Median partitioning: A novel method for the selection of representative subsets from large compound pools

Journal of Chemical Information and Computer Sciences

Volumn 42, Issue 4, 2002, Pages 885-893

  Godden, Jeffrey W ^a,b   Xue, Ling ^a,b   Kitchen, Douglas B ^a   Stahura, Florence L ^a,b   Schermerhorn, E James ^a   Bajorath, Jürgen ^a,b,c  

^a ALBANY MOLECULAR RESEARCH INC   (United States)

^b ALBANY MOLECULAR RESEARCH INC   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MEDIAN PARTITIONING (MP);

COMBINATORIAL MATHEMATICS; COMPUTATIONAL COMPLEXITY; DATABASE SYSTEMS; GENETIC ALGORITHMS;

ENTROPY;

ALGORITHM; ARTICLE; COMBINATORIAL CHEMISTRY; COMPUTER SIMULATION; DRUG DESIGN; FACTUAL DATABASE;

ALGORITHMS; COMBINATORIAL CHEMISTRY TECHNIQUES; COMPUTER SIMULATION; DATABASES, FACTUAL; DRUG DESIGN;

EID: 0036628566     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci0203693     Document Type: Article

References (39)

1. Shemetulskis, N.E.; Dunbar, J.B. Jr.; Dunbar, B.W.; Moreland, D.W.; Humblet, C. Enhancing the diversity of a corporate database using chemical database clustering and analysis. J. Comput-Aided Mol. Des. 1995, 9, 407-416.
2. Rhodes, N.; Willett, P.; Dunbar, J.B., Jr.; Humblet, C. Bit-string methods for selective compound acquisition. J. Chem. Inf. Comput. Sci. 2000, 40, 210-214.
3. Willett, P. Dissimilarity-based algorithms for selecting structurally diverse sets of compounds. J. Comput. Biol. 1999, 6, 447-457.
4. Willett, P. Similarity and Clustering in Chemical Information Systems; Research Studies Press: Letchworth, 1987.
5. Barnard, J.M.; Downs, G.M. Clustering of chemical structures on the basis of two-dimensional similarity measures. J. Chem. Inf. Comput. Sci. 1992, 32, 644-649.
6. Ward, J.H. Hierarchical grouping to optimize au objective function. J. Am. Stat. Assoc. 1963, 58, 236-244.
7. Agrafiotis, D.K. Stochastic algorithms for maximizing molecular diversity. J. Chem. Inf. Comput. Sci. 1997, 37, 841-851.
8. Snarey, M.; Terrett, N.K.; Willett, P.; Wilton, D.J. Comparison of algorithms for dissimilarity-based compound selection. J. Mol. Graph. Model. 1997, 15, 372-285.
9. Higgs, R.E.; Bemis, K.G.; Watson, I.A.; Wikel, J.H. Experimental designs for selecting molecules from large chemical databases. J. Chem. Inf. Comput. Sci. 1997, 37, 861-870.
10. Clark, R.D. OptiSim: An extended dissimilarity selection method for finding diverse representative subsets. J. Chem. Inf. Comput. Sci. 1997, 37, 1181-1188.
11. Shemetulskis, N.E.; Weininger, D.; Blankley, C.J.; Yang, J.J.; Humblet, C. Stigmata: An algorithm to determine structural commonalities in diverse datasets. J. Chem. Inf. Comput. Sci. 1996, 36, 862-871.
12. Xue, L.; Godden, J.W.; Stahura, F.L.; Bajorath, J. A dual-fingerprint based metric for the design of focused compound libraries and analogues. J. Mol. Model. 2001, 7, 125-131.
13. Holliday, J.D.; Ranade, S.S.; Willett, P.A. Fast algorithm for selecting sets of dissimilar molecules from large chemical databases. Quant. Struct.-Act. Relat. 1995, 14, 501-506.
14. Trepalin, S.V.; Gerasimenko, V.A.; Kozyukov, A.V.; Savchuk, N.P.; Ivaschenko, A.A. New diversity calculations algorithms used for compound selection. J. Chem. Inf. Comput. Sci. 2002, 42, 249-258.
15. Agrafiotis, D.K. A constant time algorithm for estimating the diversity of large chemical libraries. J. Chem. Inf. Comput. Sci. 2001, 41, 159-167.
16. Cummins, D.J.; Andrews, C.W.; Bentley, J.A.; Cory, M. Molecular diversity in chemical databases: Comparison of medicinal chemistry knowledge bases and databases of commercially available compounds. J. Chem. Inf. Comput. Sci. 1996, 36, 750-763.
17. Pearlman, R.S.; Smith, K.M. Novel software tools for chemical diversity. Perspect. Drug Discov. Design 1998, 9, 339-353.
18. Xue, L.; Bajorath, J. Molecular descriptors for effective classification of biologically active compounds based on principal component analysis identified by a genetic algorithm. J. Chem. Inf Comput. Sci. 2000, 40, 801-809.
19. Bayley, M.J.; Willett, P. Binning schemes for partition-based compound selection. J. Mol. Graph. Model. 1999, 17, 10-18.
20. Glen, W.G.; Dunn, W.J.; Scott, D.R. Principal component analysis and partial least squares regression. Tetrahedron Comput. Methodol. 1989, 2, 349-376.
21. Friedman, J.A. Recursive partitioning decision roles for nonparametric classification. IEEE Trans. Comput. 1977, 26, 404-408.
22. Rusinko, A. III; Farmen, M.W.; Lambert, C.G.; Brown, P.L.; Young, S.S. Analysis of a large structure/biological activity data set using recursive partitioning. J. Chem. Inf. Comput. Sci. 1999, 39, 1017-1026.
23. Meier, P.C.; Zünd, R.E. Statistical methods in analytical chemistry; John Wiley & Sons: New York, 2000.
24. Shannon, C.E.; Weaver, W. The Mathematical Theory of Communication; University of Illinois Press: Urbana, 1963.
25. Godden, J.W.; Stahura, F.L.; Bajorath, J. Variability of molecular descriptors in compound databases revealed by Shannon entropy calculations. J. Chem. Inf. Comput. Sci. 2000, 40, 796-800.
26. Godden, J.W.; Bajorath, J. Chemical descriptors with distinct levels of information content and varying sensitivity to differences between selected compound databases identified by SE-DSE analysis. J. Chem. Inf. Comput. Sci. 2002, 42, 87-93.
27. MOE (Molecular Operating Environment), version 2001.01, Chemical Computing Group Inc., 1255 University Street, Montreal, Quebec, Canada, H3B 3X3.
28. Available Chemicals Directory, MDL Information Systems, Inc., 14600 Catalina Street, San Leandro, CA 94577.
29. Forrest, S. Genetic algorithms - Principles of natural selection applied to computation. Science 1993, 261, 872-878.
30. Carhart, R.E.; Smith, D.H.; Vankataraghavan, R. Atom pairs as molecular features in structure-activity studies: Definition and applications. J. Chem. Inf. Comput. Sci. 1985, 25, 64-73.
31. Xue, L.; Bajorath, J. Distribution of molecular scaffolds and R-groups isolated from large compound databases. J. Mol. Model. 1999, 5, 97-102.
32. Labute, P. A widely applicable set of descriptors. J. Mol. Graph. Model. 2000, 18, 464-477.
33. Hann, M.; Hudson, B.; Lewell, X.; Lifely, R.; Miller, L.; Ramsden, N. Strategic pooling of compounds for high-throughput screening. J. Chem. Inf. Comput. Sci. 1999, 39, 897-902.
34. Muegge, I.; Heald, S.L.; Britelli, D. Simple selection criteria for drug-like chemical matter. J. Med. Chem. 2001, 44, 1841-1846.
35. Lipinski, C.A.; Lombardo, F.; Dominy, B.W., Feeney, P.J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug. Deliv. Rev. 1997, 23, 3-25.
36. Martin, Y.C. Diverse viewpoints on computational aspects of molecular diversity. J. Comb. Chem. 2001, 3, 1-20.
37. Hall, L.H.; Kier, L.B. The molecular connectivity chi indexes and kappa shape indexes in structure-property modeling. Rev. Comput. Chem. 1991, 2, 367-422.
38. Gasteiger, J.; Marsili, M. Iterative partial equalization of orbital electronegativity - A rapid access to atomic charges. Tetrahedron 1980, 36, 3219-3228.
39. Balaban, A.T. Highly discriminating distance-based topological index. Chem. Phys. Lett. 1982, 89, 399-404.