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WABI
2001
Springer

Pattern Matching and Pattern Discovery Algorithms for Protein Topologies

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Pattern Matching and Pattern Discovery Algorithms for Protein Topologies
We describe algorithms for pattern matching and pattern learning in TOPS diagrams (formal descriptions of protein topologies). These problems can be reduced to checking for subgraph isomorphism and finding maximal common subgraphs in a restricted class of ordered graphs. We have developed a subgraph isomorphism algorithm for ordered graphs, which performs well on the given set of data. The maximal common subgraph problem then is solved by repeated subgraph extension and checking for isomorphisms. Despite the apparent inefficiency such approach gives an algorithm with time complexity proportional to the number of graphs in the input set and is still practical on the given set of data. As a result we obtain fast methods which can be used for building a database of protein topological motifs, and for the comparison of a given protein of known secondary structure against a motif database. 1 Biological motivation Once the structure of a protein has been determined, the next task for biologi...
Juris Viksna, David Gilbert
Added 30 Jul 2010
Updated 30 Jul 2010
Type Conference
Year 2001
Where WABI
Authors Juris Viksna, David Gilbert
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