Lilien Lab
Department of Computer Science
Centre for Cellular and Biomolecular Research
University of Toronto

The PSMDB provides non-redundant sets of protein - small-molecule complexes that are especially suitable for structure-based drug design and protein - small-molecule interaction research.

In the construction of the database we have aimed to address the following:

• Support frequent updates -The number of new structures in the PDB is growing rapidly. In order to utilize these structures, frequent updates are required. In contrast to manual procedures which require significant time and effort per update, generation of the PSMDB database is fully automatic thereby facilitating frequent database updates.
• Consider both protein and ligand structural redundancy - In our database, two complexes are considered redundant if they share a similar protein and ligand (our protein - small-molecule non-redundant set). This allows the database to contain structural information for the same protein bound to several different ligands (and vice-versa). Additionally, for completeness, the database contains a set of non-redundant complexes when only protein structural redundancy is considered (our protein non-redundant set). The following images demonstrate the structural redundancy of the protein complexes in the PDB compared to the PSMDB.
• Efficient handling of covalent bonds -Many protein complexes contain covalently bound ligands. Typically, protein-ligand databases discard these complexes; however, the PSMDB simply removes the covalently bound ligand from the complex, retaining any non-covalently bound ligands. This increases the number of usable complexes in the database.
• Separate complexes into protein and ligand files -The PSMDB contains individual structure files for both the protein and all non-covalently bound ligands. The unbound proteins are in PDB format while the individual ligands are in SDF format (in their native coordinate frame).

Please cite:
The Protein–Small-Molecule Database (PSMDB), A Non-Redundant Structural Resource for the Analysis of Protein-Ligand Binding
Izhar Wallach, Ryan Lilien, Bioinformatics, 25(5):615-20 (2009)