PDBx/mmCIF: the foundation for the wwPDB OneDep system

Westbrook, John D.; Markley, John L.; Haruki,; Velankar, Sameer; Burley, S. J.

doi:10.1107/s2053273317082146

Cited by 1 publication

(4 citation statements)

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“…We have chosen to create the new I/H methods data representation as an extension of the existing PDBx/mmCIF data representation (Fitzgerald et al, 2005; Westbrook, 2013) used by the wwPDB to archive structures of biological macromolecules. The fundamental concepts used in creating data standards, the structure and contents of the new I/H methods data representation and the development of the PDB-Dev prototype system are discussed below.…”

Section: Resultsmentioning

confidence: 99%

“…Over time, the wwPDB worked with the NMR, 3DEM and SAS communities to extend the metadata framework, allowing for representing and exchanging the data required to archive and validate model structures obtained from these experimental methods. PDBx/mmCIF has evolved while serving as the metadata and archiving data standard for the PDB archive (Westbrook et al, 2005; Westbrook and Fitzgerald, 2009; Westbrook, 2013). It was officially adopted as the Master format for the PDB in 2011.…”

Section: Resultsmentioning

confidence: 99%

“…The IHM dictionary is built as an extension to the PDBx/mmCIF dictionary (Fitzgerald et al, 2005; Westbrook, 2013) used by the wwPDB to archive macromolecular structures. Wherever possible, existing definitions in the PDBx/mmCIF dictionary are re-used.…”

Section: Star Methodsmentioning

confidence: 99%

“…(a) Selected definitions in the PDBx/mmCIF dictionary (Westbrook, 2013) that relate to the descriptions of small molecules ( e.g. , Heme), polymers ( e.g ., Hemoglobin α chain) and molecular complexes ( e.g ., human deoxy Hemoglobin) are shown.…”

Section: Figurementioning

confidence: 99%

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Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules

et al. 2018

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Essential processes in biology are carried out by large macromolecular assemblies, whose structures are often difficult to determine by traditional methods. Increasingly, researchers combine measured data and computed information from several complementary methods to obtain "hybrid" or "integrative" structural models of macromolecules and their assemblies. These integrative/hybrid (I/H) models are not archived in the PDB because of the absence of standard data representations and processing mechanisms. Here we present the development of data standards and a prototype system for archiving I/H models. The data standards provide the definitions required for representing I/H models that span multiple spatiotemporal scales and conformational states, as well as spatial restraints derived from different experimental techniques. Based on these data definitions, we have built a prototype system called PDB-Dev, which provides the infrastructure necessary to archive I/H structural models. PDB-Dev is now accepting structures and is open to the community for new submissions.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%