Docking guidance with experimental ligand structural density improves docking pose prediction and virtual screening performance.

ABSTRACT: Recent advances in structural biology have led to the publication of a wealth of high-resolution x-ray crystallography (XRC) and cryo-EM macromolecule structures, including many complexes with small molecules of interest for drug design. While it is common to incorporate information from the atomic coordinates of these complexes into docking (e.g., pharmacophore models or scaffold hopping), there are limited methods to directly leverage the underlying density information. This is desirable because it does not rely on the determination of relevant coordinates, which may require expert intervention, but instead interprets all density as indicative of regions to which a ligand may be bound. To do so, we have developed CryoXKit, a tool to incorporate experimental densities from either cryo-EM

SUBMITTER: Hansel-Harris AT 

PROVIDER: S-EPMC11854350 | biostudies-literature | 2025 Mar

REPOSITORIES: biostudies-literature