Automated identification of small molecules in cryo-electron microscopy data with density- and energy-guided evaluation.

ABSTRACT: Methodological improvements in cryo-electron microscopy (cryoEM) have made it a useful tool in ligand-bound structure determination for biology and drug design. However, determining the conformation and identity of bound ligands is still challenging at the resolutions typical for cryoEM. Automated methods can aid in ligand conformational modeling, but current ligand identification tools - developed for X-ray crystallography data - perform poorly at resolutions common for cryoEM. Here, we present EMERALD-ID, a method capable of docking and evaluating small molecule conformations for ligand identification. EMERALD-ID identifies 43% of common ligands exactly and identifies closely related ligands in 66% of cases. We then use this tool to discover possible ligand identification errors, as well

SUBMITTER: Muenks A 

PROVIDER: S-EPMC11601544 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature