The P-gp substrates and inhibitors of the Validation set 2 were clustered using six different molecular descriptors (namely, FragFp, PathFp, SphereFp, SkelSpheres, OrgFunctions, and Flexophore) calculated with the software DataWarrior , generating one clustering set for each of the descriptor, using the Tanimoto similarity index. The FragFp, PathFp, and SphereFp are substructure-based fingerprints related to MDL keys , Daylight fingerprint , and Hose codes , respectively. The SkelPheres fingerprint is similar to the SphereFp, but also considers stereochemistry, counts duplicate fragments, and encodes heteroatom depleted skeletons with a resolution of 1024 bits. The OrgFunctions is neither a fingerprint nor an integer vector but focuses on available functional groups from a synthetic chemist's point of view. Finally, the Flexophore allows the prediction of 3D-pharmacophore similarities .