Fig. 1: Overview of EMERALD docking protocol.
From: Automatic and accurate ligand structure determination guided by cryo-electron microscopy maps
a The cryoEM map, coordinates of the receptor, and the location of the binding site (red cross) are provided as inputs. The binding pocket is calculated depending on the radius of the ligand (circle) to determine boundaries and side chains to consider when modeling. b All unmodeled density in the pocket is converted to a pseudo-atomic skeleton (independent of ligand identity), which is used to generate an initial set of ligand conformers. c Using a genetic algorithm, the pool of ligand conformers is optimized against Rosetta energy and density fit. The population of ligand conformers evolve over 10 generations with low energy conformations surviving and combining attributes with each other. d The 20 poses with lowest energy are refined in Rosetta.
