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What is the Worldwide Protein Data Bank?

According to their website, the Worldwide Protein Data Bank (wwPDB) is the one and only resource for protein, nucleic acid and complex assembly data. Below introduces the history, benefits and purpose of this unique scientific establishment.

Overview

The wwPDB is the result of an ongoing global collaboration between various scientists, researchers and students. The wwPDB manages the processing, maintenance and distribution of the data archive. The online archive is a repository that contains key information for almost 40,000 organic structures, such as proteins, nucleic acids and macromolecular complexes. These structures are analyzed through NMR, electron microscopy and X-ray crystallography techniques. The founding members of the wwPDB are actually an amalgamation of independent national organizations that include the United States’ RCSB PDB, Europe’s MSD-EBI and Japan’s PDBj organizations. In 2006, the American BMRB group joined the wwPDB and in 2006, the University of Wisconsin-Madison’s BioMagResBank (BMRB) became the newest member. The purpose of the wwPDB is to maintain a centralized archive of macromolecular structural data that is openly available to international communities.

A Brief History

The protein data bank was established in the early 1970’s in an effort to provide a repository for 3D structural data of experimental biological macromolecules. The protein data bank contains detailed information about the target item’s chemical content, such as ligand chemistry and polymer sequencing, and qualitative descriptions of the experimental process that was used to identify the structure.

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In the beginning, the protein data bank consisted of only seven data structures composed of physical texts. Today, the archive has almost contains 40, 000 structures that are carefully cataloged and categorized from international contributors. Regardless of location, all contributors follow standardized formatting and structural content specifications. All international organizations that make up the international protein data bank share responsibilities for the deposition, processing and distribution of the data archive.

Data Access and Responsibilities

The data archive is a collection of files that are submitted in three proprietary formats: the original PDB file format, the mmCIF syntax and the PDBML/XML format, which is a converted PDB exchange format. Each of the national PDB sites distributes an identical archive via FTP that is updated every week. In addition to this, screen snapshots of the archive are time stamped and added to a separate online archive. This provides a historical copy of the archive for research purposes. In addition to providing access to the local PDB archive, each site also provides research support through websites and databases that provide alternative views and contrasting analyses of the structural data. All members collaborate to ensure that the archive maintains uniformity through the PDB Exchange Dictionary that defines rules and procedures. This was accomplished through years of collaborative efforts to eliminate and correct errors. All member groups work together to improve the integrity of molecular data, to assess the accuracy of chemical definitions and the quality of official entry correspondences.

The Worldwide Protein Data Bank is an acclaimed scientific accomplishment that is shared, prompted and managed by international researchers.