Pattern Search in Molecules with FANS: Preliminary Results
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We show here how FANS, a fuzzy sets-based heuristic, is applied to a particular case of the Molecular Structure Matching problem: given two molecules A (the pattern) and B (the target) we want to find a subset of points of B whose set of intra-atomic distances is the most similar to that of A. This is a hard combinatorial problem because, first we have to determine a subset of atoms of B and then some order for them has to be established.
We analyze how the size of the pattern affects the performance of the heuristic, thus obtaining guidelines to approach the solution of real problems in the near future.
KeywordsLocal Search Pattern Size Semantic Neighborhood Protein Structure Comparison Matched Atom
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- 9.N. Leibowitz, Z. Fligerman, R. Nussinov, and H. Wolfson. Multiple structural alignment and core detection by geometric hashing. In T. L. Et.Al., editor, Procs of 7th Intern. Conference on Intelligent Systems for Molecular Biology ISMB 99., pages 167–177. AAAI Press, 1999.Google Scholar
- 11.D. Pelta, A. Blanco, and J. L. Verdegay. A fuzzy adaptive neighborhood search for function optimization. In Fourth International Conference on Knowledge-Based Intelligent Engineering Systems & Allied Technologies, KES 2000, volume 2, pages 594–597, 2000.Google Scholar
- 13.D. Pelta, A. Blanco, and J. L. Verdegay. Fuzzy adaptive neighborhood search: Examples of application. In J. L. Verdegay, editor, Fuzzy Sets based Heuristics for Optimization, Studies in Fuzziness and Soft Computing. Physica-Verlag, 2003. to appear.Google Scholar
- 16.R. N. H. Wolfson. Efficient detection of three dimensional structural motifs in biological macromolecules by computer vision techniques. Procs. of the National Academy of Sciences USA, 88:10495–10499, 1991.Google Scholar
- 17.H. J. Zimmermann. Fuzzy Sets Theory and Its Applications. Kluwer Academic, 1996.Google Scholar