#54 PDBML - Protein Data Bank Markup Language

[Geoff Hutchison]

The Protein Data Bank has yet another file format: PDBML:
http://pdbml.rcsb.org/

From the website:
The Protein Data Bank Markup Language (PDBML) provides a representation of PDB data in XML format. The description of this format is provided in XML schema of the PDB Exchange Data Dictionary. This schema is produced by direct translation of the mmCIF format PDB Exchange Data Dictionary Other data dictionaries used by the PDB have been electronically translated into XML/XSD schemas and these are also presented in the list below.

PDBML data files are provided in three forms:
fully marked-up files,
files without atom records
files with a more space efficient encoding of atom records
Data files in PDBML format can be downloaded from the RCSB PDB website or by ftp.
Software tools for manipulating PDB data in XML format can be found here.
An article describing PDBML is available.
PDBML: the representation of archival macromolecular structure data in XML.
John Wesbrook, Nobutoshi Ito, Haruki Nakamura, Kim Henrick and Helen M. Berman,
Bioinformatics, 21(7), 988-992, 2005.