Relibase

Relibase 

Cambridge Crystallography Data Centre (CCDC) 

Reviewed by Susan Boyd, CompChem Solutions, Cambridge, UK

If you’re at all interested in protein-ligand interactions, then Relibase (and Relibase+) from CCDC are certainly worth a look. Relibase is currently accessible to all, free of charge, via the web, whilst its big brother, Relibase+ comes complete with enhanced functionality and is available under license from CCDC. 

Relibase itself allows users to search the Protein Data Bank on PDB codes, keywords and resolution. Complexed ligands are easily viewable as 2D chemical sketches. Where this tool easily wins over the other freebie PDB browsers is in its full 2D/3D searching facility. Users can use this to search for 2D substructures in ligands, or for specific 3D interactions between functionalities on the protein and those on the ligand. It is even possible to search the database for similar active site cavities to a given query (done on the basis of homology) and superimpose the retrieved complexes in the supplied 3D structural viewer. 

Relibase+ extends the functionality of Relibase by supporting input of proprietary protein structures to a locally installed version of the PDB, by allowing users to store and manipulate (via Boolean algebra) retrieved hitlists and by supporting cavity similarity searching on the basis of shape and detected binding features (CavBase). WaterBase allows crystallographers and modellers to explore water clusters in crystal structures, and will warn users if it detects the likelihood of a wrongly-assigned water molecule, for example. If used alongside the Cambridge Structural Database (CSD), Relibase+ can assess whether ligand geometry is optimal by checking the occurrence of each given bond length, distance or torsion angle in the CSD, and graphing the data for ease of interpretation.  

Check out the web site to explore Relibase - but unless you’re an academic user you need to do that in the next couple of months, as, from January 2008, Relibase will only be available free of charge to academic users. 

For more information, or to arrange an evaluation of Relibase+, contact the CCDC (admin@ccdc.cam.ac.uk).