PDBMLplus

PDBMLplus is the XML format file including additional information relating to individual proteins. Currently, PDB files are lacking a detailed description of function, experimental conditions, and the like. And then such information was included to extended XML database, named PDBMLplus.

The schema of PDBMLplus is available from the PDBj Mine web page.

• http://www.pdbj.org/schema/pdbMLplus_v40.xsd

http://service.pdbj.org/mine/schema.html

The PDBMLplus file of each entry is available from following URL:

ftp://ftp.pdbj.org/XML/pdbmlplus/pdbml_xp_gz/[PDBID (lower)]-pdbmlplus.xml.gz

New PDBMLplus schema becomes available on 2011-7-13 (Wed.)

PDBj has released a new XML schema for PDBMLplus, an extension of PDBML with the publication of the PDBML v4.0 schema (http://pdbml.pdb.org/schema/pdbx-v40.xsd ). PDBMLplus schema includes some annotations are added at PDBj as below.

Annotation Categories

Following categories are added. The names of these categories have "_pdbjplus" as a suffix. Previously, the information in these categories were directly added in the corresponding mmCIF categories without "_pdbjplus" suffix, but now they are separated to make clear that annotations are done at PDBj.

• exptl_crystal_grow_comp_pdbjplusCategory
• exptl_crystal_grow_pdbjplusCategory
• exptl_crystal_pdbjplusCategory
• refine_ls_restr_pdbjplusCategory
• refine_ls_shell_pdbjplusCategory
• refine_pdbjplusCategory
• reflns_pdbjplusCategory
• reflns_shell_pdbjplusCategory
• software_pdbjplusCategory
• struct_ref_src_pdbjplusCategory
• citation_author_pdbjplusCategory
• citation_pdbjplusCategory

Automatic

The information in the following categories are augmented by references to other database resources which are extracted automatically.

• struct_site
  • Extracted from UniProt/SwissProt, Prosite, and Catalytic Site Atlas (CSA).
• struct_site_gen
  • Extracted from UniProt/SwissProt, Prosite, and Catalytic Site Atlas (CSA), CATRES.
• struct_ref
  • Extracted from UniProt
• gene_ontology
  • Gene ontology mapping is obtained from UniProt.

Japanese version:PDBMLplus