The Pharmacophore Kernel for Virtual Screening with Support Vector Machines
Pierre Joachim Mahe, Liva Ralaivola, Véronique Stoven, Jean‐Philippe Vert · Journal of Chemical Information and Modeling · 2006
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.