Three-Dimensional quantitative structure-activity relationship: The state of the art

Comprehensive Medicinal Chemistry II

Volumn 4, Issue , 2006, Pages 575-595

  Doweyko, A M ^a  

^a BRISTOL MYERS SQUIBB   (United States)

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EID: 70249139620     PISSN: None     EISSN: None     Source Type: Book    
DOI: None     Document Type: Chapter

References (221)

1. Crum-Brown, A.; Fraser, T. R. Trans. R. Soc. Edinb. 1868, 25, 151.
2. Richardson, B. J. Med. Times Gazette 1869, 2, 703.
3. Hansch, G.; Fujica, T. J. Am. Ghem. Soc. 1964, 86, 1616-1626.
4. Free, S. M" Jr.; Wilson, J. W. J. Med. Chem. 1964, 7, 395-399.
5. Verloop, A.; Hoogenscraacen, W; Tipker, J. Med. Ghem. 1976, 11, 165-207.
6. Verloop, A. Proc. Int. Congr. Pestic. Chem. 1983, 1, 339-344.
7. Boyd, D. B. Review of Computational Chemistry, Lipkowitz, B.; Boyd, D. B., Eds.; VCH: New York, 1990, pp 355-371.
8. Fujita, T The Role of QSAR in Drug Design. In Drug Design: Fact or Fantasy? Jolles, G., Wooldridge, K. R. H., Eds.; Academic Press: London, 1984, pp 19-33.
9. Hansch, C.; Leo, A.; Khoekman, D. Exploring QSAR: Hydrophobic, Electronic and Steric Constants; ACS: Washington, DC, 1995.
10. Kier, L. B. Molecular Orbital Theory in Drug Research; Academic Press: New York, 1971.
11. Holtje, H. D.; Kier, L. B. J. Pharm. Sei. 1974, 63, 1722-1725.
12. Holtje, H. D.; Kier, L. B. J. Med. Chem. 1974, 17, 814-819.
13. Marshall, G. R. Med. Chem., Proc. Int. Symp. 1979, 225-235.14
14. Marshall, G. R.; Barry, C. D.; Bosshard, H. E.; Dammkoehler, R. A.; Dunn, D. A. ACS Symp. Ser. 1979, 112, 205-226.
15. Murray, W J.; Hall, L. H.; Kier, L. B. J. Pharm. Sei. 1975, 64, 1978-1981.
16. Kier, L. B.; Hall, L. H.; Murray, W J.; Randic, M. J. Pharm. Sei. 1975, 64, 1971-1974.
17. Kier, L. B.; Murray, W J.; Hall, L. H. J. Med. Chem. 1975, 18, 1272-1274.
18. Murray, W J.; Kier, L. B.; Hall, L. H. J. Med. Chem. 1976, 19, 573-578.
19. Kier, L. B.; Hall, L. H. Medicinal Chemistry, Molecular Connectivity in Chemistry and Drug Research; Academic Press: New York, 1976; Vol. 14.
20. Hopfinger, A. J. J. Med. Chem. 1983, 26, 990-996.
21. Hopfinger, A. J. Arch. Biochem. Biophysics 1981, 206, 153-163.
22. Hopfinger, A. J.; Burke, B. J. Prog. Clin. Biol. Res. 1989, 291, 151-159.
23. Tokarski, J. S.; Hopfinger, A. J. J. Med. Chem. 1994, 37, 3639-3654.
24. Montsenigos, A.; Ciubotariu, D.; Chiriac, A.; Simon, Z. Rev. Roumaine Chimie 1989, 34, 2101-2106.
25. Simon, Z.; Dragomir, N.; Plauchitiu, M. G.; Holban, S.; Glatt, H.; Kerek, F. Eur. J. Med. Chem. 1980, 15, 521-527.
26. Simon, Z. MTD and Hyperstructure Approaches. In 3D QSAR Drug Design; Kubinyi, H., Ed.; ESCOM: The Netherlands, 1993, pp 307-319.
27. Simon, Z.; Chiriac, A.; Holban, S.; Ciubotam, D.; Mihalas, G. I. Chemometrics Series, Minimum Steric Difference. The MTD Method for QSAR Studies; Wiley: New York, 1984; Vol. 7.
28. Ghose, A. K.; Crippen, G. M. Mol. Pharmacol. 1990, 37, 725-734.
29. Ghose, A. K.; Crippen, G. M. Quant. Struct.-Act. Relat. J. Med. Chem. 1985, 28, 333-346.
30. Ghose, A. K.; Crippen, G. M.; Revankar, G. R.; McKernan, P. A.; Smee, D. F; Robins, R. K. J. Med. Chem. 1989, 32, 746-756.
31. Goodford, P. J. J. Med. Chem. 1985, 28, 849-857.
32. Boobbyer, D. N.; Goodford, P. J.; McWhinnie, P. M.; Wade, R. C. J. Med. Chem. 1989, 32, 1083-1094.
33. Semus, S. F. Med. Chem. Res. 1999, 9, 535-547.
34. Semus, S. F, Kellogg, G. E., Application of HINT Interaction Scores and Hydropathic Intermolecular Field Analysis (HIFA) to the Prediction of Ligand Binding Affinity. Abstracts of Papers, 228th ACS National Meeting, Philadelphia, PA, United States, August 22-26, 2004; American Chemical Society: Washington, DC, 2004, COMP-102.
35. Cramer, R. D., III; Bunce, J. D. Pharmacochem. Libr. 1987, 10, 3-12.
36. Wise, M.; Cramer, R.D.; Smith, D.; Exman, I. Progress in Three-Dimensional Drug Design: The Use of Real Time Colour Graphics and Computer Postulation of Bioactive Molecules in DYLOMMS. In Quantitative Approaches to Drug Design; Proceedings of the 4th European Symposium on Chemical Structure-Biological Activity: Quantitative Approaches; Dearden, J., Ed.; Elsevier: Amsterdam, 1983, pp 145-146.
37. Wise, M. Evolution of QSAR Methodology and the Role of Newer Computational Techniques. In QSAR and Strategies in the Design of Bioactive Compounds; Proceedings of the 5th European Symposium on QSAR; VCH: Weinheim, 1985, pp 19-29.
38. Cramer, R. D., III; Patterson, D. E.; Bunce, J. D. J. ACS 1988, 110, 5959-5967.
39. Skagerberg, B.; Dunn, W J., III; Hellberg, S.; Wold, S. The PLS Data Analytic Method in QSAR. In Fed. Rep. Ger. QSAR Strategies in the Design of Bioactive Compounds; Seydel, J. K., Ed.; 1985, 305-310.
40. Geladi, P.; Kowalski, B. R. Anal. Chim. Acta 1986, 185, 1-17.
41. Doweyko, A. M. J. Med. Chem. 1988, 31, 1396-1406.
42. Green, S. M.; Marshall, G. R. Trends Pharm. Sei 1995, 16, 285-291.
43. Oprea, T I.; Waller, C. L. Rev. Comput. Chem. 1997, 127-182.
44. Greco, G.; Novellino, E.; Martin, Y C. Rev. Comput. Chem. 1997, 183-240.
45. Lewis, R. A. Chem. Model. 2002, 2, 271-292.
46. Akamatsu, M. Curr. Top. Med. Chem. 2002, 2, 1381-1394.
47. Kellogg, G. E.; Semus, S. F. 3D QSAR in Modern Drug Design. In Modern Methods of Drug Discovery (Experientia Supplementum Vol. 93); Hillisch, A., Hilgenfeld, R., Eds.; Verlag: Birkhauser, Switzerland, 2003, pp 223-241.
48. Cruciani, G.; Carosati, E.; Clementi, S. Three-Dimensional Quantitative Structure-Property Relationships. In The Practice of Medicinal Chemistry, 2nd ed.; Wermuth, C. G., Ed.; Elsevier: London, 2003, pp 405-416.
49. Oprea, T I. 3D-QSAR Modeling in Drug Design. In Computational Medicinal Chemistry for Drug Discovery; Bultinck, P, Ed.; Marcel Dekker: New York, 2004, pp 571-616.
50. Greener, M. QSAR: Predictions Beyond the Fourth Dimension. In Drug Discovery and Development; Reed Business Information, div of Reed Elsevier, Inc., 2005.
51. Cramer, R. D., III; Wold, S. B. Comparative molecular field analysis (CoMFA); U.S. Patent 5025388A, June, 18, 1991, 22 pp.
52. Kim, K. H. Perspect. Drug Disc. Design 1998, 12-14, 317-338.
53. Clark, M. R. C.; Jones, D.; Patterson, D.; Simeroth, P. Tetrahedron Comp. Methods 1990, 3, 47.
54. Sun, H.; Xie, Q.; Zhou, J.; Xu, Z. Huaxue Jinzhan 1996, 8, 79-85.
55. Kim, K. H.; Greco, G.; Novellino, E. Perspect. Drug Disc. Design 1998, 12/13/14, 257-315.
56. Norinder, U. Perspect. Drug Disc. Design 1998, 12/13/14, 25-39.
57. SYBYL Molecular Modeling Software; Tripos, Inc.: St. Louis, MO 63144, US.
58. Cho, S. J.; Tropsha, A. J. Med. Chem. 1995, 38, 1060-1066.
59. Tropsha, A.; Cho, S. J. Perspect. Drug Disc. Design 1998, 12/13/14, 57-69.
60. Kimura, T; Hasegawa, K.; Funatsu, K. J. Chem. Inf. Comp. Sei. 1998, 38, 276-282.
61. Baroni, M. G. C.; Cruciani, G.; Riganelli, D.; Valigi, R.; Clementi, S. Quant. Struct.-Act. Rßlat. 1993, 12, 9.
62. Cruciani, G.; Watson, K. A. J. Med. Chem. 1994, 37, 2589-2601.
63. Nilsson, J.; Wikstrom, H.; Smilde, A.; Glase, S.; Pugsley, T; Cruciani, G.; Pastor, M.; Clementi, S. J. Med. Chem. 1997, 40, 833-840.
64. Sulea, T; Purisima, E. O. Quant. Struct.-Act. Relat. 1999, 18, 154-158.
65. Nicholls, A.; Honig, B. J. Comput. Chem. 1991, 12, 435-445.
66. Waller, C. L.; Marshall, G. R. J. Med. Chem. 1993, 36, 2390-2403.
67. DELPHI; Accelrys, Inc.: San Diego, CA.
68. Klebe, G.; Abraham, U.; Mietzner, T. J. Med. Chem. 1994, 37, 4130-4146.
69. Bringmann, G.; Rummey, C. J. Chem. Inf. Comp. Sei. 2003, 43, 304-316.
70. Kellogg, G. E.; Semus, S. F; Abraham, D. J. J. Comput.-AidedMol. Design 1991, 5, 545-552.
71. Aurenhammer, F. ACM Comput. Surv 1991, 23, 345-305.
72. Srivastava, S. W W R.; Bradley, M. P; Crippen, G. M. Three-Dimensional Receptor Modeling Using Distance Geometry and Voronoi Polyhedra. In 3D QSAR in Drug Design: Theory, Methods and Applications'; Kubinyi, H., Ed.; ESCOM: Leiden, 1993, pp 409-430.
73. Chuman, H.; Karasawa, M.; Fujita, T. Quant. Struct.-Act. Relat. 1998, 17, 313-326.
74. Audry, E.; Dallet, P; Langlois, M. H.; Colleter, J. C.; Dubost, J. P. Prog. Clin. Biol Res. 1989, 291, 63-66.
75. Gaillard, P.; Carrupt, P. A.; Testa, B.; Boudon, A. J. Comput.-Aided Mol. Design 1994, 8, 83-96.
76. Carrupt, P. A.; Billois, F; Weber, P; Testa, B.; Meyer, C.; Perez, S. The Molecular Lipophilicity Potential (MLP): A New Tool for LogP Calculation and Docking, and in Comparative Molecular Field Analysis (CoMFA). In Lipophilicity in Drug Action and ; Pliska, V, Testa, B., van de Waterbeemd, H., Eds.; VCH: Weinheim, 1995, pp 195-215.
77. Floersheim, P; Nozulak, J.; Weber, H. P. Experience with Comparative Molecular Field Analysis. In Trends in QSAR and Proceedings of the European Symposium in Structure-Activity Relationships: QSAR and Molecular Modelling; Wermuth, C.-G., Ed.; ESCOM: Leiden, The Netherlands, 1993, pp 227-232.
78. Ghose, A. K.; Crippen, G. M. J. Comput. Chem. 1986, 7, 333-346.
79. Amat, L.; Robert, D.; Besalu, E.; Carbo-Dorca, R. J. Chem. Inf. Comp. Sei. 1998, 38, 624-631.
80. Girones, X.; Amat, L.; Carbo-Dorca, R. SAR QSAR Environ. Res. 1999, 10, 545-556.
81. Carbo, R.; Besalu, E.; Amat, L.; Fradera, X. J. Math. Chem. 1995, 18, 237-246.
82. Fradera, X.; Amat, L.; Besalu, E.; Carbo-Dorca, R. Quant. Struct.-Act. Relat. 1997, 16, 25-32.
83. Robinson, D. D.; Winn, P. J.; Richards, W G. Self-Organizing Molecular Field Analysis. Book of Abstracts, 216th ACS National Meeting, Boston, August 23-27; American Chemical Society: Washington, DC, 1998, COMP-082.
84. Winn, P. J.; Robinson, D. D.; Richards, W. G. Self-Organizing Molecular Field Analysis (SOMFA): A Tool for Structure-Activity Studies. In Fundamental of Molecular Similarity; Carbo-Dorca, R., Girones, X., Mezey, P. G., Eds.; Kluwer: New York, 2001, pp 321-332.
85. Horwell, D. C.; Howson, W; Higginbottom, M.; Naylor, D.; Ratcliffe, G. S.; Williams, S. J. Med. Chem. 1995, 38, 4454-4462.
86. Klebe, G.; Abraham, U. J. Med. Chem. 1993, 36, 70-80.
87. Mestres, J.; Rohrer, D. C.; Maggiora, G. M. J. Mol. Graphics Model 1997, 15, 114-121, 103-116.
88. Doweyko, A. M. ACS Symposium Ser. 1989, 413, 82-104.
89. Nowakowski, M.; Tishler, M.; Doweyko, A. M. Phosphorus Sulfur Silicon Relat. Elements 1989, 45, 183-188.
90. Doweyko, A. M. J. Math. Chem. 1991, 7, 273-285.
91. Doweyko, A. M.; Mattes, W B. Biochemistry 1992, 31, 9388-9392.
92. Kaminski, J. J.; Doweyko, A. M. J. Med. Chem. 1997, 40, 427-436.
93. Woolfrey, J. R.; Avery, M. A.; Doweyko, A. M. J. Comput.-Aided Mol. Design 1998, 12, 165-181.
94. Doweyko, A. M.; Kellogg, G. E. www.edusoft-lc.com (accessed Aug 2006).
95. Vedani, A.; Zbinden, P; Snyder, J. P. J. Receptor Res. 1993, 13, 163-177.
96. Schmetzer, S.; Greenidge, P; Kovar, K. A.; Schulze-Alexandru, M.; Folkers, G. J. Comput.-Aided Mol. Design 1997, 11, 278-292.
97. Sippl, W; Stark, H.; Hoeltje, H. D. Pharmazie 1998, 53, 433-437.
98. Gurrath, M.; Muller, G.; Holtje, H.-D. Perspect. Drug Disc. Design 1998, 12/13/14, 135-157.
99. Zbinden, P; Dobler, M.; Folkers, G.; Vedani, A. Quant. Struct.-Act. Relat. 1998, 17, 122-130.
100. Hahn, M. J. Med. Chem. 1995, 38, 2080-2090.
101. Hahn, M.; Rogers, D. Receptor surface models. Perspect. Drug Disc. Design 1998, 12/13/14, 117-133.
102. Potemkin, V A.; Bartashevich, E. V; Grishina, M. A.; Guccione, S. An Alternative Method for 3D-QSAR and the Alignment of Molecular Structures: BiS (Biological Substrate Search). In Rational Approaches to Drug Design; Proceedings of the European Symposium on Quantitative Structure-Activity Relationships, 13th, Duesseldorf, Germany; Holtje, H.-D., Sippl, W, Eds.; Prous Science: Philadelphia, 2001, pp 349-353.
103. Walters, D. E. Perspect. Drug Disc. Design 1998, 12/13/14, 159-166.
104. Walters, D. E.; Hinds, R. M. J. Med. Chem. 1994, 37, 2527-2536.
105. Hirashima, A.; Eiraku, T; Kuwano, E.; Eto, M. Combinat. Chem. High Throughput Screen. 2004, 7, 83-91.
106. Santagati, M.; Doweyko, A.; Santagati, A.; Modica, M.; Guccione, S.; Chen, H.; Barretta, G. U.; Balzano, F. 5-HT1A Receptors Mapping by Conformational Analysis (2D NOESY/MM) and Molecular Modeling and Prediction of Bioactivity; Proceedings of the European Symposium on Quant. Struct.-Act. Relat.: Molecular Modeling and Prediction of Bioactivity, 12th, Copenhagen, Denmark; Kluwer: New York, 2000, pp 183-194.
107. Chen, H. M.; Zhou, J. J.; Ren, T R.; Xie, G. R. Chin. Chem. Lett. 1997, 8, 975-978.
108. Albuquerque, M. G.; Hopfinger, A. J.; Barreiro, E. J.; de Alencastro, R. B. J. Chem. Inf. Comp. Sei. 1998, 38, 925-938.
109. Klein, C. D.; Hopfinger, A. J. Pharm. Res. 1998, 15, 303-311.
110. Ravi, M.; Hopfinger, A. J.; Hormann, R. E.; Dinan, L. J. Chem. Inf. Comput. Sei. 2001, 41, 1587-1604.
111. Hopfinger, A. J.; Tokarski, J. S.; Jin, B.; Albuquerque, M.; Madhav, P. J.; Duraiswami, C. J. Am. Chem. Soc. 1997, 119, 10509-10524.
112. Hopfinger, A. J.; Tokarski, J. 3D-QSAR Analysis. In Practical Application of Computer-Aided Drug Design; Charifson, P. S., Ed.; Dekker: New York, 1997, p 105.
113. Tsujishita, H.; Hirono, S. J. Comput.-Aided Mol. Design 1997, 11, 305-315.
114. Kearsley, S. K.; Smith, G. M. Tetrahedron Comput. Methodol 1990, 3, 615-633.
115. McMartin, C.; Bohacek, R. S. J. Comput.-Aided Mol. Design 1997, 11, 333-344.
116. Iwase, K.; Hirono, S. J. Comput.-Aided Mol. Design 1999, 13, 499-512.
117. Lemmen, C.; Lengauer, T; Klebe, G. J. Med. Chem. 1998, 41, 4502-4520.
118. De Esch, I. J.; Mills, J. E.; Perkins, T. D.; Romeo, G.; Hoffmann, M.; Wieland, K.; Leurs, R.; Menge, W. M. B.; Nederkoorn, P. H. J.; Dean, P M. et al. J. Med. Chem. 2001, 44, 1666-1674.
119. Mills, J. E. J.; De Esch, I. J. P; Perkins, T. D. J.; Dean, P M. J. Comput.-Aided Mol. Design 2001, 15, 81-96.
120. Kroonenberg, P. M.; Dunn, W. J.; Commandeur, J. J. F. J. Chem. Inf. Comput. Sci. 2003, 43, 2025-2032.
121. Commandeur, J. J. F; Kroonenberg, P. M.; Dunn, W J., III. J. Chemo 2004, 18, 37-42.
122. Kearsley, S. K.; Smith, G. M. Tetrahedron Comput. Methodol. 1990, 3, 615-633.
123. Waller, C. L.; Marshall, G. R. J. Med. Chem. 1993, 36, 2390-2403.
124. Hermann, R. B.; Herron, D. K. J. Comput.-Aided Mol. Design 1991, 5, 511-524.
125. Good, A. C.; Hodgkin, E. E.; Richards, W G. J. Chem. Inf. Comput. Sei. 1992, 32, 188-191.
126. Namasivayam, S.; Dean, P. M. J. Mol. Graph. 1986, 4, 46-50.
127. Dean, P. M.; Chau, P L. J. Mol Graph. 1987, 5, 152-164.
128. Martin, Y C. IUL Biotechnol Ser. 2000, 2, 49-68.
129. Martin, Y. C.; Bures, M. G.; Danaher, E. A.; DeLazzer, J.; Lico, I.; Pavlik, P. A. J. Comput.-Aided Mol. Design 1993, 7, 83-102.
130. Mason, J. S. Pharmacochem. Library 1993, 20, 147-156.
131. Halova, J.; Zak, P.; Strouf, O.; Uchida, N.; Yuzuri, T.; Sakakibara, K.; Hirota, M. Organic Reactivity (Tartu) 1997, 31, 31-43.
132. Kristam, R.; Gillet, V J.; Lewis, R. A.; Thorner, D. J. Chem. Inf. Model. 2005, 45, 461-476.
133. Sprague, P. W. Perspect. Drug Disc. Design 1995, 3, 1-20.
134. CATALYST 3D-QSAR Program; Accelrys, Inc.: San Diego, CA.
135. Doweyko, A. M. J. Med. Chem. 1994, 37, 1769-1778.
136. Golender, V; Vesterman, B.; Vorpagel, E. APEX-www.netsci.org (accessed Aug 2006).
137. Golender, V E.; Vorpagel, E. R. 3D QSAR Drug Des. 1993, 137-149.
138. Hongmei, S.; Xie, Q.; Xie, G.; Jiaju, Z.; Zhihong, X.; Zhengmin, L.; Guofeng, J.; Lingxiu, W. Wuli Huaxue Xuebao 1995, 11, 773-776.
139. Chow, M. M.; Meyer, E. F, Jr.; Bide, W; Kam, C. M.; Radhakrishnan, R.; Vijayalakshimi, J.; Powers, J. C. J. Am. Chem. Soc 1990, 112, 7783-7789.
140. Bolin, J. T; Matthews, D. J.; Hamlin, D. A.; Kraut, J. J. Biol Chem. 1982, 257, 13650-13662.
141. Kester, W R.; Matthews, B. W. Biochemistry 1977, 16, 2506-2516.
142. Case, D. A.; Karplus, M. J. Mol. Biol. 1979, 132, 343-368.
143. Shoichet, B. K.; Stroud, R. M.; Santi, D. V; Kuntz, I. D.; Perry, K. M. Science 1993, 259, 1445-1449.
144. Mattos, C.; Ringe, D. Multiple Binding Modes. In 3D QSAR in Drug Design: Theory, Methods and Applications; Kubinyi, H., Ed.; ESCOM: Leiden, 1993, pp 226-254.
145. Nicklaus, M. C.; Milne, G. W; Burke, T R., Jr. J. Comput.-Aided Mol Design 1992, 6, 487-504.
146. Guccione, S.; Doweyko, A. M.; Chen, H.; Barretta, G. U.; Balzano, F. J. Comput.-Aided Mol. Design 2000, 14, 647-657.
147. Dimitrov, S. D.; Mekenyan, O. G. Chemometrics Intelligent Lab. Systems 1997, 39, 1-9.
148. Mekenyan, O. Curr. Pharm. Design 2002, 8, 1605-1621.
149. Mekenyan, O. G.; Ivanov, J. M.; Veith, G. D.; Bradbury, S. P. Quant. Struct.-Act. Relat. 1994, 13, 302-307.
150. Doweyko, A. M., Multiple Conformer Protocol: A New Method for the Identification of Preferred Ligand Binding Motifs Using Crossvalidated 3D-QSAR models. In Rational Approaches to Drug Design; Proceedings of the European Symposium on Quantitiative Structure-Activty Relationships, 13th, Duesseldorf, Germany; Holtje, H.-D., Sippl, W, Eds.; Prous Science: Philadelphia, 2001, pp 307-315
151. Lukacova, V; Balaz, S. Incorporation of Multiple Binding Modes into 3D-QSAR Methods. Rational Approaches to Drug Design; Proceedings of the European Symposium on Quantitiative Structure-Activty Relationships, 13th, Duesseldorf, Germany, 2001, pp 354-358.
152. Hasegawa, K.; Arakawa, M.; Funatsu, K. Chemometrics Intell. Lab. Systems 2000, 50, 253-261.
153. Hasegawa, K.; Arakawa, M.; Funatsu, K. Curr Comput.-Aided Drug Design 2005, 1, 129-145.
154. Jain, A. N.; Harris, N. L.; Park, J. Y. J. Med. Chem. 1995, 38, 1295-1308.
155. Jain, A. N.; Koile, K.; Chapman, D. J. Med. Chem. 1994, 37, 2315-2327.
156. Broto, P; Moreau, G.; Vandycke, C. QSAR Des. Bioact Compd. 1984, 393-401.
157. Broto, P; Moreau, G.; Vandycke, C. Eur. J. Med. Chem. 1984, 19, 61-65.
158. Moreau, G.; Broto, P. Nouv. J. Chimie 1980, 4, 757-764.
159. Moreau, G.; Broto, P. The autocorrelation of a topological structure: a new molecular descriptor. Nouv. J. Chimie 1980, 4, 359-360.
160. Clementi, S.; Cruciana, G.; Riganelli, D.; Valigi, R.; Constantino, G.; Baroni, M.; Wold, S. Pharm. Pharmacol. Lett. 1993, 3, 5-8.
161. Wagener, M.; Sadowski, J.; Gasteiger, J. J. ACS 1995, 117, 7769-7775.
162. Pastor, M.; Cruciani, G.; McLay, I.; Pickett, S.; Clementi, S. J. Med. Chem. 2000, 43, 3233-3243.
163. Afzelius, L.; Zamora, I.; Masimirembwa, C. M.; Karlén, A.; Andersson, T B.; Mecucci, S.; Baroni, M.; Cruciani, G. J. Med. Chem. 2004, 47, 907-914.
164. Gratteri, P.; Cruciani, G.; Scapecchi, S.; Romanelli, M. N. GRID Independent Descriptors (GRIND) in the Rational Design of Muscarinic Antagonists. Rational Approaches to Drug Design; Proceedings of the European Symposium on Quantitiative Structure-Activity Relationships, 13th, Duesseldorf, Germany, 2001, 241-243.
165. ALMOND; Molecular Discovery: Ponte San Giovanni, PG, Italy.
166. Todeschini, R.; Lasagni, M.; Marengo, E. J. Chemometrics 1994, 8, 263-272.
167. Todeschini, R.; Gramatica, P. SAR QSAR Environ. Res. 1997, 7, 89-115.
168. Todeschini, R.; Moro, G.; Boggia, R.; Bonati, L.; Cosentino, U.; Lasagni, M.; Pitea, D. Chemometrics Intell. Lab. Systems 1997, 36, 65-73.
169. Bravi, G.; Gancia, E.; Mascagni, P; Pegna, M.; Todeschini, R.; Zaliani, A. J. Comput.-Aided Mol. Design 1997, 11, 79-92.
170. Gancia, G. B.; Mascagni, P; Zaliani, A. J. Comput.-Aided Mol. Design 2000, 14, 293-306.
171. Bravi, G.; Wikel, J. H. Quant. Struct.-Act. Relat. 2000, 19, 29-38.
172. Bravi, G.; Wikel, J. H. Quant Struct.-Act. Relat. 2000, 19, 39-49.
173. Silverman, B. D.; Platt, D. E. J. Med. Chem. 1996, 39, 2129-2140.
174. Silverman, B. D.; Platt, D. E.; Pitman, M.; Rigoutsos, I. Perspect. Drug Disc. Design 1998, 12/13/14, 183-196.
175. Turner, D. B.; Willett, P.; Ferguson, A. M.; Heritage, T. J. Comput.-Aided Mol. Design 1997, 11, 409-422.
176. Heritage, T. W; Ferguson, A. M.; Turner, D. B.; Willett, P. Perspect. Drug Disc. Design 1998, 9/10/11, 381-398.
177. Turner, D. B.; Ferguson, A. M.; Heritage, T. W. J. Comput.-Aided Mol. Design 1999, 13, 271-296.
178. Asikainen, A.; Ruuskanen, J.; Tuppurainen, K. J. Chem. Inf. Comput. Sri. 2003, 43, 1974-1981.
179. Hurst, T. HQSAR-A Highly Predictive QSAR Technique Based on Molecular Holograms. Book of Abstracts, 213th ACS National Meeting, San Francisco, April 13-17; American Chemical Society: Washington, DC, 1997, CINF-019.
180. Tong, W; Lowis, D. R.; Perkins, R.; Chen, Y; Welsh, W J.; Goddette, D. W; Heritage, T. W; Sheehan, D. M. J. Chem. Inf. Comput. Sri. 1998,38, 669-677.
181. Wold, S.; Esbensen, K.; Geladi, P. Chemometrics Intell. Lab. Systems 1987, 2, 37-52.
182. Kubinyi, H.; Hamprecht, F A.; Mietzner, T. J. Med. Chem. 1998, 41, 2553-2564.
183. Filipponi, E.; Cruciani, G.; Tabarrini, O.; Cecchetti, V; Fravolini, A. J. Comput.-Aided Mol. Design 2001, 15, 203-217.
184. Cianchetta, G.; Singleton, R. W; Zhang, M.; Wildgoose, M.; Giesing, D.; Fravolini, A.; Cruciani, G.; Vaz, R. J. J. Med. Chem. 2005, 48, 2927-2935.
185. Wold, S.; Johansson, E.; Cocchi, M. PLS-Partial Least Squares Projections to Latent Structures. In 3D-QSAR in Drug Design: Theory, Methods and Applications; Kubinyi, H., Ed.; ESCOM: Leiden, 1993, pp 523-550.
186. Bhagat, P. Chem. Eng. Prog. 1990, 86, 55-60.
187. Wythoff, B. J. Chemometrics Intell. Lab. Systems 1993, 18, 115-155.
188. Zupan, J.; Gasteiger, J. Anal. Chim. Acta 1991, 248, 1-30.
189. Polanski, J. J. Chem. Inf. Comput. Sei. 1997, 37, 553-561.
190. Livingstone, D. J.; Manallack, D. T. QSAR Comb. Sei. 2003, 22, 510-518.
191. Zhang, X.; Zhou, J. Jisuanji Yu Yngyong Huaxue 1995, 12, 186-191.
192. Tetko, I. V; Livingstone, D. J.; Luik, A. I. J. Chem. Inf. Comput. Sei. 1995, 35, 826-833.
193. Agrafiotis, D. K.; Cedeno, W; Lobanow, V S. J. Chem. Inf. Comput. Sei. 2002, 42, 903-911.
194. Kubinyi, H. Quant. Struct.-Act. Relat. 1994, 13, 285-294.
195. Clark, D. E.; Westhead, D. R. J. Comput.-Aided Mol. Design 1996, 10, 337-358.
196. So, S.-S.; Karplus, M. J. Med. Chem. 1996, 39, 1521-1530.
197. Gillet, V J. Struct. Bond. (Berl Germany) 2004, 110, 133-152.
198. Holland, J. H. Sci. Am. 1992, 267, 66.
199. Boser, B. E.; Guyon, I. M.; Vapnik, V N. A Training Algorithm for Optimal Margin Classifiers. In 5th Annual ACM Workshop on COLT; Haussler, D., Ed.; ACM Press: Pittsburgh, PA, 1992, pp 144-152.
200. Platt, J. Fast Training of Support Vector Machines Using Squential Minimum Optimisation. In Advances in Kernel Methods-Support Vector Learning, Scholkopf, B., Burges, C. J. C., Smola, A. J., Eds.; MIT Press: Cambridge, MA, 1998, pp 185-208.
201. Czerminski, R.; Yasri, A.; Hartsough, D. Quant. Struct.-Act. Relat. 2001, 20, 227-240.
202. Apostolakis, J.; Hofmann, D.; Lengauer, T. Using Simple Learning Machines to Derive a New Potential for Molecular Modeling. In Rational Approaches to Drug Design; Holtje, H.-D., Sippl, W, Eds.; Prous Science: Philadelphia, 2001, pp 125-134.
203. Datar, P. A.; Coutinho, E. C.; Srivastava, S. Lett. Drug Design Disc. 2004, 1, 115-120.
204. Votano, J. R.; Parham, M.; Hall, L. H.; Kier, L. B.; Oloff, S.; Tropsha, A.; Xie, Q.; Tong, W. Mutagenesis 2004, 19, 365-377.
205. Doweyko, A. M. J. Comput. Aided Mol. Design 2004, 18, 587-596.
206. Doweyko, A. M.; Bell, A. R.; Minatelli, J. A.; Relyea, D. I. J. Med. Chem. 1983, 26, 475-478.
207. Martin, Y C. Pharmacochem. Library 1993, 20, 129-137.
208. Bohacek, R. S.; McMartin, C. ACS Symposium Ser 1995, 589, 82-97.
209. DeWitte, R. S.; Shakhnovich, E. I. J. ACS 1996, 118, 11733-11744.
210. Vinkers, H. M.; de Jonge Marc, R.; Daeyaert, F F D.; Heeres, J.; Koymans, L. M. H.; van Lenthe, J. H.; Lewi, P J.; Timmerman, H.; Aken, K. V; Janssen, P. A. J. Med. Chem. 2003, 46, 2765-2773.
211. Kubinyi, H. Pharmazie unserer Zeit 1994, 23, 281-290.
212. Oprea, T I.; Ho, C. M. W; Marshall, G. R. ACS Symposium Ser. 1995, 589, 64-81.
213. Erickson, J. A.; De Novo Design Using a 3-D QSAR Derived Receptor. Book of Abstracts, 212th ACS National Meeting, Orlando, FL, August 25-29; American Chemical Society: Washington, DC, 1996, COMP-165.
214. Pearlman, R. S.; Balducci, R.; Smith, K. M.; Brusniak, M. Y. Dirty Comfa, Dirty Docking, and a Clean Method for Inverse-QSAR-based Drug Design. Book of Abstracts, 217th ACS National Meeting, Anaheim, Calif., March 21-25; American Chemical Society: Washington, DC, 1999, COMP-048.
215. Doweyko, A. M.; Johnson, S. R. Q. A Novel Method to Simulate the Solvation of Hydrophobic Surfaces by Water and Its Application to the Estimation of Protein-Ligand Binding Constants. Abstracts of Papers, 229th ACS National Meeting, San Diego, CA, United States, March 13-17, 2005; American Chemical Society: Washington, DC, 2005, COMP-218.
216. Steinberg, I. Z.; Scheraga, H. A. J. Biol. Chem. 1963, 238, 172-181.
217. Tunon, I.; Silla, E.; Pascual-Ahuir, J. L. Protein Eng. 1992, 5, 715-716.
218. Soda, K. Adv. Biophysics 1993, 29, 1-54.
219. Lazaridis, T. J. Phys. Chem. B 2000, 104, 4964-4979.
220. Scheraga, H. A. J. Phys. Chem. 1961, 65, 1071-1072.
221. Venkatarangan, P.; Hopfinger, A. J. J. Chem. Inf. Comput. Sei. 1999, 39, 1141-1150.