With this week's update, the PDB archive contains 99,624 entries and will soon pass the milestone of 100,000. In the weeks leading up to this event, wwPDB is looking back at other PDB milestones.
Through lively conversations, debates, and planning for the future, a community of structural biologists banded together to establish the PDB in 1971 at Brookhaven National Laboratory (1) as an archive for the experimentally-determined 3D structures of biological macromolecules. Today, the PDB archive is managed by the Worldwide Protein Data Bank (2), a unique collaboration of organizations that act as deposition, curation and distribution centers for PDB data (3). The wwPDB's mission is to maintain a single PDB archive of macromolecular structural data that is freely and publicly available to the global community (4,5).
In support of this mission, wwPDB works closely with the various communities that rely on the archive. wwPDB has convened Task Forces for  ,  ,  and  that bring together acknowledged experts in these fields to advise wwPDB on issues of method-specific validation, deposition and annotation. Their recommendations are implemented in wwPDB validation pipelines that are an integral part of the new  . produced by this pipeline have recently been released for all X-ray structures in the current archive; reports for NMR and EM structures will follow later.
Through a dedicated  , wwPDB works with software developers from the major macromolecular crystallographic software packages on the representation of large structures, complex chemistry, and new and hybrid experimental methods in the PDB. Recommendations about essential extensions to PDBx/mmCIF have been developed to accommodate large structures, and CCP4 and Phenix can now produce PDBx/mmCIF files suitable for deposition.
An international  , made up of experts in X-ray crystallography, 3DEM, NMR, and bioinformatics, advises the wwPDB and meets annually.
In addition, wwPDB reaches out to the wider community through symposia and publications. One notable event was the celebrating the 40th anniversary of the Protein Data Bank (PDB40) held at Cold Spring Harbor Laboratory, the intellectual birthplace of the PDB. Many distinguished speakers described structural biology's past, present and future. Selected presentations from this event are .
Recently, the wwPDB created a  in celebration of the International Year of Crystallography. This calendar is available for  .
Many publications describe the development and future of the PDB archive and wwPDB organization, including: How community has shaped the Protein Data Bank (), The future of the Protein Data Bank (), and Creating a Community Resource for Protein Science (). A full list is .
- Protein Data Bank. (1971) Protein Data Bank. Nature New Biol. 233: 223.
- H. M. Berman, K. Henrick, H. Nakamura. (2003) Announcing the worldwide Protein Data Bank. Nat Struct Biol 10: 980.
- H. M. Berman, G. J. Kleywegt, H. Nakamura, et al. (2013) The future of the protein data bank. Biopolymers 99: 218-222.
- H. M. Berman, G. J. Kleywegt, H. Nakamura, et al. (2013) How community has shaped the Protein Data Bank. Structure 21: 1485-1491.
- H. M. Berman, G. J. Kleywegt, H. Nakamura, et al. (2012) The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future. Structure 20: 391â€�396.Â
