New collaborative agreement to establish Worldwide Protein Data Bank

New Brunswick 21 November 2003The Research Collaboratory for Structural Bioinformatics (RCSB), the Macromolecular Structure Database at the EMBL-European Bioinformatics Institute (MSD-EBI), and Protein Data Bank Japan (PDBj) have signed a collaboration to form the Worldwide Protein Data Bank. An announcement of the agreement appears in the December issue of Nature Structural Biology.


The Protein Data Bank (PDB), an international resource for biomedical research with facilities at Rutgers, The State University of New Jersey, has become the focus of an international collaborative agreement. The agreement establishes the Worldwide Protein Data Bank (wwPDB) and, in doing so, ensures a single, uniform and enduring archive of three-dimensional models of biological structures, proteins specifically.

"The PDB is an important tool for biomedical and pharmaceutical researchers and a critical asset to 21st century genomic research and drug design", stated Rutgers Board of Governors Professor of Chemistry and Chemical Biology Helen M. Berman, director of the Protein Data Bank. "The agreement ensures and simplifies access to this important source of information for researchers worldwide."

The collaboration reflects the growing international and interdisciplinary nature of scientific research, and formalizes the global character of the Protein Data Bank (PDB), which has been used as an international resource for the collection and sharing of three-dimensional information on proteins and other large molecules since its inception 32 years ago. The formation of the wwPDB will be transparent to users and will ensure the overall quality and consistency of data directly available through the PDB.

"By providing a formal mechanism for standardizing the presentation of PDB data, software developers and users of the data will be assured of consistent data. At the same time, it is hoped that this wwPDB will allow for individual creativity in how the data are presented and made available to the community", stated Helen Berman.

The archived structures represent an increasingly large fraction of all the molecules of life - ones that will interact with new drugs being designed. These large molecular structures are determined by the most modern experimental methods, including X-ray crystallography, NMR spectroscopy and cryo-electron microscopy.

Kim Henrick, head of the MSD-EBI, stated: "The PDB is a canonical research resource that transcends both scientific and political boundaries. The wwPDB agreement among the three equal partners elevates the responsibility for the deposition and accessibility of the data to a global level. The EBI has been a longtime deposition site and advisor to the PDB and the evolution of that role is a welcome development."

The Research Collaboratory for Structural Bioinformatics (RCSB), of which Rutgers is a member; the Macromolecular Structure Database at the European Bioinformatics Institute (MSD-EBI); and the Protein Data Bank Japan (PDBj) will maintain sites through which new protein data may be deposited and processed. The processed data will be forwarded to the RCSB and entered into a data bank archive by the RCSB: the "archive keeper" with sole direct access to the database and control over its directory structure and contents.

Head of the PDBj group at the Institute for Protein Research in Osaka University, Haruki Nakamura stated: "The PDBj has become the representative for the PDB throughout Asia and Oceania. With the recent explosion of interest in structural biology and bioinformatics research in the region, which would not be possible without the PDB, it is a natural step for us to formalize our involvement through the wwPDB."

Prior to the agreement, RCSB members including Rutgers, the San Diego Supercomputer Center at the University of California, San Diego and the Center for Advanced Research in Biotechnology of the National Institute of Standards and Technology, managed the PDB. The PDB is the single archive of biological macromolecular structure data, which is made freely and publicly available to researchers, educators, and students.

Worldwide, the PDB receives over 60 million hits per year. As of October 28, 2003, it contained 22.984 structures, a number that has been growing exponentially. According to a 10-year agreement signed by the 3 founding members of the wwPDB, the sites will share responsibilities in data deposition, data processing, and distribution. An international advisory board will be formed to support the collaboration. The PDB is supported by funds from the National Science Foundation, the Department of Energy and the National Institutes of Health.

Leslie Versweyveld

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