The pharmacophore kernel for virtual screening with support vector machines.
We introduce a family of positive definite kernels specifically optimized for the manipulation of 3D structures of molecules with kernel methods. The kernels are based on the comparison of the three-point pharmacophores present in the 3D structures of molecules, a set of molecular features known to be particularly relevant for virtual screening applications. We present a computationally demanding exact implementation of these kernels, as well as fast approximations related to the classical fingerprint-based approaches. Experimental results suggest that this new approach is competitive with state-of-the-art algorithms based on the 2D structure of molecules for the detection of inhibitors of several drug targets.
Mahé
Pierre
P
Center for Computational Biology, Ecole des Mines de Paris, 35 rue Saint Honoré, 77305 Fontainebleau, France. pierre.mahe@ensmp.fr
Ralaivola
Liva
L
Stoven
Véronique
V
Vert
Jean-Philippe
JP
D000465:Algorithms; D004364:Pharmaceutical Preparations
D004364:Pharmaceutical Preparations