Fig. 2: Benchmarking EMERALD against the EMDB.
From: Automatic and accurate ligand structure determination guided by cryo-electron microscopy maps
a A comparison of EMERALD models to the deposited structures for 1053 EMDB-deposited complexes. In total, 57% of EMERALD-docked models were placed within 1 Å RMSD of the deposited ligand (match, green); 38% were more than 1 Å RMSD of the deposited ligand but had similar or better density correlations and numbers of hydrogen bonds (similar or better quality, orange), and 5% were more than 1 Å RMSD from the deposited ligand and had worse density correlations or number of hydrogen bonds (worse quality, blue). b, c Bins of binding pocket local resolution (b) and number of torsion angles in the small molecule (c) shown as percentage by docking result. d–f The convergence of the best ranking models across multiple runs for matches (d), worse quality (e), and similar or better quality (f) cases. The darkest shade had multiple runs converge with all atoms within 1 Å of each other, the middle shade had multiple runs converge with at least 60% of atoms within 1 Å, and the lightest shade had divergent top-scoring models.
