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Similarity Search for Ligand Binding Sites at Atomic Resolution [Help]

Given a query protein structure, GIRAF searches for ligand binding sites in the PDB that are structurally similar to substructures of the query. As a query, you can specify a PDB ID or upload your own PDB-formatted file. For more information, please refer to the help page.

Note: This service is currently under development. Submitted jobs may be terminated prematurely at any time.

GIRAF query upload

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Chain IDs (optional): (comma-separated multiple IDs [e.g., "A,B"] or "all" are allowed.)

Limit target PDB entries (optional): (comma-separated multiple IDs [e.g., "101m,1a00"] or "all" are allowed.)

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DB version: 2017-06-17: 619311 interfaces


  1. Similarity search for local protein structures at atomic resolution by exploiting a database management system.
    Kinjo, A. R.; Nakamura, H. BIOPHYSICS 3:75-84 (2007) [for the description of the method]
  2. Comprehensive structural classification of ligand binding motifs in proteins.
    Kinjo, A. R.; Nakamura, H. Structure 17:234-246 (2009) [for the identification of structural motifs]
  3. Geometric similarities of protein-protein interfaces at atomic resolution are only observed within homologous families: An exhaustive structural classification study.
    Kinjo, A. R.; Nakamura, H. J. Mol. Biol 399:526-540 (2010) [application to protein-protein interfaces]
  4. GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution.
    Kinjo, A. R.; Nakamura, H. BIOPHYSICS 8:79-94 (2012) [for the description of the improved method]

Protein Data Bank Japan 2010-04-30