PDBML Resources
PDBML
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.
PDBML Schema
- PDB Exchange Dictionary in support of PDB Data File Format V3.3 |
| current version
| alternative atom record markup
||
XML Schema for Exchange Data dictionary developed as a collaboration
between PDBe, PDBj and RCSB and used by wwPDB members for data exchange.
- PDB Exchange Dictionary in support of PDB Data File Format V3.2/3.15 (frozen) |
| current version
| previous versions
| alternative atom record markup
||
XML Schema for Exchange Data dictionary developed as a collaboration
between PDBe, PDBj and RCSB and used by wwPDB members for data exchange.
- PDB Exchange Dictionary in support of PDB Format V3.1 (frozen) |
| current version
| previous versions
| alternative atom record markup
||
XML Schema for Exchange Data dictionary developed as a collaboration
between PDBe, PDBj and RCSB and used by wwPDB members for data exchange.
-
mmCIF Dictionary |
| current version
| previous versions
||
IUCr Standard Dictionary
Originial working group members: Paula M. Fitzgerald, Helen Berman,
Phil Bourne, Brian McMahon, Keith Watenpaugh, and John Westbrook
- DDL2 Dictionary |
| current version
| previous versions
||
Syd Hall and John Westbrook
- NMRSTAR Dictionary |
| current version
| previous versions
||
Developed by the BioMagResBank
- imgCIF/CBF Extension Dictionary |
| current version
| previous versions
||
Andy Hammersley, Herbert J. Bernstein, I. David Brown, and John Westbrook
- BIOSYNC Extension Dictionary |
| current version
| previous versions
||
Anne Kuller and John Westbrook
- MDB Modeling Extension Dictionary |
| current version
| previous versions
||
Alexei Adzhubei and Eugenia Migliavacca
- Provisional Symmetry Extension Dictionary |
| current version
| previous versions
||
I. David Brown, Editor
- 3D EM Extension Dictionary |
| current version
| previous versions
||
Community extension data dictionary describing 3D EM structure and experimental data
to be deposited in the EMDB and PDB databases.
- 3D EM Exchange Dictionary |
| current version
| previous versions
||
Development version of the 3D EM data dictionary for program to program data exchange.
- CCP4 Harvest Extension Dictionary |
| current version
| previous versions
||
Data dictionary developed by CCP4 in collaboration with EBI for data harvesting.
