Molecular Library Design Using Multi-Objective Optimization Methods (original) (raw)

References

1. Ekins, S., Boulanger, B., Swaan, P. W., Hupcey, M. A. (2002) Towards a new age of virtual ADME/TOX and multidimensional drug discovery. J Comput Aided Mol Des 16, 381–401.
   Article PubMed CAS Google Scholar
2. Agrafiotis, D. K., Lobanov, V. S., Salemme, F. R. (2002) Combinatorial informatics in the post-genomics era. Nat Rev Drug Discov 1, 337–346.
   Article PubMed CAS Google Scholar
3. Baringhaus, K. –H., Matter, H. (2004) Efficient strategies for lead optimization by simultaneously addressing affinity, selectivity and pharmacokinetic parameters, in (Oprea, T., ed.) Chemoinformatics in Drug Discovery. Wiley-VCH, Weinheim, Germany, pp. 333–379.
   Google Scholar
4. Nicolaou, C. A., Brown, N., Pattichis, C. S. (2007) Molecular optimization using computational multi-objective methods. Curr Opin Drug Discov Dev 10, 316–324.
   CAS Google Scholar
5. Soltanshahi, F., Mansley, T. E., Choi, S., Clark, R. D. (2006) Balancing focused combinatorial libraries based on multiple GPCR ligands. J Comput Aided Mol Des 20, 529–538.
   Article PubMed CAS Google Scholar
6. Gillet, V. J., Willet, P., Fleming, P. J., Green, D. V. (2002) Designing focused libraries using MoSELECT. J Mol Graph Model 20, 491–498.
   Article PubMed CAS Google Scholar
7. Gillet, V. J., Khatib, W., Willett, P., Fleming, P. J., Green, D. V. (2002) Combinatorial library design using a multiobjective genetic algorithm. J Chem Inf Comput Sci 42, 375–385.
   Article PubMed CAS Google Scholar
8. Agrafiotis, D. K. (2000) Multiobjective optimization of combinatorial libraries. Mol Divers 5, 209–230.
   Article CAS Google Scholar
9. Nicolaou, C. A., Apostolakis, J., Pattichis, C. S. (2009) De novo drug design using multi-objective evolutionary graphs. J Chem Inf Model 49, 295–307.
   Article PubMed CAS Google Scholar
10. Coello Coello, C. A. (2002) Evolutionary multiobjective optimization: a critical review, in (Sarker, R., Mohammadian, M., Yao, X. eds.) Evolutionary Optimization. New York: Springer 48, pp. 117–146.
    Google Scholar
11. Yann, C., Siarry, P. (eds.) (2004) Multiobjective Optimization: Principles and Case Studies, Springer, Berlin, Germany.
    Google Scholar
12. Fonseca, C. M., Fleming, P. J. (1998) Multiobjective optimization and multiple constraint handling with evolutionary algorithms. I: a unified formulation. IEEE Trans Syst Man Cybernet 28, 26–37.
    Article Google Scholar
13. Zitzler, E., Thiele, L. (1999) Multiobjective evolutionary algorithms: a comparative case study and the strength Pareto approach. IEEE Trans Evol Comput 3, 257–271.
    Article Google Scholar
14. Gillet, V. J. (2004) Designing combinatorial libraries optimized on multiple objectives in methods in molecular biology, in (Bajorath, J., ed.) Chemoinformatics: Concepts, Methods, and Tools for Drug Discovery. Humana Press, Totowa, NJ, 275, pp. 335–354.
    Google Scholar
15. Gillet, V. J., Willett, P., Bradshaw, J., Green, D. V. S. (1999) Selecting combinatorial libraries to optimize diversity and physical properties. J Chem Inf Comput Sci 39, 169–177.
    Article CAS Google Scholar
16. Zheng, W., Hung, S. T., Saunders, J. T., Seibel, G. L. (2000) PICCOLO: a tool for combinatorial library design via multicriterion optimization. Pac Symp Biocomput 5, 585–596.
    Google Scholar
17. Bemis, A. G. W., Murcko, M. A. (1999) Designing libraries with CNS activity. J Med Chem 42, 4942–4951.
    Article PubMed Google Scholar
18. Wright, T., Gillet, V. J., Green, D. V., Pickett, S. D. (2003) Optimizing the size and configuration of combinatorial libraries. J Chem Inf Comput Sci 43, 381–390.
    Article PubMed CAS Google Scholar
19. Noesis Chemoinformatics, Ltd. http://www.noesisinformatics.com (accessed August 12, 2009).
20. MoDest. http://www.chil2.de (accessed June 30, 2009).
21. OpenEye, Inc. http://www.eyesopen.com (accessed July 3, 2009).
22. Nicolaou, C. A., Pattichis, C. S. (2006) Molecular substructure mining approaches for computer-aided drug discovery: a review. Proceedings of the 2006 ITAB Conference, October 26–28, Ioannina, Greece.
    Google Scholar
23. Lewell, X. O., Budd, D. B., Watson, S. P., Hann, M. M. (1998) RECAP – Retrosynthetic Combinatorial Analysis Procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry. J Chem Inf Comput Sci 38, 511–522.
    Article PubMed CAS Google Scholar
24. Barone R., Chanon, M. (2001) A new and simple approach to chemical complexity. Application to the synthesis of natural products. J Chem Inf Comput Sci 41, 269–272.
    Article PubMed CAS Google Scholar
25. Angelis, M. D., Stossi F., Waibel M., Katzenellenbogen, B. S., Katzenellenbogen, J. A. (2005) Isocoumarins as estrogen receptor beta selective ligands: isomers of isoflavone phytoestrogens and their metabolites. Bioorg Med Chem 13, 6529–6542.
    Article PubMed Google Scholar
26. Wheeler, D. L., et al. (2006) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 34, 173–180.
    Article Google Scholar
27. Wild, D. J., Blankley, C. J. (2000) Comparison of 2D fingerprint types and hierarchy level selection methods for structural grouping using wards clustering. J Chem Inf Comput Sci 40, 155–162.
    Article PubMed CAS Google Scholar
28. Kearsley, S. K., Sallamack, S., Fluder, E. M., Andose, J. D., Mosley, R. T., Sheridan, R. P. (1996) Chemical similarity using physiochemical property descriptors. J Chem Inf Comput Sci 36, 118–127.
    Article CAS Google Scholar
29. Tietze, S., Apostolakis, J. (2007) GlamDock: development and validation of a new docking tool on several thousand protein-ligand complexes. J Chem Inf Model 47, 1657–1672.
    Article PubMed CAS Google Scholar
30. Willet, P., Barnard, J. M., Downs, G. M. (1998) Chemical similarity searching. J Chem Inf Comput Sci 39, 983–996.
    Google Scholar
31. Lipinski, C. A., Lombardo, F., Dominy, B. W., Feeney, P. J. (1997) Experimental and computational approaches to estimate solubility and permeability. Drug discovery and development settings. Adv Drug Discovery Rev 23, 3–25.
    Article CAS Google Scholar
32. Prien, O. (2005) Target-family-oriented focused libraries for kinases – conceptual design aspects and commercial availability. ChemBioChem 6, 500–505.
    Article PubMed CAS Google Scholar

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