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PDBj stands for the Protein Data Bank Japan. From the PDBj website, one can access macromolecular structures, deposit experimental data, and also make use of a variety of structural bioinformatics web services. PDBj is a member of the Worldwide PDB.

PDBj's services are mostly based on the XML (extensible markup language) files called PDBML and PDBMLplus (see also Data Format ).

In PDBj, following service are available.

  • Data Deposition
    • ADIT (Molecular structure deposition tool solved by X-ray crystallography)
    • ADIT-NMR (Molecular structure deposition tool solved by NMR spectroscopy)
  • Search
  • Services and Software
    • jV (PDBj Viewer, molecular visualizing software)
    • Yorodumi (a website to easily watch, move, rotate, learn, and enjoy 3D structures of biological molecules)
    • Protein Globe (A service to visualize the protein world)
    • ASH (A calculating program to molecular structural similarity)
    • MAFFTash (A tool to calculate molecular similarity considering both sequence and structure)
    • SEALA (SEquence ALignment Analyzer)
    • NMRToolBox (Useful tools for NMR data evaluation)
    • CRNPRED (Structure prediction service based on the sequence)
    • Spanner (Structure prediction service using structure known molecules with similar sequence)
    • SFAS (Multiple service both sequence alignment and structure prediction)
  • Derived database
    • eF-site (Database for molecular surfaces of their functional sites)
    • eF-surf (Calculating the molecular electrostatic potential and surface)
    • eF-seek (Searching similar ligand binding sites)
    • ProMode Elastic (Database of normal mode analysis of PDB data)
  • Educational Service
    • eProtS (Encyclopedia of protein structures)
    • Molecule of the Month (Articles about topical matter related molecules in RCSB, translated into Japanese by PDBj)
    • Previous workshop (materials used in the previous workshop)
    • PDBj Games
2012-07-13 (last edited: 3 months ago)2015-12-09
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