Fuzzy clustering as a means of selecting representative conformers and molecular alignments

Journal of Chemical Information and Computer Sciences

Volumn 43, Issue 3, 2003, Pages 810-818

  Feher, Miklos ^a   Schmidt, Jonathan M ^a  

^a Signalgene Inc Canada   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CLUSTERING PROCESSES; CONFORMATIONS;

ALGORITHMS; COMPUTER SIMULATION; FUZZY SETS; MATRIX ALGEBRA; MOLECULAR DYNAMICS; MOLECULAR ORIENTATION;

MOLECULAR STRUCTURE;

EID: 0037498095     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci0200671     Document Type: Article

References (18)

1. Feher, M.; Schmidt, J. M. Metric and Multidimensional Scaling: Efficient Tools for Clustering Molecular Conformations. J. Chem. Inf. Comput. Sci. 2001, 41, 346-353.
2. Feher, M.; Schmidt, J. M. Identifying potential binding modes and explaining partitioning behavior using flexible alignments and multidimensional scaling. J. Comput.-Aided Mol. Des. 2001, 75, 1065-1083.
3. Labute, P.; Williams, C.; Feher, M.; Sourial, E.; Schmidt, J. M. Flexible Alignment of Small Molecules. J. Med. Chem. 2001, 44, 1483-1490.
4. Bezdek, J. C. Cluster Validity with Fuzzy Sets. J. Cybernetics 1974, 3, 58-71.
5. Dunn, J. A fuzzy relative of the ISODATA process and its use in detecting compact, well separated clusters. J. Cybernetics 1974, 3, 32-57.
6. Bezdek, J. C. Pattern Recognition with Fuzzy Objective Function Algorithms; Plenum Press: New York, 1981; pp 43-93.
7. Krzanowski, W. J. Principles of Multivariate Analysis; Clarendon Press: Oxford, 1988.
8. Xie, X. L.; Beni, G. A Validity Measure for Fuzzy Clustering. IEEE Trans. Pattern Anal. Mach. Intellig. 1991, 13, 841-847.
9. Dunn, J. C. Indices of partition fuzziness and detection of clusters in large data sets. In Fuzzy Automata and Decision Processes; Elsevier: New York, 1977.
10. Molecular Operating Environment, Version 2000.02; Chemical Computing Group Inc.: Montreal, Quebec, Canada.
11. MATLAB, version 6.1; The MathWorks Inc.: Natick, MA.
12. Shenkin, P. S.; McDonald, D. Q. Cluster Analysis of Molecular Conformations. J. Comput. Chem. 1994, 75, 899-916.
13. Kelley, L. A., Gardner, S. P., Sutcliffe, M. An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies. J. Prot. Eng. 1996, 9, 1063-1065.
14. Torda, A. E.; Gunsteren, W. F. Algorithms for Clustering Molecular Dynamics Configurations. J. Comput. Chem. 1994, 75, 1331-1340.
15. Tung, W. L.; Quek, C. DIC: A novel discrete incremental clustering technique for the derivation of fuzzy membership functions. Lect. Notes Comput. Sci. 2002, 2417, 178-188.
16. Devillez, A.; Billaudel, P.; Lecolier, G. V. A fuzzy hybrid hierarchical clustering method with a new criterion able to find the optimal partition. Fuzzy Sets Syst. 2002, 728, 323-338.
17. Turhan, M. Genetic Fuzzy Clustering by Means of Discovering Membership Functions. Lect. Notes Comput. Sci. 1997, 1280, 383-393.
18. Nascimento, S.; Moura-Pires, F. A Genetic Approach to Fuzzy Clustering with a Validity Measure Fitness Function. Lect. Notes Comput. Sci. 1997, 1280, 325-337.