%0 Journal Article
%T The pharmacophore kernel for virtual screening with support vector machines
%A Pierre Mah¨¦
%A Liva Ralaivola
%A V¨¦ronique Stoven
%A Jean-Philippe Vert
%J Quantitative Biology
%D 2006
%I arXiv
%X 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-points pharmacophores present in the 3D structures of molecul es, 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 approa ches. Experimental results suggest that this new approach outperforms state-of-the-art algorithms based on the 2D structure of mol ecules for the detection of inhibitors of several drug targets.
%U http://arxiv.org/abs/q-bio/0603006v1