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Worldwide Protein Data Bank breaks 100,000 structures mark
The Worldwide Protein Data Bank (wwPDB), an international partnership which maintains a freely accessible archive of protein and nucleic acid 3-D structures, has announced that they have broken the 100,000 entry mark. The archive was established in 1971 but in recent years it growth has greatly accelerated. It has doubled in size since 2008 and currently releases approximately 200 new structures weekly.

The archive is made possible by the efforts of the scientific community who deposit their experimentally determined structures. Once submitted, each structure is carefully checked and curated by wwPDB staff. The value to the whole scientific community is maximised by addition of value-added annotations and linking to other important biological data to ensure that it is of use to a wide variety of scientists of different skills, interests and backgrounds. Nobel Laureate Venki Ramakrishnan of the MRC Laboratory of Molecular Biology in Cambridge, UK says: “The PDB is a critical resource for the international community of working scientists which includes everyone from geneticists to pharmaceutical companies interested in drug targets."

The archive is maintained by PDB data centres in the USA, the UK and Japan. It consists of the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB; at Rutgers, The State University of New Jersey and the San Diego Supercomputer Center (SDSC) and Skaggs School of Pharmacy and Pharmaceutical Sciences at the University of California San Diego and BioMagResBank (BMRB; at the University of Wisconsin in the USA, the Protein Data Bank in Europe (PDBe; at the EMBL European Bioinformatics Institute, and the Protein Data Bank Japan (PDBj; at Osaka University.

They ensure that the data are securely stored, expertly managed, and made freely available. They are advised by community experts in defining deposition and annotation policies, resolution of data representation issues, and implementation of community validation standards. The result is a resource that is accessed hundreds of millions of times every year by researchers, students and educators. They are able to inform themselves on how different proteins might be related as well as gaining insights into how form influences fundamental biological functions and mechanisms. The knowledge gained feeds into new discoveries in biomedicine, agriculture, and ecology.

The structures of myoglobin and haemoglobin were two of the first to be deposited with the PDB. This week, 219 more structures were deposited, bringing the total to 100,147 entries. There are challenges ahead for the wwPDB as the number of structures as well as size and complexity increases and new hybrid structure determination methods emerge. These use a variety of biophysical, biochemical, and modelling techniques to determine the shapes of biologically relevant molecules which present challenges for data management and representation. Building on its ethos of community-driven enterprise, the wwPDB will continue to strive to meet these challenges.


Press release: Rutgers University; available at
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