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.
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.
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
The list of all BindingDB Monomer IDs, with their associated SMILES strings, is available here: http://www.bindingdb.org/bind/BindingDB_SMILES.txt
The list of all SMILES strings in BindingDB is available here: http://www.bindingdb.org/bind/BindingDB_SMILES.txt
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
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.