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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.

Also, the schema file is available from following URL:

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.
2013-11-08 (last edited: 5 months ago)2017-05-12
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