Note: This service is currently under development.

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.

GIRAF query upload

Input PDB ID:

or upload a PDB file:

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

Your email address (optional):

DB version: 2008-06-13 (186485 ligand binding sites)

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References

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. Structure17:234-246 (2009) [for the identification of structural motifs]

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Protein Data Bank Japan 2008-11-24