PDBMLadd is the XML format file consisting 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 extracted for each entry, named PDBMLadd.

The schema of PDBMLadd is available from the following page.

• PDBMLadd schema

Also, the schema file is available from following URL:

• https://pdbj.org//schema/PDBMLadd_v40.xsd

And can also be viewed using our interactive XML viewer.

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

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

See also About data download for details.

PDBMLadd files and schema become available on 2013-11-6 (Wed.)

PDBj has released a new XML schema for PDBMLadd, an extension of PDBML with the publication of the PDBML schema ( pdbx-v40.xsd / pdbx-v42.xsd ). PDBMLadd schema consists of some annotations are added at PDBj as below.

Annotation Categories

Following categories are added. The names of these categories have _pdbmlplus as a suffix. They are separated to make clear that annotations are done at PDBj.

• exptl_crystal_grow_comp_pdbmlplusCategory
• exptl_crystal_grow_pdbmlplusCategory
• exptl_crystal_pdbmlplusCategory
• refine_ls_restr_pdbmlplusCategory
• refine_ls_shell_pdbmlplusCategory
• refine_pdbmlplusCategory
• reflns_pdbmlplusCategory
• reflns_shell_pdbmlplusCategory
• software_pdbmlplusCategory
• struct_ref_pdbmlplusCategory
• struct_ref_seq_pdbmlplusCategory
• struct_ref_src_pdbmlplusCategory
• citation_author_pdbmlplusCategory
• citation_pdbmlplusCategory

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, PFam and SIFTS.
• struct_ref_seq
  • Extracted from UniProt, PFam and SIFTS.
• gene_ontology
  • Gene ontology mapping is obtained from UniProt.