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IBM Journal of Research and Development  
Volume 45, Numbers 3/4, 2001
Deep computing for the life sciences
 Table of contents: arrowHTML arrowPDF arrowASCII   This article: arrowHTML arrowPDF arrowASCII arrowCopyright info
   

Multiobjective optimization of combinatorial libraries - References

by D. K. Agrafiotis

References

  1. L. A. Thompson and J. A. Ellman, Chem. Rev. 96, 555–600 (1996).
  2. V. Pareto, Manual of Political Economy, 1906, p. 106.
  3. H. A. Eschenauer, J. Koski, and A. Osyczka, Multicriteria Design Optimization: Procedures and Applications, Springer-Verlag, New York, 1986.
  4. E. J. Martin, J. M. Blaney, M. A. Siani, D. C. Spellmeyer, A. K. Wong, and W. H. Moos, “Measuring Diversity: Experimental Design of Combinatorial Libraries for Drug Discovery,” J. Med. Chem. 38, 1431–1436 (1995).
  5. D. K. Agrafiotis, R. F. Bone, F. R. Salemme, and R. M. Soll, U.S. Patents 5,463,564, 1995; 5,574,656, 1996; 5,684,711, 1997; and 5,901,069, 1999.
  6. R. P. Sheridan and S. K. Kearsley, “Using a Genetic Algorithm to Suggest Combinatorial Libraries,” J. Chem. Inf. Comput. Sci. 35, 310–320 (1995).
  7. L. Weber, S. Wallbaum, C. Broger, and K. Gubernator, “Optimization of the Biological Activity of Combinatorial Compound Libraries by a Genetic Algorithm,” Angew. Chem. Int. Ed. Eng. 34, 2280–2282 (1995).
  8. J. Singh, M. A. Ator, E. P. Jaeger, M. P. Allen, D. A. Whipple, J. E. Soloweij, S. Chowdhary, and A. M. Treasurywala, “Application of Genetic Algorithms to Combinatorial Synthesis: A Computational Approach for Lead Identification and Lead Optimization,” J. Amer. Chem. Soc. 118, 1669–1676 (1996).
  9. D. K. Agrafiotis, “Stochastic Algorithm for Maximizing Molecular Diversity,” presented at the 3rd Electronic Computational Chemistry Conference, http://hackberry.chem.niu.edu/ECCC3/paper48, 1996.
  10. D. K. Agrafiotis, “Stochastic Algorithms for Maximizing Molecular Diversity,” J. Chem. Inf. Comput. Sci. 37, 841–851 (1997).
  11. D. K. Agrafiotis, “On the Use of Information Theory for Assessing Molecular Diversity,” J. Chem. Inf. Comput. Sci. 37, 576–580 (1997).
  12. D. K. Agrafiotis and V. S. Lobanov, “An Efficient Implementation of Distance-Based Diversity Metrics Based on k-d Trees,” J. Chem. Inf. Comput. Sci. 39, 51–58 (1999).
  13. M. Hassan, J. P. Bielawski, J. C. Hempel, and M. Waldman, “Optimization and Visualization of Molecular Diversity of Combinatorial Libraries,” Mol. Diversity 2, 64–74 (1996).
  14. M. Waldman, H. Li, and M. Hassan, “Novel Algorithms for the Optimization of Molecular Diversity of Combinatorial Libraries,” J. Mol. Graphics Mod. (special issue on combinatorial library design, D. K. Agrafiotis and E. Martin, Eds.) 18, 412–426 (2000).
  15. A. C. Good and R. A. Lewis, “New Methodology for Profiling Combinatorial Libraries and Screening Sets: Cleaning Up the Design Process with HARPcik,” J. Med. Chem. 40, 3926 (1997).
  16. W. Zheng, S. J. Cho, and A. Tropsha, “Rational Combinatorial Library Design: 1) Focus-2D: A New Approach to the Design of Targeted Combinatorial Chemical Libraries,” J. Chem. Inf. Comput. Sci. 38, 251 (1998).
  17. R. D. Brown and Y. C. Martin, “Designing Combinatorial Library Mixtures Using Genetic Algorithms,” J. Med. Chem. 40, 2304–2313 (1997).
  18. V. J. Gillet, P. Willett, J. Bradshaw, and D. V. S. Green, “Selecting Combinatorial Libraries to Optimize Diversity and Physical Properties,” J. Chem. Inf. Comput. Sci. 39, 169–177 (1999).
  19. D. N. Rassokhin and D. K. Agrafiotis, “Kolmogorov– Smirnov Statistic and Its Applications in Library Design,” J. Mol. Graphics Mod. 18, 370–384 (2000).
  20. R. D. Brown, M. Hassan, and M. Waldman, “Combinatorial Library Design for Diversity, Cost Efficiency and Druglike Character,” J. Mol. Graphics Mod. 18, 427–437 (2000).
  21. R. P. Sheridan, S. G. SanFeliciano, and S. K. Kearsley, “Designing Targeted Libraries with Genetic Algorithms,” J. Mol. Graphics Mod. 18, 320–334 (2000).
  22. G. M. Downs and P. Willett, “Similarity Searching and Clustering of Chemical-Structure Databases Using Molecular Property Data,” J. Chem. Inf. Comput. Sci. 34, 1094–1102 (1994).
  23. R. D. Brown and Y. C. Martin, J. Chem. Inf. Comput. Sci. 36, 572–584 (1996).
  24. D. E. Patterson, R. D. Cramer, A. M. Ferguson, R. D. Clark, and L. E. Weinberger, J. Med. Chem. 39, 3049–3059 (1996).
  25. R. D. Brown and Y. C. Martin, “The Information Content of 2D and 3D Structural Descriptors Relevant to Ligand-Receptor Binding,” J. Chem. Inf. Comput. Sci. 37, 1–9 (1997).
  26. H. Matter, “Selecting Optimally Diverse Compounds from Structure Databases: A Validation Study of Two-Dimensional and Three-Dimensional Molecular Descriptors,” J. Med. Chem. 40, 1219 (1997).
  27. Y. C. Martin, M. G. Bures, and R. D. Brown, “Validated Descriptors for Diversity Measurements and Optimization,” Pharm. Pharmacol. Commun. 4, 147 (1998).
  28. V. J. Gillet, P. Willett, and J. Bradshaw, J. Chem. Inf. Comput. Sci. 37, 731–740 (1997).
  29. E. A. Jamois, M. Hassan, and M. Waldman, J. Chem. Inf. Comput. Sci. 40, 63–70 (2000).
  30. A. Polinsky, R. D. Feinstein, S. Shi, and A. Kuki, Molecular Diversity and Combinatorial Chemistry, I. M. Chaiken and K. D. Janda, Eds., American Chemical Society: Washington, DC, 1996, pp. 219–232.
  31. E. J. Martin, D. C. Spellmeyer, R. E. Critchlow, and J. M. Blaney, “Does Combinatorial Chemistry Obviate Computer-Aided Drug Design?” Reviews in Computational Chemistry, Volume 10, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1997, pp. 75–100.
  32. P. Willett, Similarity and Clustering in Chemical Information Systems, Research Studies Press, Letchworth, UK, 1987.
  33. R. Taylor, J. Chem. Inf. Comput. Sci. 35, 59–67 (1995).
  34. D. Chapman, J. Comput.-Aided Mol. Design 10, 501–512 (1996).
  35. D. J. Cummins, C. W. Andrews, J. A. Bentley, and M. Cory, J. Chem. Inf. Comput. Sci. 36, 750–763 (1996).
  36. R. S. Pearlman and R. S. Smith, Perspect. Drug Discovery Design 9, 339–353 (1998).
  37. S. Pickett, J. S. Mason, and I. M. McLay, J. Chem. Inf. Comput. Sci. 36, 1214–1223 (1996).
  38. E. K. Davies and C. Briant, Network Sci., 1995, http://www.netsci.org/Science/Combichem/feature05.html.
  39. N. E. Shemetulsksis, D. Weininger, C. J. Blankley, J. J. Yang, and C. Humblet, J. Chem. Inf. Comput. Sci. 36, 862–871 (1996).
  40. S. M. Boyd, M. Beverly, L. Norskov, and R. E. Hubbard, J. Comput.-Aided Mol. Design 9, 417–424 (1995).
  41. D. K. Agrafiotis and V. S. Lobanov, “Ultrafast Algorithm for Designing Focused Combinatorial Arrays,” J. Chem. Inf. Comput. Sci. 40, 1030–1038 (2000).
  42. R. V. Stanton, J. Mount, and J. L. Miller, “Combinatorial Library Design: Maximizing Model Fitting Compounds with Matrix Synthesis Constraints,” J. Chem. Inf. Comput. Sci. 40, 701–705 (2000).
  43. D. K. Agrafiotis, “The Diversity of Chemical Libraries,” The Encyclopedia of Computational Chemistry, P. v. R. Schleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. A. Kollman, H. F. Schaefer III, and P. R. Schreiner, Eds., John Wiley & Sons, Chichester, UK, 1998, pp. 742–761.
  44. D. K. Agrafiotis, J. C. Myslik, and F. R. Salemme, “Advances in Diversity Profiling and Combinatorial Series Design,” Mol. Diversity 4, 1–22 (1999).
  45. D. K. Agrafiotis, V. S. Lobanov, D. N. Rassokhin, and S. Izrailev, “The Measurement of Molecular Diversity,” Virtual Screening of Bioactive Molecules, H.-J. Böhm and G. Schneider, Eds., Wiley–VCH Verlag GmbH, Weinheim, Germany, 2000.
  46. M. S. Lajiness, in QSAR: Rational Approaches to the Design of Bioactive Compounds, C. Silipo and A. Vittoria, Eds., Elsevier, Amsterdam, Netherlands, 1991, pp. 201–204.
  47. D. S. Dhanoa, V. Gupta, A. Sapienza, and R. M. Soll, Poster 26, American Chemical Society National Meeting, Anaheim, CA, 1999.
  48. L. H. Hall and L. B. Kier, “The Molecular Connectivity Chi Indexes and Kappa Shape Indexes in Structure– Property Relations,” Reviews of Computational Chemistry, D. B. Boyd and K. B. Lipkowitz, Eds., VCH Publishers, New York, 1991, Ch. 9, pp. 367–422.
  49. D. Bonchev and N. Trinajstic, J. Chem. Phys. 67, 4517–4533 (1977).
  50. V. S. Lobanov and D. K. Agrafiotis, “Stochastic Similarity Selections from Large Combinatorial Libraries,” J. Chem. Inf. Comput. Sci. 40, 460–470 (2000).
  51. D. K. Agrafiotis, “A New Method for Analyzing Protein Sequence Relationships Based on Sammon Maps,” Prot. Sci. 6, 287–293 (1997).
  52. D. K. Agrafiotis and V. S. Lobanov, “Nonlinear Mapping Networks,” J. Chem. Inf. Comput. Sci. 40, 1356–1362 (2000).
  53. D. N. Rassokhin, V. S. Lobanov, and D. K. Agrafiotis, “Nonlinear Mapping of Massive Data Sets by Fuzzy Clustering and Neural Networks,” J. Comput. Chem. 22, 373–386 (2000).
  54. D. K. Agrafiotis, D. N. Rassokhin, and V. S. Lobanov, “Multidimensional Scaling of Large Molecular Similarity Tables,” J. Comput. Chem. 22, 488–500 (2000).
  55. A. K. Ghose, V. N. Viswanadhan, and J. J. Wendoloski, J. Phys. Chem. A 102, 3762–3772 (1998).
  56. D. K. Agrafiotis, “Constant Time Algorithm for Estimating the Diversity of Large Chemical Libraries,” J. Chem. Inf. Comput. Sci. 41, 159–167 (2000).
  57. E. J. Martin and R. E. Critchlow, “Beyond Mere Diversity: Tailoring Combinatorial Libraries for Drug Discovery,” J. Comb. Chem. 1, 32–45 (1999).
  58. E. J. Martin and A. Wong, “Sensitivity Analysis and Other Improvements to Tailored Combinatorial Library Design,” J. Chem. Inf. Comput. Sci. 40, 215–220 (2000).
  59. R. T. Koehler, S. L. Dixon, and O. H. Villar, “LASSOO: A Generalized Directed Diversity Approach to the Design and Enrichment of Chemical Libraries,” J. Med. Chem. 42, 4695–4704 (1999).
  60. C. A. Lipinski, F. Lombardo, B. W. Dominy, and P. J. Feeny, Adv. Drug Delivery Rev. 23, 3–25 (1997).