Dimensionality reduction in patch-signature based protein structure matching
ADC '06 Proceedings of the 17th Australasian Database Conference - Volume 49
An algebraic view of the relation between largest common subtrees and smallest common supertrees
Theoretical Computer Science
Bit-vector algorithms for binary constraint satisfaction and subgraph isomorphism
Journal of Experimental Algorithmics (JEA)
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Subgraph isomorphism and maximum common subgraph isomorphism algorithms from graph theory provide an effective and an efficient way of identifying structural relationships between biological macromolecules. They thus provide a natural complement to the pattern matching algorithms that are used in bioinformatics to identify sequence relationships. Examples are provided of the use of graph theory to analyze proteins for which three-dimensional crystallographic or NMR structures are available, focusing on the use of the Bron-Kerbosch clique detection algorithm to identify common folding motifs and of the Ullmann subgraph isomorphism algorithm to identify patterns of amino acid residues. Our methods are also applicable to other types of biological macromolecule, such as carbohydrate and nucleic acid structures. © 2005 Wiley Periodicals, Inc.