • 655 nucleic acids
  • 12 carbohydrates

Experimental Technique

  • 214 theoretical modeling
  • 1504 NMR
  • 7913 diffraction and other
  • 2716 structure factor files
  • 527 NMR restraint files

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The Research Collaboratory for Structural Bioinformatics (RCSB) is a non-profit consortium dedicated to improving our understanding of the function of biological systems through a study of 3-D biological macromolecular structure.

Welcome from Helen M. Berman
Welcome to the second Research Collaboratory for Structural Bioinformatics (RCSB) newsletter. The communication with PDB users and the development of RCSB PDB tools has made the past several months very exciting. We really appreciate your feedback, which guides the further development of the system. [MORE...]

Summer Events
The PDB will have an exhibition booth at the IUCr meeting to provide computer demonstrations of the query and deposition software, and to meet with PDB users.. [MORE...]

Transition Update
Due to the advances made by the PDB project in data deposition and processing, and query and distribution, the RCSB will be taking over complete responsibility for the PDB starting July 1, 1999. [MORE...]

Structure Validation at the RCSB PDB
Introduction to Structure Checking by the RCSB
In order to provide the community with high quality data, the RCSB has developed a number of tools that are used to deposit and process X-ray and NMR structures. Deposition is accomplished through ADIT, which collects all the information necessary for data processing. Data processing involves checking various aspects of the structure and the data collected through ADIT. [MORE...]

Phase II of PDB Query
RCSB plans call for three releases of the PDB Web query interface in the first year of RCSB operation, that is through October 1, 1999. Phase I provided a simple text search interface called SearchLite, as described in the previous newsletter. [MORE...]

A Fast Topology-Based Structural Comparison Service
Users are invited to use an updated release of a fast topology- based structural comparison service at http://tops.ebi.ac.uk/tops/compare.html. The service uses TOPS topology diagrams and patterns, and is part of the suite of programs available on the TOPS web-site at http://tops.ebi.ac.uk. [MORE...]

The Most Wanted Structures in the PDB
The BNL PDB Web logs from the last six months of 1998 were analyzed in order to determine which structures were the most broadly accessed. A structure was considered to be "broadly accessed" if it was frequently investigated across a spectrum of Web pages and activities, namely, saving the PDB file to disk in 3DB and PDB Lite, viewing the full coordinate set, and viewing the structure in RasMol and Chime. [MORE...]

Citing the Protein Data Bank
Several users of the PDB have recently asked what is the best way to cite structures that they have obtained from the PDB. In the same time-frame, some members of the crystallographic community have also expressed the concern that when a structure is downloaded from the PDB for analysis, it is sometimes the PDB rather than the workers who were responsible for the original structure determination that is referenced. [MORE...]

Developments in the PDB Newsletter
In the future, the RCSB PDB newsletter will carry submitted articles, such as Gilbert, Westhead, and Thornton’s article in this issue. [MORE...]

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