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Celebrating 10 Years of the wwPDB

Celebrating 10 Years of wwPDB

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Click on the birthday cake for a slideshow of wwPDB milestones through the years.

July 1st 2013 marks the 10-year anniversary of the founding of the wwPDB, the international collaboration that manages the PDB archive.

From modest beginnings

Starting from just 7 protein crystal structures in 1971, the PDB archive has grown rapidly over the past 42 years. Last year alone, 9,972 new structures were deposited, more than in the first 25 years of the PDB combined. Today, the archive contains over 90,000 structures and at its current rate of growth will reach the 100,000 structure mark in 2014, the International Year of Crystallography.

On July 1st 2003, the way in which the PDB archive was managed was transformed by the founding of the Worldwide Protein Data Bank organization. From its inception, the PDB has been an international archive and the establishment of the wwPDB ensured that these valuable data will continue to be stored, managed and kept freely available for the benefit of scientists worldwide.

The wwPDB organization nowadays consists of four partners: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) and BioMagResBank (BMRB) in the USA, Protein Data Bank in Europe (PDBe), and Protein Data Bank Japan (PDBj).

wwPDB activities

The wwPDB partner sites each act as deposition, processing and distribution centres for PDB data. They work together and in consultation with the wider community to define deposition and annotation policies, file formats and validation standards for structural data. This close collaboration between the member organizations is vital to guarantee that the global community of PDB users is provided with reliable and consistent data.

While working jointly on all aspects of data representation and processing, each partner site also offers independent tools and services that help make the wealth of data about biomacromolecular structure and function easily accessible to the user community.

wwPDB activities are overseen by an international advisory committee comprising of experts in X-ray crystallography, 3DEM, NMR, and bioinformatics.

Future Challenges

The increasing volume, diversity and complexity of biological data being deposited in the PDB and the emergence of hybrid techniques to obtain structural insights into biologically relevant molecules, complexes and molecular machines all present major challenges for the management and presentation of structural data.

To address these challenges, the wwPDB partners are jointly developing a software system that will allow deposition, validation and annotation of complex and diverse macromolecular structures along with the underlying experimental data using a single interface. This new system will go into full production at all the wwPDB deposition sites early in 2014 and will be able to handle depositions of structures of any size, determined using diffraction, NMR and/or EM methods.

Validation will be an integral part of the new deposition and annotation system. Assessment of coordinates, experimental data and associated meta data at the time of deposition is vital for improving the quality of the archive. In addition, it will help users with no or limited structural biology background to select the most appropriate structural models for their purposes.

Whatever new challenges the next 10 years will bring, the wwPDB will remain committed to maintain high standards of quality, integrity and consistency of the macromolecular structure archive and to make it freely available to an increasingly large, diverse and demanding global community of users.

(1) Announcing the worldwide Protein Data Bank. Berman H, Henrick K, Nakamura H. Nat. Struct. Biol. 10, 980 (2003) doi:10.1038/nsb1203-980

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2013-07-02 (last edited: more than 1 year ago)2013-08-06
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