V.J. van Geerestein, N.C. Perry, P.D.J. Grootenhuis, C.A.G. Haasnoot
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3D Database searching on the basis of ligand shape using the sperm prototype method
This paper describes a method for the rapid searching of 3d structural databases for molecules showing 3d shape similarity to a query structure. In the sperm program, molecular properties are projected onto the surface of a sphere and icosahedral symmetry is used to minimise storage requirements and accelerate comparison over all of 3d rotational space. The results of searches of a 30,000 compound database for molecules with a 3d shape resembling netropsin and daunomycin are described. In addition to molecules showing topological similarity to the query, hits are obtained showing considerable structural diversity. The results demonstrate that the method might be useful in the selection of new lead compounds as potential ligands for a given receptor.
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