Table 1 Fingerprints used in this study

3DAPfp

Shape

16-bit scalar 3D-fp, each bit is the sum of atom pair gaussian function values sampled at 16 different through-space distances between 1 and 20 Å, normalized to HAC^1.5

^b)

3DXfp

Pharmacophore

80-bit scalar 3D-fp, equivalent to 3DAPfp extended to 5 categories: Hyb, HBA, HBD, sp2, and cross-pair HBA-HBD

^b)

R3DAPfp

Shape

40-bit scalar 3D-fp, each bit counts the number of atom pairs within the corresponding 0.5 Å through-space distance interval between 0 and 20 Å, normalized to HAC (R = regular binning)

^b)

R3DXfp

Pharmacophore

200-bit scalar fp, category extended version of R3DAPfp

^b)

APfp

Shape

20-bit scalar 2D-fp, each bit counts the number of atom pairs at one particular topological distance between 1 and 20 bonds, normalized to HAC

[28]

Xfp

Pharmacophore

55-bit scalar 2D-fp, category extended version of APfp

[28]

PMIfp

Shape

3-bit scalar 3D-fp, measures the principal moments of inertia scaled to molecular weight

[17]

USR

Shape

12-bit scalar 3D-fp, represents euclidean distance distributions calculated with respect to four chosen reference points by three statistical moments: average, standard deviation and kurtosis

[30]

USRCAT

Pharmacophore

60-bit scalar 3D-fp, version of USR extended with categories: All atoms, Hyb, HBA, HBD, aromatic atoms

[31]

MQN

Composition

42-bit scalar 2D-fp, counts 42 Molecular Quantum Numbers (MQN) counting atom types, bond types, polar groups and topologies

[7,8]

Sfp

Substructure

1024-bit binary 2D-fp, perceives the presence of substructures

[15]