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Protein Data Bank Releases 100,000th Structure

14 May, 2014

Protein Data Bank

The Worldwide Protein Data Bank (wwPDB) is proud to announce that it has today released its 100,000th biological molecular structure to the community. Established in 1971, this central, public archive of experimentally-determined protein and nucleic acid structures has reached this important milestone thanks to the efforts of structural biologists all over the world. The Wellcome Trust is a supporter of the Protein Data Bank and to mark this occasion, Gary Battle, from PDB Europe and Tom Collins, from the Wellcome Trust take a look at how it has grown into such a wonderful resource… 

2014 marks the centennial of the discovery of X-ray diffraction by Max von Laue and the father and son team of William Henry Bragg and William Laurence Bragg, and provides an opportunity to look back on how the sharing of structural information has been fundamental to enabling scientific discovery. The landmark 100,000th entry into the Protein Data Bank (PDB) comes fittingly within the International Year of Crystallography (IYCr).

The PDB contains and supports online access to more than 100,000 structures of biological macromolecules and complexes. The resource is accessed hundreds of millions of times every year by researchers, students, and educators wishing to explore how different proteins are related to one another, to clarify biological mechanisms and to develop new medicines.

“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,” comments Nobel laureate Venki Ramakrishnan of the MRC Laboratory of Molecular Biology in Cambridge, UK.

The PDB was established in 1971 with just seven structures as an international collaboration to provide both a home and an access point to these information-rich structures. It is a testament to the vision and foresight of the pioneers in the field that they understood the value and potential of archiving and sharing data in an era when computer networking was virtually non-existent.

Since its inception, the PDB has grown rapidly. The size of the archive has increased by a factor of 10 approximately every 10-15 years: the PDB reached 100 released entries in 1982, 1000 entries in 1993, and 10,000 in the year 2000. As we pass the 100,000 structure milestone, ~90% of the archive will have been released in the past 14 years.

Screen Shot 2014-05-14 at 12.21.41

Growth of the number of structures available in the PDB through May 14, 2014, with selected examples. Early structures included myoglobin (1), the first structure solved by X-ray crystallography, and small enzymes (2). As the methodology, software and instrumentation developed, the archive rapidly grew to host examples of tRNA (3), viruses (4), antibodies (5), protein-DNA complexes (6), ribosomes (7), and chaperones (8).

The way in which the PDB archive was managed was transformed in 2003, with the founding of the Worldwide Protein Data Bank organisation. From the beginning, the PDB has been an international archive and the establishment of the wwPDB ensured that these valuable data would continue to be stored, managed and kept freely available for the benefit of scientists worldwide. The wwPDB organisation nowadays consists of four partners: the Protein Data Bank in Europe (PDBe), the Protein Data Bank Japan, and the Research Collaboratory for Structural Bioinformatics Protein Data Bank and BioMagResBank in the USA.

PDBe, based at the European Bioinformatics Institute (EMBL-EBI) in Hinxton, UK, has benefited from Wellcome Trust funding since 1996. This continued support has ensured that this vital resource remains freely available to an increasingly large, diverse and demanding global community of users.

Free and open data sharing, which is enabled by projects such as the PDB, is an example of the Wellcome Trust’s efforts to maximise the distribution of results from the scientific research that it funds, thereby ensuring that the current knowledge base can be effectively built on in the future

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