Combining crystallographic and binding affinity data towards a novel dataset of small molecule overlays.

ABSTRACT: Although small molecule superposition is a standard technique in drug discovery, a rigorous performance assessment of the corresponding methods is currently challenging. Datasets in this field are sparse, small, tailored to specific applications, unavailable, or outdated. The newly developed LOBSTER set described herein offers a publicly available and method-independent dataset for benchmarking and method optimization. LOBSTER stands for "Ligand Overlays from Binding SiTe Ensemble Representatives". All ligands were derived from the PDB in a fully automated workflow, including a ligand efficiency filter. So-called ligand ensembles were assembled by aligning identical binding sites. Thus, the ligands within the ensembles are superimposed according to their experimentally determined binding o

SUBMITTER: Honig SMN 

PROVIDER: S-EPMC11618164 | biostudies-literature | 2024 Dec

REPOSITORIES: biostudies-literature