The paper describes the goals of the Protein Data Bank (PDB) and the systems in place in 2000 for data deposition, processing, distribution, and query.

The PDB archive of biological macromolecules has been in existence since 1971. In 1998, the management was moved from Brookhaven National Laboratory to the Research Collaboratory for Structural Bioinformatics (RCSB). This is the first paper that discusses the work of the RCSB PDB.

At that time, we had created new systems for managing all aspects of the data pipeline. New tools were available for users to validate and deposit their structures. The RCSB PDB website supported a database that could be used to search and report on the archive. This paper also describes the beginnings of our "data uniformity" project that eventually developed into an international collaboration to make the entire archive uniform. The worldwide PDB (wwPDB) just released the remediated archive this summer!

The RCSB PDB is currently managed by two members of the RCSB: Rutgers, The State University of New Jersey and the University of California, San Diego. It is supported by funds from the National Science Foundation, the National Institute of General Medical Sciences, the Office of Science, Department of Energy, the National Library of Medicine, the National Cancer Institute, the National Center for Research Resources, the National Institute of Biomedical Imaging and Bioengineering, the National Institute of Neurological Disorders and Stroke, and the National Institute of Diabetes and Digestive and Kidney Diseases.

Using the RCSB PDB systems, it is possible to access and download the coordinate files, query the database about specific features of the data, create reports about groups of structures, access summaries of individual structures, visualize the structures using different tools, browse the database for information that has been integrated from other data resources, and access educational materials for learning about biological molecules. The Molecule of the Month feature in particular is very useful for teachers and students.

The PDB is used by many people: structural biologists who contribute and access structural data; biologists who need a molecular explanation for their research findings; computational biologists who are developing methods for relating sequence, structure, and function; pharmaceutical companies who use the data for drug discovery; teachers and students in K-12, as well as undergraduate and graduate teachers and students.

The PDB is a very heavily used resource. Depositions have increased from a few per month to more than 7,000 per year. Usage of the ftp site is very heavy—more than 6,235,000 files were downloaded in June 2007 alone. When people deposit data or when they use the resources of the RCSB PDB, they cite the 2000 paper.

The PDB archive has been under continuous development. One striking change is the globalization of data deposition and distribution services. In contrast to the earlier days of the PDB, data are now deposited at three data centers: RCSB PDB, Macromolecular Structure Database at the EMBL's European Bioinformatics Institute (MSD-EBI), and Protein Data Bank Japan (PDBj). In 2003, these centers formed the wwPDB to ensure that the PDB archive would continue to be single and uniform. The BioMagResBank joined the wwPDB in 2005. Each week, the data centers forward data to the RCSB PDB (the "archive keeper") for release into the PDB archive at ftp://ftp.wwpdb.org. Each wwPDB site has a website that offers different views of the underlying data.

Another development has been the remediation of the archive by the wwPDB. This project worked to remove inconsistencies, update and check data, and to utilize the IUPAC-standard nomenclature. The release of these data makes the PDB archive even more useful—the more uniform the data are, the more powerful and accurate the searches can be.

The RCSB PDB site has grown both in terms of the underlying architecture and in terms of improved query and browsing functionality since the publication of that 2000 paper. The underlying database was reengineered in 2006, and again in 2007 to support the remediated data. New features and resources are continually being developed to support our broad community of users.

Yet much of our work as described in that paper is still current. We still find the times to be exciting and challenging, and depend heavily on user input to improve the resource. When that paper was written, the archive held approximately 10,500 structures, and we thought that it could triple or quadruple in five years. Seven years later, there are more than 45,000 structures, with individual structures growing in size themselves. We look forward to what challenges the coming years will bring.

Helen M. Berman, Ph.D.
Chemistry and Chemical Biology Department
Rutgers University
New Brunswick, NJ, USA