Algorithms for the identifications of three-dimensional maximal common substructures
Journal of Chemical Information & Computer Sciences
Algorithm 457: finding all cliques of an undirected graph
Communications of the ACM
Multiobjective evolutionary algorithms: classifications, analyses, and new innovations
Multiobjective evolutionary algorithms: classifications, analyses, and new innovations
Multiobjective Optimization in Bioinformatics and Computational Biology
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Deterministic pharmacophore detection via multiple flexible alignment of drug-like molecules
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
A point-matching based algorithm for 3d surface alignment of drug-sized molecules
CompLife'06 Proceedings of the Second international conference on Computational Life Sciences
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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 molecule, multiple conformers drawn from molecular ensembles generated by conformational analysis are used. To address the varying degree of similarity 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 applied to generate feasible start transformations, which are used to compute common substructures. The results of these pairwise comparisons are efficiently merged using binary matching trees. Despite considering the full atomic information for identifying multiple structural similarities, the algorithm is well suited as an interactive tool for exploring drug-sized molecules, and has been integrated into the molecular visualization package AmiraMol. The algorithm's capabilities are demonstrated on two sets of molecules.