The pharmacophore kernel for virtual screening with support vector machines |
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Authors: | Mahé Pierre Ralaivola Liva Stoven Véronique Vert Jean-Philippe |
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Institution: | Center for Computational Biology, Ecole des Mines de Paris, 35 rue Saint Honoré, 77305 Fontainebleau, France. pierre.mahe@ensmp.fr |
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Abstract: | 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. |
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