New Paper: Redocking the PDB

20. Dezember 2023

Foto: Florian Flachsenberg

Redocking the PDB - How to get an honest estimate on docking success rate?

Docking tools are usually evaluated on relatively small subselections of PDB protein-ligand complexes. In practice, docking scenarios are various, not all ligands might be drug-like, binding site properties and crystal structure quality vary.

In our recent publication, we present an automated workflow based on our docking tool JAMDA enabling a redocking experiment on almost all complexes in the PDB. We show the influence of preparation steps as well as key dependence factors for success rate. While not yet a cross-docking scenario (next step!), the process points towards a realistic estimate of docking performance, which is urgently needed for upcoming deep learning-based docking workflows. Big thanks to @Florian for developing JAMDA and @Torben and @Christiane for a great job in analyzing the results. The full paper is here.