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 following page.

• PDBMLplus schema

Also, the schema file is available from following URL:

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

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_pdbjplusas a suffix. Previously, the information in these categories were directly added in the corresponding mmCIF categories without_pdbjplussuffix, 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.