Automated identification of small molecules in cryoelectron microscopy data with density- and energy-guided...

Methodological improvements in cryoelectron microscopy (cryo-EM) have made it useful in ligand-bound structure determination for biology and drug design. However, determining ligand conformation and identity is challenging at the resolutions typical for cryo-EM. 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 cryo-EM. Here, we present EMERALD-ID, a method capable of docking and evaluating small molecule conformations for ligand identification. EMERALD-ID identifies 44% 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 as previously unidentified ligands. Furthermore, we show EMERALD-ID identifying ligands from custom ligand libraries of various small molecule types, including human metabolites and drug fragments. Our method provides a valuable addition to cryo-EM modeling tools to improve small molecule model accuracy and quality.