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.
- Protein ("target") Links
- Link/query by BindingDB Target Name
- The following URL retrieves all enzyme inhibition data for a given target protein, based upon its BindingDB Target Name.
- http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_ki.jsp?tag=tg&kiunit=nM&icunit=nM&column=ki&submit=Search&energyterm=kJ%2Fmole&target=target
- The following URL retrieves all ITC data for a given target protein, based upon its BindingDB Target Name.
- http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_itc.jsp?tag=tg&column=delta_G0&energyterm=kJ%2Fmole&startPg=0&Increment=50&submit=Search&target=target
The list of BindingDB Target Names is here http://www.bindingdb.org/bind/BindingDB_targets.txt and here http://www.bindingdb.org/bind/ByTargetNames.jsp
Other options: Units of Ki and IC50 can be changed from nanomolar to micromolar by specifying kiunit=uM, icunit=uM instead of kiunit=nM, icunit=nM. Energy units can be changed from kJ/mol to kcal/mol by specifying kcal instead of kJ. Number of data per page can be changed from 50 to, for example, 100, by changing Increment=50 to Increment=100.
- Link/query by BLAST search
- The following URL searches BindingDB for proteins with sequences similar to the query sequence:
- http://www.bindingdb.org/bind/blastResult.jsp?DATASOURCE=protein&Search=B2&blastSeq=Protein Sequence
The list of all BindingDB protein sequences is available here http://www.bindingdb.org/bind/BindingDB_sequences.txt and see also http://www.bindingdb.org/bind/BySequence.jsp
- Link/query by BindingDB Target Name
- Small molecule ("compound") Links
- Link by BindingDB Monomer ID
- If you know the Monomer ID of a compund in BindingDB, you can directly link to it in BindingDB with the following URL:
- http://www.bindingdb.org/bind/chemsearch/marvin/MolStructure.jsp?monomerid=BindingDB Monomer ID
The list of all BindingDB Monomer IDs, with their associated SMILES strings, is available here: http://www.bindingdb.org/bind/BindingDB_SMILES.txt
Example: http://www.bindingdb.org/bind/chemsearch/marvin/MolStructure.jsp?monomerid=100
- Link by SMILES strings
- Exact compound match
- http://www.bindingdb.org/bind/searchby_smiles.jsp?SearchType=4&submit=Search&smilesStr=SMILES string
- Similar compounds, based upon Jmol bitstrings and Tanimoto similarity
- http://www.bindingdb.org/bind/searchby_smiles.jsp?SearchType=3&similarity=similarity&submit=Search&smilesStr=SMILES string
- Substructure search
- http://www.bindingdb.org/bind/searchby_smiles.jsp?SearchType=2&submit=Search&smilesStr=SMILES string
The list of all SMILES strings in BindingDB is available here: http://www.bindingdb.org/bind/BindingDB_SMILES.txt
- Link by BindingDB Monomer ID
- 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
- 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.