Similarity Search for Ligand Binding Sites at Atomic Resolution

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.

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  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]

Created: 2010-04-30 (last edited: more than 1 year ago)2019-04-30
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PDB entries from 2021-06-09