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Multiple Semi-flexible 3D Superposition of Drug-sized Molecules

Summary: Multiple Semi-flexible 3D Superposition of
Drug-sized Molecules
Daniel Baum
Zuse Institute Berlin (ZIB), Germany
Abstract. A new algorithm for multiple semi-flexible superpositioning
of drug-sized molecules is described. It identifies structural similarities
between two or more molecules. To account for the flexibility of a mole-
cule, multiple conformers drawn from molecular ensembles generated by
conformational analysis are used. To address the varying degree of sim-
ilarity among the molecules, similar substructures present in different
subsets of the molecules are identified.
All molecules are compared to a preselected reference molecule. Clique
detection on the correspondence graph of two molecular structures is ap-
plied to generate feasible start transformations, which are used to com-
pute common substructures. The results of these pairwise comparisons
are efficiently merged using binary matching trees.
Despite considering the full atomic information for identifying multi-
ple structural similarities, the algorithm is well suited as an interactive
tool for exploring drug-sized molecules, and has been integrated into the


Source: Andrzejak, Artur - Konrad-Zuse-Zentrum für Informationstechnik Berlin


Collections: Computer Technologies and Information Sciences