Macs in Chemistry

Insanely Great Science

Getting PDB information

 

A while back I published two scripts that use UniChem a web resource provided by the EBI, a 'Unified Chemical Identifier' system, designed to assist in the rapid cross-referencing of chemical structures, and their identifiers, between multiple databases.

Chambers, J., Davies, M., Gaulton, A., Hersey, A., Velankar, S., Petryszak, R., Hastings, J., Bellis, L., McGlinchey, S. and Overington, J.P. UniChem: A Unified Chemical Structure Cross-Referencing and Identifier Tracking System. Journal of Cheminformatics 2013, 5:3 (January 2013). DOI: http://dx.doi.org/10.1186/1758-2946-5-3

The first script uses the ChEMBL ID to search for other identifiers, the second script allows more flexible searching using any of the identifiers available within UnicChem. One of the identifiers returned is from the PDBe (Protein Data Bank Europe) and represents the ID of the ligand in the PDB. Whilst this is interesting it would also be very useful to have the identity of the crystal structures that contain the ligand. Fortunately PBDe provide a series of web services that can be used to interrogate the database, together with a really useful page to help build the calls.

Full details of the script are here..

There is a comprehensive listing of scripts, tips, jupyter notebooks etc here.