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Linking into BindingDB


The following generic search URLs allow you to link into BindingDB by protein, small molecule, PDB ID, and/or PubMed ID. Please feel free to suggest other search methods.

  1. Protein ("target") Links
  2. Small molecule ("compound") Links
  3. Protein Data Bank ID (PDB ID)
    BindingDB provides hard links to binding data corresponding to a specific PDB entry if the BindingDB Target is >85% identical to the protein in the PDB entry, according to BLAST, and if the ligand in the PDB entry is identical to the ligand in BindingDB.
    http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_pdbids.jsp?pdbids_submit=Search&pdbids=PDB ID
    BindingDB provides hard links to binding data corresponding to a specific PDB entry if the BindingDB Target is >85% identical to the protein in the PDB entry, according to BLAST.
    http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_pdbids.jsp?pdbids_submit=Target&pdbids=PDB ID

    Example: http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_pdbids.jsp?pdbids_submit=Search&pdbids=1OKZ

    The list of all PDB IDs represented in BindingDB is available here (might give blank page with Search): http://www.bindingdb.org/bind/BindingDB_PDB.txt

  4. PubMedID
    The following generic URL returns all BindingDB data obtained from the article with the selected PubMed ID.
    http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_pubmed.jsp?pubmed_submit=Search&pubmed=PubMed ID

    Example: http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_pubmed.jsp?pubmed_submit=Search&pubmed=17408953

    The list of all PubMed IDs in BindingDB is available here:  http://www.bindingdb.org/bind/BindingDB_PubMed.txt and see also http://www.bindingdb.org/bind/ByPubMed.jsp.