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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.

Also, the schema file is available from following URL:

And via our tree viewer.

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

http://127.0.0.1/#!rest/downloadPDBfile?format=pdbmlplus-all&id=PDBID
http://127.0.0.1/#!rest/downloadPDBfile?format=pdbmlplus-noatom&id=PDBID

(e.g. PDBID=100d)
http://127.0.0.1/#!rest/downloadPDBfile?format=pdbmlplus-noatom&id=100d

PDBMLplus schema has been updated on 2014-1-20 (Mon.)

PDBj has released a new XML schema for PDBMLplus, an extension of PDBML based on the latest 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_pdbmlplus as a suffix. Previously, the information in these categories were directly added in the corresponding mmCIF categories without_pdbmlplus suffix, but now 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
  • gene_ontology
    • Gene ontology mapping is obtained from UniProt.
2012-07-13 (last edited: 4 weeks ago)2014-08-22
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entries available on 2014-09-17
00:00 UTC / 09:00 JST