LOBSTER (Ligand Overlays from Binding SiTe Ensemble Representatives)

LOBSTER ("Ligand Overlays from Binding SiTe Ensemble Representatives")  is a dataset of ligand overlays designed to evaluate small molecule superposition tools.

Based on all structures from the RCSB PDB, the dataset generation and filtering protocols are fully automated to avoid subjectivity in the selection of protein-ligand complexes and to gain the largest possible set of refined compounds. Affinity and activity data have been processed to select ligands with a high ligand efficiency.
Ligands were superimposed in their crystal pose by aligning the corresponding binding pockets to so-called ensembles. For poses generated in benchmark experiments, this offers an objective comparison to the superimposed ligand crystal poses. A clustering of ensembles created with the same protein-ligand complexes ensures the diversity of the LOBSTER set.
The 671 ligand ensembles comprise a total of 3212 unique ligands from 3521 different protein-ligand complexes. A total of 72 734 ligand pairs have been derived from the ensembles. Ten subsets were generated from the pairs according to the shape overlap of the pairs, quantified by the Shape Tversky Index.