Figure 2

Identification of a threshold for SurfaceShapeSignatures. SSS distances obtained by querying the ATP binding site of cAMP-dependent kinase (PDB:1atp) against the GPSS ligand surface library are plotted against the molecular weight of the ligand corresponding to the library surface (a). Ligands with MW ± 100 D of ATP are highlighted in yellow. The molecular shape similarity Taniomoto score between ATP and the ligand corresponding to the library surface is plotted in (b). Tanimoto scores greater than 0.7 (blue) are generally regarded as similar. The correlation coefficients for molecular weight and shape similarity are 0.46 and 0.45, respectively, and the corresponding regression lines are shown in red. Our selected threshold distance of 0.3 (green) for use in our SurfaceScreen methodology eliminates less than 1% of true-positive surfaces in our benchmarking exercises.