wwPDB Frequently Asked Questions
WHAT IS THE VISION AND MISSION OF THE WWPDB?
Vision: Sustain freely accessible, interoperating Core Archives of structure data and metadata for biological macromolecules as an enduring public good to promote basic and applied research and education across the sciences.
Mission:
- Manage the wwPDB Core Archives as a public good according to the FAIR Principles.
- Provide expert deposition, validation, biocuration, and remediation services at no charge to Data Depositors worldwide.
- Ensure universal open access to public domain structural biology data with no limitations on usage.
- Develop and promote community-endorsed data standards for archiving and exchange of global structural biology data.
WHAT IS THE PDB ARCHIVE?
The "PDB archive" is the collection of flat files in the PDBx/mmCIF format and, where possible, the legacy PDB file format. Each wwPDB site is distributing the same PDB archive.
HOW CAN I ACCESS THE PROTEIN DATA BANK ARCHIVE?
The RCSB PDB, PDBe, and PDBj serve as deposition, data processing and
distribution sites of the PDB Archive. Each wwPDB site provides its
own view of the primary data, thus providing a variety of tools and
resources for the global community.
HOW IS THE PDB ARCHIVE MANAGED?
The wwPDB members agree that the RCSB will be the
'archive keeper' and will have sole write access to the PDB
archive and control over the directory structure and contents.
The archive keeper distributes new PDB identifiers to all
deposition sites. The members of the
wwPDB will undertake to use PDB 4-letter codes as set out in the agreement.
The four-letter PDB identifier currently consists of
a number (0-9) followed by 3 letters or numbers.
The archival PDB files will be distributed with the reserved
conventional names, in the form pdbentry_id.ent, where
entry_id is a PDB 4-letter code, e.g. pdb1abc.ent, for PDB
format entries; rentry_idsf.ent, e.g. r1abcsf.ent, for X-ray
experimental data; entry_id.mr, e.g. 1abc.mr, for NMR
experimental/constraints; entry_id.cif, e.g. 1abc.cif, for
mmCIF format entries; and entry_id.xml, e.g. 1abc.xml, for
canonical XML format entries.
WHY WAS THE wwPDB FORMED?
wwPDB formalizes the international character of the PDB and
ensures that the archive will remain single and uniform.
Formation of the wwPDB will be transparent to depositors.
PDB depositions will continue to be accepted at all three sites
and will not appear any different than it does now. Data will be
equally well validated and annotated at all wwPDB sites.
By providing a formal mechanism for standardizing the
presentation of PDB data, software developers and users of
the data will be assured of consistent data. At the same time, it
is hoped that this agreement will allow for individual creativity
in how the data are presented and made available to the
community.
HOW IS THE wwPDB FUNDED?
The RCSB PDB is supported by the National Science Foundation, the National Institutes of Health, and the Department of Energy.
PDBe is supported by the European Molecular Biology Laboratory, Wellcome Trust, Biotechnology and Biological Sciences Research Council, the National Institutes of Health and the European Union.
PDBj is supported by National Bioscience Database Center-Japan Science and Technology Agency.
The BMRB is supported by the National Institute of General Medical Sciences.
EMDB is funded by the Wellcome Trust and EMBL-EBI.
Other funding awards to RCSB PDB by the NSF and to PDBe by the UK Biotechnology and Biological Research Council are jointly supporting development of a Next Generation PDB archive (DBI-2019297, PI: S.K. Burley; BB/V004247/1, PI: Sameer Velankar) and new Mol* features (DBI-2129634, PI: S.K. Burley; BB/W017970/1, PI: Sameer Velankar).