Performance of machine learning methods for ligand-based virtual screening

Combinatorial Chemistry and High Throughput Screening

Volumn 12, Issue 4, 2009, Pages 358-368

  Plewczynski, Dariusz ^a   Spieser, Stéphane A H ^b   Koch, Uwe ^b  

^a UNIVERSITY OF WARSAW   (Poland)

^b IRBM   (Italy)

Author keywords

Drug discovery; Machine learning; QSAR; Virtual screening

Indexed keywords

LIGAND;

ANALYTIC METHOD; ARTIFICIAL NEURAL NETWORK; BAYES THEOREM; CLUSTER ANALYSIS; DATA BASE; DECISION TREE; HIGH THROUGHPUT SCREENING; MACHINE LEARNING; MATHEMATICAL MODEL; PRIORITY JOURNAL; REVIEW; SUPPORT VECTOR MACHINE; VIRTUAL SCREENING;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; COMPUTER SIMULATION; DATABASES, FACTUAL; DRUG EVALUATION, PRECLINICAL; LIGANDS; REGRESSION ANALYSIS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 66249104368     PISSN: 13862073     EISSN: None     Source Type: Journal    
DOI: 10.2174/138620709788167962     Document Type: Review

References (140)

1. 1 McGaughey, G. B.; Sheridan, R. P.; Bayly, C. I.; Culberson, J. C.; Kreatsoulas, C.; Lindsley, S.; Maiorov, V.; Truchon, J. F.; Cornell, W. D. J. Chem. Inf. Model., 2007, 47, 1504-1519.
2. Martin, Y. C.; Kofron, J. L.; Traphagen, L. M. J. Med. Chem., 2002, 45, 4350-4358.
3. Cleves, A. E.; Jain, A. N. J. Med. Chem., 2006, 49, 2921-2938.
4. Fliri, A. F.; Loging, W. T.; Thadeio, P. F.; Volkmann, R. A. Proc. Natl. Acad. Sci. USA, 2005, 102, 261-266.
5. Krejsa, C. M.; Horvath, D.; Rogalski, S. L.; Penzotti, J. E.; Mao, B.; Barbosa, F.; Migeon, J. C. Curr. Opin. Drug Discov. Dev., 2003, 6, 470-480.
6. Maggiora, G. M. J. Chem. Inf. Model., 2006, 46, 1535.
7. Friedman, J. H. IEEE Trans. Comput., 1977, 26, 404-408.
8. Quinlan, J. R. Mach. Learn., 1986, 1, 81-106.
9. Amimoto, R.; Prasad, M. A.; Gifford, E. M. J. Biomol. Screen., 2005, 10, 197-205.
10. Burton, J.; Ijjaali, I.; Barberan, O.; Petitet, F.; Vercauteren, D. P.; Michel, A. J. Med. Chem., 2006, 49, 6231-6240.
11. Svetnik, V.; Liaw, A.; Tong, C.; Culberson, J. C.; Sheridan, R. P.; Feuston, B. P. J. Chem. Inf. Comput. Sci., 2003, 43, 1947-1958.
12. van Rhee, A. M. J. Chem. Inf. Comput. Sci., 2003, 43, 941-948.
13. Zhang, Q. Y.; Aires-de-Sousa, J. J. Chem. Inf. Model., 2007, 47, 1-8.
14. van de Waterbeemd, H.; Gifford, E. Nature Rev. Drug Discov., 2003, 2, 192-204.
15. Xu, J.; Hagler, A. Molecules, 2002, 7, 566-600.
16. Muegge, I. Med. Res. Rev., 2003, 23, 302-321.
17. Wagener, M.; van Geerestein, V. J. J. Chem. Inf. Comput. Sci., 2000, 40, 280-292.
18. Young, S. S. J. Chem. Inf. Comput. Sci., 1999, 39, 1017-1026.
19. Rusinko Iii, A.; Young, S. S.; Drewry, D. H.; Gerritz, S. W. Comb. Chem. High Throughput Screen., 2002, 5, 125-133.
20. Xue, L.; Bajorath, J. Comb. Chem. High Throughput Screen., 2000, 3, 363-372.
21. Woods, K.; Kegelmeyer, W. P.; Bowyer, K. IEEE Trans. Pattern Anal. Machine Intell., 1997, 19, 405-410.
22. Kuncheva, L. I. IEEE Trans. Pattern Anal. Machine Intell., 2002, 24, 281-286.
23. Jordan, M. I.; Jacobs, R. A. Proceedings of 1993 International Joint Conference on Neural Networks, 1993. IJCNN'93-Nagoya., 1993, 2.
24. Krogh, A.; Vedelsby, J. Adv. Neural Inf. Process. Syst., 1995, 7, 231-238.
25. Gama, J. AI Commun., 2000, 13, 135-136.
26. Dietterich, T. G. Lect. Notes Comput. Sci., 2000, 1857, 1-15.
27. Opitz, D.; Maclin, R. J. Artif. Intell. Res., 1999, 11, 12.
28. Freund, Y. Inform. Comput., 1995, 121, 256-285.
29. Freund, Y.; Schapire, R. E. Machine Learning: Proceedings of the Thirteenth International Conference, 1996, 148, 156.
30. Breiman, L. Mach. Learn., 1996, 24, 123-140.
31. Witten, I. H.; Frank, E. Data Mining: Practical Machine Learning Tools and Techniques; Elsevier: New York, 2005.
32. Schapire, R. E.; Freund, Y.; Bartlett, P.; Lee, W. S. Ann. Statist., 1998, 26, 1651-1686.
33. Banfield, R. E.; Hall, L. O.; Bowyer, K. W.; Kegelmeyer, W. P. IEEE Trans. Pattern Anal. Machine Intell., 2007, 29, 173-180.
34. Svetnik, V.; Wang, T.; Tong, C.; Liaw, A.; Sheridan, R. P.; Song, Q. J. Chem. Inf. Model., 2005, 45, 786-799.
35. Friedman, J. H. Comput. Stat. Data Anal. 2002, 38, 367-378.
36. Breiman, L. Mach. Learn., 2001, 45, 5-32.
37. Ho, T. K. IEEE Trans. Pattern Anal. Machine Intell., 1998, 20, 832-844.
38. Breiman, L. Mach. Learn., 2001, 45, 5-32.
39. Tong, W.; Hong, H.; Fang, H.; Xie, Q.; Perkins, R. J. Chem. Inf. Comput. Sci., 2003, 43, 525-531.
40. Hawkins, D. M. Am. Stat., 1991, 45, 155-155.
41. Young, S. S.; Hawkins, D. M. J. Med. Chem., 1995, 38, 2784-2788.
42. Miller, D. W. J. Chem. Inf. Comput. Sci., 2001, 41, 168-175.
43. Izrailev, S.; Agrafiotis, D. J. Chem. Inf. Comput. Sci., 2001, 41, 176-180.
44. Blower, P.; Fligner, M.; Verducci, J.; Bjoraker, J. J. Chem. Inf. Comput. Sci., 2002, 42, 393-404.
45. Dixon, S. L.; Villar, H. O. J. Comput. Aided Mol. Des., 1999, 13, 533-545.
46. Vapnik, V. Estimation of Dependencies Based on Empirical Data; Nauka: Moscow, 1979.
47. Vapnik, V. The Nature of Statistical Learning Theory, Springer: New York, 1995.
48. Vapnik, V. N. Statistical learning theory. Adaptive and learning systems for signal processing, communications, and control; Wiley: New York, 1998.
49. Christianini, N.; Shawe-Taylor, J. An Introduction to Support Vec- tor Machines and Other Kernel-based Learning Methods; Cam- bridge University Press: Cambridge (UK), 2000.
50. Schölkopf, B.; Burges, C. J. C.; Smola, A. J. Advances in kernel methods: support vector learning; MIT Press Cambridge, MA, USA, 1999.
51. Scholkopf, B.; Smola, A. J. Learning with Kernels: Support Vector Machines, Regularization, Optimization, and Beyond; MIT Press Cambridge, MA: USA, 2001.
52. Smola, A. J.; Schölkopf, B. Statistics and Computing, 2004, 14, 199-222.
53. Burges, C. J. C. Data Mining Knowledge Discov., 1998, 2, 121-167.
54. Byvatov, E.; Schneider, G. Appl. Bioinformatics, 2003, 2, 67-77.
55. Cai, Y. D.; Liu, X. J.; Xu, X.; Zhou, G.P. BMC Bioinformatics, 2001, 2, 3.
56. Cherkassky, V.; Ma, Y. Neural Netw., 2004, 17, 113-126.
57. Cristianini, N.; Schölkopf, B. AI Magazine, 2002, 23, 31-41.
58. Ivanciuc, O. In Reviews in Computational Chemistry; T. R. Cundari K. B. Lipkowitz, E d.; Wiley-VCH: Weinheim, 2007; 23, 291-400.
59. Byvatov, E.; Schneider, G. J. Chem. Inf. Comput. Sci., 2004, 44, 993-999.
60. Burbidge, R.; Trotter, M.; Buxton, B.; Holden, S. Comput. Chem., 2001, 26, 4-15.
61. Doniger, S.; Hofmann, T.; Yeh, J. J. Comput. Biol., 2002, 9, 849-864.
62. Lengauer, T.; Lemmen, C.; Rarey, M.; Zimmermann, M. Drug Discov. Today, 2004, 9, 27-34.
63. Trotter, M. W. B.; Buxton, B. F.; Holden, S. B. Measure. Control, 2001, 34, 235-239.
64. Trotter, M. W. B.; Holden, S. B. QSAR Comb. Sci., 2003, 22, 533-548.
65. Warmuth, M. K.; Liao, J.; Ratsch, G.; Mathieson, M.; Putta, S.; Lemmen, C. J. Chem. Inf. Comput. Sci., 2003, 43, 667-673.
66. Fausett, L. Fundamentals of neural networks: architectures, algo- rithms, and applications; Prentice-Hall, Inc. Upper Saddle River, NJ: USA, 1994.
67. Hagan, M. T.; Demuth, H. B.; Beale, M. Neural network design, PWS Publishing Co. Boston, MA: USA, 1997.
68. Hassoun, M. H. Fundamentals of Artificial Neural Networks; MIT Press: Cambridge, MA: 1995.
69. Haykin, S. Neural Networks: A Comprehensive Foundation; Pren- tice Hall PTR Upper Saddle River, NJ: USA, 1994.
70. Kohonen, T. Self-organization and associative memory; Springer- Verlag New York, Inc. New York, NY: USA, 1989.
71. Chem, A. Anal. Chem., 2004, 76, 1726-1732.
72. Cronin, M. T. D.; Livingstone, D. J. J. Med. Chem., 2005, 48, 661-663.
73. Delaney, J. S. Drug Discov. Today, 2005, 10, 289-295.
74. Dudek, A. Z.; Arodz, T.; Galvez, J. Comb. Chem. High Throughput Screen., 2006, 9, 213-228.
75. Gasteiger, J.; Zupan, J. Angew. Chem. Intern. Ed., 1993, 32, 503-527.
76. Niculescu, S. P. J. Mol. Struct. (Theochem), 2003, 622, 71-87.
77. Rost, B.; Sander, C. Proteins, 1994, 19, 55-72.
78. Schneider, G.; Wrede, P. Progr. Biophys. Mol. Biol., 1998, 70, 175-222.
79. Tsoi, A. C.; Back, A. D. IEEE Trans. Neural Netw., 1994, 5, 229-239.
80. Ivanciuc, O.; Rabine, J. P.; Cabrol-Bass, D.; Panaye, A.; Doucet, J. P. J. Chem. Inf. Comput. Sci, 1996, 36, 644-653.
81. Lim, C. W.; Fujiwara, S.; Yamashita, F.; Hashida, M. Biol. Pharm. Bull., 2002, 25, 361-366.
82. Ozdemir, M.; Embrechts, M. J.; Arciniegas, F.; Breneman, C. M.; Lockwood, L.; Bennett, K. P. Soft Computing in Industrial Appli- cations, 2001. SMCia/01. Proceedings of the 2001 IEEE Mountain Workshop on, 2001, 53-57.
83. Sardari, S.; Sardari, D. Curr. Pharm. Des., 2002, 8, 659-670.
84. Taskinen, J.; Yliruusi, J. Adv. Drug Deliv. Rev., 2003, 55, 1163-1183.
85. Oja, M.; Kaski, S.; Kohonen, T. Neural Comput. Surveys, 2003, 3, 1-156.
86. Gasteiger, J.; Teckentrup, A.; Teroth, L.; Spycher, S. J. Phys. Org. Chem., 2003, 16, 232-245.
87. Polanski, J. Adv. Drug Deliv. Rev., 2003, 55, 1149-1162.
88. Ochoa, C.; Chana, A.; Stud, M. Curr. Med. Chem. Central Nervous System Agents, 2001, 1, 247-256.
89. von Korff, M.; Sander, T. J. Chem. Inf. Model., 2006, 46, 536-544.
90. Bayram, E.; Santago, P.; Harris, R.; Xiao, Y. D.; Clauset, A. J.; Schmitt, J. D. J. Comp.-Aided Mol. Des., 2004, 18, 483-493.
91. Schneider, G. Curr. Med. Chem., 2002, 9, 2095-2101.
92. Stahura, F. L.; Bajorath, J. Comb. Chem. High Throughput Screen., 2004, 7, 259-269.
93. Hartigan, J. A. Clustering Algorithms; John Wiley & Sons, Inc. New York, NY: USA, 1975.
94. Jain, A. K.; Dubes, R. C. Algorithms for clustering data; Prentice- Hall, Inc. Upper Saddle River, NJ: USA, 1988.
95. Johnson, S. C. Psychometrika, 1967, 32, 241-254.
96. Jarvis, R. A.; Patrick, E. A. Trans. Comput., 1973, 100, 1025-1034.
97. Kanungo, T.; Mount, D. M.; Netanyahu, N. S.; Piatko, C. D.; Sil- verman, R.; Wu, A. Y.; Center, A. R.; San Jose, C. A. IEEE Trans. Pattern Anal. Machine Intell., 2002, 24, 881-892.
98. Binder, D. A. Biometrika, 1978, 65, 31.
99. Zheng, W.; Tropsha, A. J. Chem. Inf. Comput. Sci., 2000, 40, 185-194.
100. Bocker, A.; Derksen, S.; Schmidt, E.; Teckentrup, A.; Schneider, G. J. Chem. Inf. Model., 2005, 45, 807-815.
101. Brown, R. D.; Martin, Y. C. J. Chem. Inf. Comput. Sci, 1996, 36, 572-584.
102. Bayes, T. Philos. Trans. R. Soc. London, 1763, 53, 370-418.
103. Kononenko, I. Artificial Intelligen. Med., 2001, 23, 89-109.
104. Cannon, E. O.; Amini, A.; Bender, A.; Sternberg, M. J. E.; Muggle- ton, S. H.; Glen, R. C.; Mitchell, J. B. O. J. Comput.-Aided Mol. Des., 2007, 21, 269-280.
105. Carhart, R. E.; Smith, D. H.; Venkataraghavan, R. J. Chem. Inf. Comput. Sci., 1985, 25, 64-73.
106. Sheridan, R. P.; Nachbar, R. B.; Bush, B. L. J. Comput.-Aided Mol. Des., 1994, 8, 323-340.
107. Willett, P.; Wilton, D.; Hartzoulakis, B.; Tang, R.; Ford, J.; Madge, D. J. Chem. Inf. Model., 2007, 47, 1961-1966.
108. Wilton, D. J.; Harrison, R. F.; Willett, P.; Delaney, J.; Lawson, K.; Mullier, G. J. Chem. Inf. Model., 2006, 46, 471-477.
109. Harper, G.; Bradshaw, J.; Gittins, J. C.; Green, D. V.; Leach, A. R. J. Chem. Inf. Comput. Sci., 2001, 41, 1295-1300.
110. Abidi, M. A.; Gonzalez, R.C. Data Fusion in Robotics and Machine Intelligence; Academic Press, New York, NY: USA, 1992.
111. Hall, D. L.; Llinas, J. Handbook of multisensor data fusion; Boca Raton, FL: CRC Press, 2001.
112. Bajorath, J. Chemoinformatics: Concepts, Methods, and Tools for Drug Discovery; Humana Press: Totowa, 2004.
113. Buxton, B. F.; Langdon, W. B.; Barrett, S. J. Measurement+ Con- trol, 2001, 34, 229-234.
114. Hassan, M.; Brown, R. D.; Varma-O'Brien, S.; Rogers, D. Mol. Div., 2006, 10, 283-299.
115. Whittle, M.; Gillet, V. J.; Willett, P.; Alex, A.; Loesel, J. J. Chem. Inf. Comput. Sci., 2004, 44, 1840-1848.
116. Willett, P. Drug Discov Today, 2006, 11, 1046-1053.
117. Whittle, M.; Gillet, V. J.; Willett, P.; Alex, A.; Loesel, J. J. Chem. Inf. Comput. Sci., 2004, 44, 1840-1848.
118. Truchon, J. F.; Bayly, C. I. J. Chem. Inf. Model., 2007, 47, 488-508.
119. Bruce, C. L.; Melville, J. L.; Pickett, S. D.; Hirst, J. D. J. Chem. Inf. Model., 2007, 47, 219-227.
120. Plewczynski, D.; Spieser, S. A.; Koch, U. J. Chem. Inf. Model., 2006, 46, 1098-1106.
121. Zhang, Q.; Muegge, I. J. Med. Chem., 2006, 49, 1536-1548.
122. Glick, M.; Jenkins, J. L.; Nettles, J. H.; Hitchings, H.; Davies, J. W. J. Chem. Inf. Model., 2006, 46, 193-200.
123. Burbidge, R.; Trotter, M.; Buxton, B.; Holden, S. Comput. Chem., 2001, 26, 5-14.
124. Byvatov, E.; Fechner, U.; Sadowski, J.; Schneider, G. J. Chem. Inf. Comput. Sci., 2003, 43, 1882-1889.
125. Zernov, V. V.; Balakin, K. V.; Ivaschenko, A. A.; Savchuk, N. P.; Pletnev, I. V. J. Chem. Inf. Comput. Sci., 2003, 43, 2048-2056.
126. Muller, K. R.; Ratsch, G.; Sonnenburg, S.; Mika, S.; Grimm, M.; Heinrich, N. J. Chem. Inf. Model., 2005, 45, 249-253.
127. Hii, J. T.; Wyse, D. G.; Gillis, A. M.; Duff, H. J.; Solylo, M. A.; Mitchell, L. B. Circulation, 1992, 86, 1376-1382.
128. Yap, C. W.; Cai, C. Z.; Xue, Y.; Chen, Y. Z. Toxicol. Sci, 2004, 79, 170-177.
129. Doniger, S.; Hofmann, T.; Yeh, J. J. Comput. Biol., 2002, 9, 849-864.
130. Serra, J. R.; Thompson, E. D.; Jurs, P. C. Chem. Res. Toxicol., 2003, 16, 153-163.
131. Sorich, M. J.; Miners, J. O.; McKinnon, R. A.; Winkler, D. A.; Burden, F. R.; Smith, P. A. J. Chem. Inf. Comput. Sci., 2003, 43, 2019-2024.
132. Zhao, C. Y.; Zhang, R. S.; Zhang, H. X.; Xue, C. X.; Liu, H. X.; Liu, M. C.; Hu, Z. D.; Fan, B. T. SAR QSAR Environ. Res., 2005, 16, 349-367.
133. DeLisle, R. K.; Dixon, S. L. J. Chem. Inf. Comput. Sci., 2004, 44, 862-870.
134. Chen, B.; Harrison, R. F.; Pasupa, K.; Willett, P.; Wilton, D. J.; Wood, D. J.; Lewell, X. Q. J. Chem. Inf. Model., 2006, 46, 478-486.
135. Chen, B.; Harrison, R. F.; Papadatos, G.; Willett, P.; Wood, D. J.; Lewell, X. Q.; Greenidge, P.; Stiefl, N. J. Comput.-Aided Mol. Des., 2007.
136. Bender, A.; Mussa, H. Y.; Glen, R. C.; Reiling, S. J. Chem. Inf. Comput. Sci., 2004, 44, 1708-1718.
137. Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P.; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A. J. Chem. Inf. Comput. Sci., 2004, 44, 1177-1185.
138. Wilton, D.; Willett, P.; Lawson, K.; Mullier, G. J. Chem. Inf. Com- put. Sci., 2003, 43, 469-474.
139. Salim, N.; Holliday, J.; Willett, P. J. Chem. Inf. Comput. Sci., 2003, 43, 435-442.
140. Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P.; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A. J. Chem. Inf. Model., 2006, 46, 462-470.