The pharmacophore kernel for virtual screening with support vector machines

Details The pharmacophore kernel for virtual screening with support vector machines The pharmacophore kernel for virtual screening with support vector machines

2006-03-03

arxiv.org/abs/q-bio/0603006v1

Biology

Quantitative Biology

Quantitative Methods

Scientific paper

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.

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