ActivityFinder

Overview

ActivityFinder automatically links protein–ligand crystal structures to bioactivity and affinity data eliminating the need for external services or continuous data connections. It relies on structural information retrieved from PDB files and activity and affinity data in a structured SQL database such as ChEMBL. The linking procedure is based on sequence alignments, mutation tracking, and detailed chemical structure matching. It captures and reports variations such as binding-site mutations and inconsistencies in ligand modeling. Therefore, the method prevents unintended errors in the derived data sets and subsequent analyses. Although the published ActivityDB is built on public data, ActivityFinder can also handle proprietary data sets.

Limitations

The PDB files must contain ligands for annotating the corresponding bioactivity and affinity data. A differentiation between cases of contradicting stereoisomers and unspecified stereocenters is currently not possible. For ligand data with multiple components, only the largest component is retained. The ligand topology is annotated based on the ligand coordinates in the PDB files. An update functionality for the resulting ActivityDB has not yet been implemented.

Software Availability

ActivityFinder is freely available for non-commercial and academic users for Linux, macOS, and Windows as part of our NAOMI ChemBio Suite. To download ActivityFinder, register at https://software.zbh.uni-hamburg.de. Non-academic users can get an evaluation license free of charge. Only minimal setup steps are required to run ActivityFinder. All feedback (software.zbh(at)uni-hamburg.de) is highly appreciated.

References

Ehmki, E. S. R.; Gutermuth, T.; Harren, T.; Kurtz, S.; Rarey, M. ActivityFinder: Toward the Fully Automatic Integration of Structural and Binding Affinity Data. J Chem Inf Model 2026. DOI: https://doi.org/10.1021/acs.jcim.5c02505