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[PDB Format]

A text format consists of 80 columns. It is the most traditional format.

[mmCIF]

This format is modified from CIF, used to describe crystal structures, to adapt macromolecules.

The mmCIF dictionary is available from following URL:

The format PDBML is based on it.

[PDBML]

PDBML is the canonical XML format of PDB entries, originally-introduced in the following reference:

PDBML: the representation of archival macromolecular structure data in XML.
Westbrook J, Ito N, Nakamura H, Henrick K, Berman HM.
Bioinformatics, 2005, 21(7):988-992. PubMed:15509603 full text

The schema file to define PDBML data description rule is available from following URL:

There are 3 variants of PDBML files

[PDBMLplus]

PDBMLplus is also XML formatted data based on PDBML. The additional information such as functional annotation and experimental condition is added by PDBj. It is also available in PDBj Mine. See also PDBMLplus for details.

[RDF]

PDB data are also available in RDF (Resource Description Framework) format. The RDF files are automatically generated from PDBML files using XSLT. The ontology is also defined based on the PDB mmCIF Exchange Dictionary. An RDF file is created for each PDB entry. For example, the RDF data for PDB entry 1GOF is accessible at http://rdf.wwpdb.org/pdb/1GOF.

(last edited: 10 months ago)2013-11-11
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