A Scalable Approach to Combinatorial Library Design

Methods in Molecular Biology

Volumn 685, Issue , 2011, Pages 71-89

  Sharma, Puneet ^a   Salapaka, Srinivasa ^b   Beck, Carolyn ^b  

^a SIEMENS CORPORATE RESEARCH   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

Author keywords

combinatorial optimization; deterministic annealing; Library design

Indexed keywords

ALGORITHM; ARTICLE; CHEMISTRY; CLUSTER ANALYSIS; COMBINATORIAL CHEMISTRY; DRUG DEVELOPMENT; METHODOLOGY; MOLECULAR LIBRARY; SYNTHESIS; TIME;

ALGORITHMS; CLUSTER ANALYSIS; COMBINATORIAL CHEMISTRY TECHNIQUES; DRUG DISCOVERY; SMALL MOLECULE LIBRARIES; TIME FACTORS;

MLCS; MLOWN;

EID: 79952202679     PISSN: 10643745     EISSN: 19406029     Source Type: Book Series    
DOI: 10.1007/978-1-60761-931-4_4     Document Type: Chapter

References (21)

1. Gordon, E. M., Barrett, R. W., Dower, W. J., Fodor, S. P. A., Gallop, M. A. (1994) Applications of combinatorial technologies to drug discovery. 2. Combinatorial organic synthesis, library screening strategies, and future directions. J Med Chem 37(10), 1385–1401.
2. Blaney, J., Martin, E. (1997) Computational approaches for combinatorial library design and molecular diversity analysis. Curr Opin Chem Biol 1, 54–59.
3. Willett, P. (1997) Computational tools for the analysis of molecular diversity. Perspect Drug Discov Design, 7/8, 1–11.
4. Rassokhin, D. N., Agrafiotis, D. K. (2000) Kolmogorov-Smirnov statistic and its applications in library design. J Mol Graph Model 18(4–5), 370–384.
5. Lipinski, C. A., Lomabardo, F., Dominy, B. W., Feeny, P. J. (1997) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development setting. Adv Drug Del Review 23, 2–25.
6. Higgs, R. E., Bemis, K. G., Watson, I. A., Wikel, J. H. (1997) Experimental designs for selecting molecules from large chemical databases. J Chem Inf Comput Sci 37, 861–870.
7. Clark, R. D. (1997) Optisim: an extended dissimilarity selection method for finding diverse representative subsets. J Chem Inf Comput Sci 37(6), 1181–1188.
8. Agrafiotis, D. K., Lobanov, V. S. (2000) Ultrafast algorithm for designing focussed combinatorial arrays. J Chem Inf Comput Sci 40, 1030–1038.
9. Salapaka, S., Khalak, A. (2003) Constraints on locational optimization problems. Proceedings of the IEEE Control and Decisions Conference. Maui, HI, 9–12 December 2003, pp. 1741–1746.
10. Sharma, P., Salapaka, S., Beck, C. (2008) A scalable approach to combinatorial library design for drug discovery. J Chem Inf Model 48(1), 27–41.
11. Gersho, A., Gray, R. (1991) Vector Quantiza-tion and Signal Compression. Kluwer, Boston, Massachusetts.
12. Drezner, Z. (1995) Facility location: a survey of applications and methods. Springer Series in Operations Research, Springer, New York.
13. Du, Q., Faber, V., Gunzburger, M. (1999) Centroidal Voronoi tessellations: applications and algorithms. SIAM Rev 41(4), 637–676.
14. Therrien, C. W. (1989) Decision, Estimation and Classification: An Introduction to Pattern Recognition and Related Topics, 1st ed. Wiley, New York.
15. Haykin, S. (1998) Neural Networks: A Comprehensive Foundation, Prentice Hall, Engle-woods Cliffs, NJ.
16. Gray, R., Karnin, E. D. (1982) Multiple local minima in vector quantizers. IEEE Trans Inform Theor 28, 256–361.
17. Lloyd, S. P. (1982) Least squares quanti-zation in PCM. IEEE Trans Inform Theory 28(2), 129–137.
18. Rose, K. (1998) Deterministic annealing for clustering, compression, classification, regression and related optimization problems. Proc IEEE 86(11), 2210–2239.
19. Mcmaster hts lab competition. HTS data mining and docking competition. http://hts.mcmaster.ca/downloads/82bfbeb4-f2a4-4934-b6a8-804cad8e25a0.html (accessed June 2006).
20. Guha, R. (2006) Chemistry Development Kit (CDK) descriptor calculator GUI (v 0.46). http://cheminfo.informatics. indiana.edu/rguha/code/java/cdkdesc.html (accessed October 2006).
21. Steinbeck, C., Hoppe, C., Kuhn, S., Floris, M., Guha, R., Willighagen, E. L. (2006) Recent developments of the Chemistry Development Kit (CDK) – an open-source JAVA library for chemo and bioinformatics. Curr Pharm Des 12(17), 2110–2120.