LigandScout provides several scoring functions for ranking intermediate solutions during the
ligand-based pharmacophore generation. All scoring functions were
developed to deliver robust results for several investigated targets. However, different scoring functions may
deliver different results, depending on whether shape (i.e., molecular volume) or chemical functionality is
considered to be more relevant for the assumed binding mode. Available scoring functions comprise
Pharmacophore-Fit (only taking into account chemical feature overlap), Atom Overlap
(“
Fast Shape
”), Gaussian
Shape Similarity, and a combination of Pharmacophore-Fit and Atom Overlap.
These scoring functions are described in detail below.
S FCR | is the feature count/RMS distance score |
S RMS | is the matched feature pair RMS distance score in the range [0,9] |
RMS FP | is the RMS of the matched feature pair distances |
N MFP | is the number of geometrically matched feature pairs |
c | is a weighting factor for the number of matched feature pairs (currently 10.0) |
S ARO | is the atom radius overlap score in the range [0,1] |
n | is total number of atoms of all involved molecules |
V i max | is the maximum pseudo overlap volume of the ith atom with an atom of another involved molecule and lies in the range [0,1]. For the overlap volume to become non-zero, the atom has to overlap with at least one atom from each other involved molecule |
S DOF | is the pharmacophore-fit and atom overlap score |
S MFC | is the matched feature pair score |
N MFP | is the number of geometrically matched feature pairs |
NF 1 | is the number of features in the first pharmacophore |
NF 2 | is the number of features in the second pharmacophore |
S FD | is the matched feature pair distance score |
d i | is the distance of the ith matched feature pair if the distance is greater than 1, and zero otherwise |
S RMS | is the matched feature pair RMS distance score [0,1] |
RMS max | is the maximum RMS to consider (set to 5.0) |
RMS FP | is the RMS of the matched feature pair distances |
S ARO | is the atom radius overlap score in the range [0,1] |