wwPDB 2003 News





Today the Research Collaboratory for Structural Bioinformatics (RCSB), the Macromolecular Structure Database at the EMBL's European Bioinformatics Institute (PDBe), and Protein Data Bank Japan (PDBj) announced a collaboration to form the Worldwide Protein Data Bank (wwPDB; www.wwpdb.org). The announcement is published in the December issue of Nature Structural Biology [H.M. Berman, K. Henrick, H. Nakamura (2003): Announcing the worldwide Protein Data Bank. Nature Structural Biology 10 (12), p. 980].

The collaboration reflects the growing international and interdisciplinary nature of scientific research, and formalizes the global character of the 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," said Helen Berman, director of the RCSB PDB and Board of Governors Professor of Chemistry at Rutgers, The State University of New Jersey.

Kim Henrick, head of the PDBe said, "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."

Head of the PDBj group at the Institute for Protein Research in Osaka University, Haruki Nakamura said, "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."

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.