Expert systems for toxicity prediction

Issues in Toxicology

Volumn , Issue , 2010, Pages 478-507

  Dearden, J C ^a  

^a LIVERPOOL JOHN MOORES UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84897493756     PISSN: 17577179     EISSN: 17577187     Source Type: Book Series    
DOI: None     Document Type: Article

References (127)

1. V. K. Gombar, B. E. Mattioni, C. Zwickl and J. T. Deahl, in Computational Toxicology: Risk Assessment for Pharmaceutical and Environmental Chemicals, ed. S. Ekins, Wiley, Hoboken, NJ, 2007, pp. 183-215.
2. D. E. Johnson, A. D. Rodgers and S. Sudarsanam, in Computational Toxicology: Risk Assessment for Pharmaceutical and Environmental Chemicals, ed. S. Ekins, Wiley, Hoboken, NJ, 2007, pp. 725-749.
3. J. C. Dearden, M. D. Barratt, R. Benigni, D. W. Bristol, R. D. Combes, M. T. D. Cronin, P. N. Judson, M. P. Payne, A. M. Richard, M. Tichý, A. P. Worth and J. J. Yourick, Altern. Lab. Anim., 1997, 25, 223.
4. A. M. Richard, Mutat. Res., 1994, 305, 73.
5. R. D. Combes and P. N. Judson, Pestic. Sci., 1995, 45, 179.
6. A.M. Richard, C. Yang and R. S. Judson, Toxicol. Mech. Meth., 2008, 18, 103.
7. B. Simon-Hettich, A. Rothfuss and T. Steger-Hartmann, Toxicology, 2006, 224, 156.
8. K. Langton, G. Y. Patlewicz, A. Long, C. A. Marchant and D. A. Basketter, Contact Derm., 2006, 55, 342.
9. T. I. Netzeva, A. P. Worth, T. Aldenberg, R. Benigni, M. T. D. Cronin, P. Gramatica, J. S. Jaworska, S. Kahn, G. Klopman, C. A. Marchant, G. Myatt, N. Nikolova-Jeliaskova, G. Y. Patlewicz, R. Perkins, D. W. Roberts, T. W. Schultz, D. W. Stanton, J. J. M. van de Sandt, W. Tong, G. Veith and C. Yang, Alt. Lab. Anim., 2005, 33, 155.
10. J. Jaworska, N. Nikolova-Jeliaskova and T. Aldenberg, Alt. Lab. Anim., 2005, 33, 445.
11. V. K. Gombar, SAR QSAR Environ. Res., 1999, 10, 371.
12. W. Muster, A. Breidenbach, H. Fischer, S. Kirchner, L. Müller and A. Pä hler, Drug Discov. Today, 2008, 13, 303.
13. Organisation for Economic Co-operation and Development, OECD Principles for the Validation, for Regulatory Purposes, of (Quantitative) Structure-Activity Relationship Models, OECD, Paris, 2004, www.oecd.org/ dataoecd/33/37/37849783.pdf [accessed March 2010].
14. Organisation for Economic Co-operation and Development, The Report from the Expert Group on (Quantitative) Structure-Activity Relationships [(Q)SARs] on the Principles for the Validation of (Q)SARs, OECD, Paris, 2004, OECD Environment Health and Safety Publications Series on Testing and Assessment No. 49, ENV/JM/MONO(2004)24, www.olis.oecd.org/olis/2004doc.nsf/LinkTo/NT00009192/ $FILE/JT00176183.PDF [accessed March 2010].
15. E. J. Matthews and J. F. Contrera, Expert Opin. Drug Metab. Toxicol., 2007, 3, 125.
16. J. C. Dearden, M. T. D. Cronin and K. L. E. Kaiser, SAR QSAR Environ. Res., 2009, 20, 241.
17. E. Gottmann, S. Kramer, B. Pfahringer and C. Helma, Environ. Health Perspect., 2001, 109, 509.
18. D. Young, T. Martin, R. Venkatapathy and P. Harten, QSAR Comb. Sci., 2008, 27, 1337.
19. M. T. D. Cronin, ALTEX, 2006, 23, Special Issue, 365.
20. R. Judson, A. Richard, D. J. Dix, K. Houck, M. Martin, R. Kavlock, V. Dellarco, T. Henry, T. Holderman, P. Sayre, S. Tan, T. Carpenter and E. Smith, Environ. Health Perspect., 2009, 117, 685.
21. http://ec.europa.eu/environment/chemicals/reach/reviews-en.htm [accessed March 2010].
22. A. Bassan and A. P. Worth, in Computational Toxicology: Risk Assessment for Pharmaceutical and Environmental Chemicals, ed. S. Ekins, Wiley, Hoboken, NJ, 2007, pp. 751-775.
23. J. C. Dearden, in Computer Applications in Pharmaceutical Research and Development, ed. S. Ekins, Wiley, Hoboken, NJ, 2006, pp. 469-494.
24. C. A. Marchant, in Virtual ADMET Assessment in Target Selection and Maturation, ed. B. Testa and L. Turski, IOS Press, Amsterdam, 2006, pp. 237-248.
25. P. N. Judson, in Computational Toxicology: Risk Assessment for Pharmaceutical and Environmental Chemicals, ed. S. Ekins, Wiley, Hoboken, NJ, 2007, pp. 521-543.
26. K. Enslein, Toxicol. Ind. Health, 1988, 4, 479.
27. www.accelrys.com
28. K. Enslein, V. K. Gombar and B. W. Blake, Mutat. Res., 1994, 305, 47.
29. V. K. Gombar, K. Enslein and B. W. Blake, Chemosphere, 1995, 31, 2499.
30. E. Mombelli, Alt. Lab. Anim., 2008, 36, 15.
31. G. Patlewicz, A. O. Aptula, E. Uriarte, D. W. Roberts, P. S. Kern, G. F. Gerberick, I. Kimber, R. J. Dearman, C. A. Ryan and D. A. Basketter, SAR QSAR Environ. Res., 2007, 18, 515.
32. R. Venkatapathy, C. J. Moudgal and R. M. Bruce, J. Chem. Inf. Comput. Sci., 2004, 44, 1623.
33. C. A. Marchant, K. A. Briggs and A. Long, Toxicol. Mech. Meth., 2008, 18, 177.
34. www.lhasalimited.org
35. D.M. Sanderson and C. G. Earnshaw, Hum. Exp. Toxicol., 1991, 10, 261.
36. P. Crettaz and R. Benigni, J. Chem. Inf. Model., 2005, 45, 1864.
37. E. M. Hulzebos and R. Posthumus, SAR QSAR Environ. Res., 2003, 14, 285.
38. E. Hulzebos, D. Sijm, T. Traas, R. Posthumus and L. Maslankiewicz, SAR QSAR Environ. Res., 2005, 16, 385.
39. G. Klopman, J. Am. Chem. Soc., 1984, 106, 7315.
40. E. J. Matthews, R. D. Benz and J. F. Contrera, J. Mol. Graphics Model., 2000, 18, 605.
41. G. Klopman, J. Ivanov, R. Saiakhov and S. Chakravarti, in Predictive Toxicology, ed. C. Helma, Taylor & Francis, Boca Raton, FL, 2005, pp. 423-457.
42. R. D. Saiakhov and G. Klopman, Toxicol. Mech. Meth., 2008, 18, 159.
43. J. F. Contrera, N. L. Kruhlak, E. J. Matthews and R. D. Benz, Regul. Toxicol. Pharmacol., 2007, 49, 172.
44. V. Poroikov and D. Filimonov, in Predictive Toxicology, ed. C. Helma, Taylor & Francis, Boca Raton, FL, 2005, pp. 459-478.
45. A. A. Lagunin, J. C. Dearden, D. A. Filimonov and V. V. Poroikov, Mutat. Res., 2005, 586, 138.
46. www.chem.ac.ru/Chemistry/Soft/PASS.en.html [accessed March 2010].
47. V. Poroikov, D. Akimov, E. Shabelnikova and D. Filimonov, SAR QSAR Environ. Res., 2001, 12, 327.
48. A. Lagunin, D. Filimonov, A. Zakharov, W. Xie, Y. Huang, F. Zhu, T. Shen, J. Yao and V. Poroikov, QSAR Comb. Sci., 2009, 28, 806.
49. www.leadscope.com
50. C. Yang, K. Cross, G. J. Myatt, P. E. Blower and J. F. Rathman, J. Med. Chem., 2004, 47, 5984.
51. G. Roberts, G. J. Myatt, W. P. Johnson, K. P. Cross and P. E. Blower, J. Chem. Inf. Comput. Sci., 2000, 40, 1302.
52. www.compudrug.com
53. M. P. Smithing and F. Darvas, in Food Safety Assessment, ed. J. W. Finley, S. F. Robinson and D. J. Armstrong, American Chemical Society, Washington DC, 1992, ACS Symposium Series 484, pp. 191-200.
54. S. J. Brown, A. A. Raja and D. F. V. Lewis, Alt. Lab. Anim., 1994, 22, 482.
55. Much of the content of the Pharma Algorithms website (www.ap-algorithms. com) has moved to the ACDLabs website or is no longer available..
56. www.acdlabs.com
57. P. Japertas, R. Didziapetris and A. Petrauskas, Mini-Revs. Med. Chem., 2003, 3, 797.
58. R. Didziapetris, K. Lanevskij and P. Japertas, Chem. Res. Toxicol., 2008, 21, 2450.
59. L. Juska, R. Didziapetris and P. Japertas, Toxicol. Lett., 2008, 180S, S153.
60. P. Japertas, R. Didziapetris and A. Petrauskas, Chem. Res. Toxicol., 2007, 20, 1998.
61. P. J. Jurgutis, R. Didziapetris and P. Japertas, Chem. Res. Toxicol., 2007, 20, 2010.
62. www.simulations-plus.com
63. http://q-pharm.com
64. A. F. Fliri, W. T. Loging, P. F. Thadeio and R. A. Volkmann, Proc. Nat. Acad. Sci. U. S. A., 2005, 102, 261.
65. A. Fliri, W. Loging, P. Thadeio and R. Volkmann, J. Med. Chem., 2005, 48, 6918.
66. http://lazar.in-silico.de
67. C. Helma, in Predictive Toxicology, ed. C. Helma, Taylor & Francis, Boca Raton, FL, 2005, pp. 479-499.
68. C. Helma, Mol. Divers., 2006, 10, 147.
69. www.terrabase-inc.com
70. K. L. E. Kaiser, S. P. Niculescu and T. W. Schultz, SAR QSAR Environ. Res., 2002, 13, 57.
71. K. L. E. Kaiser and S. P. Niculescu, Chemosphere, 1999, 38, 3237.
72. K. L. E. Kaiser and S. P. Niculescu, Water Qual. Res. J. Canada, 2001, 36, 619.
73. M. Pavan, A. P. Worth and T. I. Netzeva, Comparative Assessment of QSAR Models for Aquatic Toxicity, European Commission Joint Research Centre, Ispra, Italy, 2005, EUR 21750, http://ecb.jrc.ec.europa.eu/qsar/information-sources/ [accessed March 2010].
74. K. L. E. Kaiser, personal communication to J. C. Dearden, 31 July 2009.
75. www.oasis-lmc.org/?section=software&swid=4
76. S. D. Dimitrov, L. K. Low, G. Y. Patlewicz, P. S. Kern, G. D. Dimitrova, M. H. I. Comber, R. D. Phillips, J. Niemela, P. T. Baily and O. G. Mekenyan, Int. J. Toxicol., 2005, 24, 189.
77. O. G. Mekenyan, S. D. Dimitrov, T. S. Pavlov and G. D. Veith, Curr. Pharm. Des., 2004, 10, 1273.
78. O. G. Mekenyan, J. M. Ivanov, S. H. Karabunarliev, S. P. Bradbury, G. T. Ankley and W. Karcher, Environ. Sci. Technol., 1997, 31, 3702.
79. O. G. Mekenyan, N. Nikolova, S. Karabunarliev, S. Bradbury, G. Ankley and B. Hansen, Quant. Struct.-Act. Relat., 1999, 18, 139.
80. S. Bradbury, V. Kamenska, P. Schmieder, G. Ankley and O. Mekenyan, Toxicol. Sci., 2000, 58, 253.
81. D. W. Roberts, G. Patlewicz, S. D. Dimitrov, L. K. Low, A. O. Aptula, P. S. Kern, G. D. Dimitrova, M. I. H. Comber, R. D. Phillips, J. Niemelä, C. Madsen, E. B. Wedebye, P. T. Bailey and O. G. Mekenyan, Chem. Res. Toxicol., 2007, 20, 1321.
82. G. Patlewicz, S. D. Dimitrov, L. K. Low, P. S. Kern, G. D. Dimitrova, M. I. H. Comber, A. O. Aptula, R. D. Phillips, J. Niemelä, C. Madsen, E. B. Wedebye, D. W. Roberts, P. T. Bailey and O. G. Mekenyan, Regul. Toxicol. Pharmacol., 2007, 48, 225.
83. www.caesar-project.eu/software
84. www.epa.gov/nrmrl/std/cppb/qsar
85. J. F. Contrera, E. J. Matthews and R. D. Benz, Regul. Toxicol. Pharmacol., 2003, 38, 243.
86. www.epa.gov/oppt/newchems/tools/21ecosar.htm
87. P. Reuschenbach, M. Silvano, M. Dammann, D. Warnecke and T. Knacker, Chemosphere, 2008, 71, 1986.
88. www.chemsilico.com
89. L. B. Kier and L. H. Hall, Molecular Connectivity in Structure-Activity Analysis, Wiley, New York, 1986.
90. L. H. Hall and L. B. Kier, Molecular Structure Description: The Electrotopological State, Academic Press, New York, 1999.
91. L. B. Kier and L. H. Hall, in Topological Indices and Related Descriptors in QSAR and QSPR, ed. J. Devillers and A. T. Balaban, Gordon & Breach, Reading, UK, 1999, pp. 491-562.
92. www.epa.gov/oppt/newchems/tools/oncologic.htm
93. Y.-T. Woo and D. Y. Lai, in Predictive Toxicology, ed. C. Helma, Taylor & Francis, Boca Raton, FL, 2005, pp. 385-413.
94. http://ntp.niehs.nih.gov
95. R. Benigni and R. Zito, Mutat. Res., 2004, 566, 49.
96. www.schrodinger.com
97. R. Farid, T. Day, R. A. Friesner and R. A. Pearlstein, Bioorg. Med. Chem., 2006, 14, 3160.
98. www.optibrium.com/stardrop
99. www.fqs.pl
100. http://research.chem.psu.edu/pcjgroup/adapt.html
101. www.openmopac.net
102. D. V. Parke, C. Ioannides and D. F. V. Lewis, Alt. Lab. Anim., 1990, 18, 91.
103. D. F. V. Lewis, C. Ioannides and D. V. Parke, Mutat. Res., 1993, 291, 61.
104. S. Zinke and I. Gerner, Alt. Lab. Anim., 2000, 28, 609.
105. I. Gerner, S. Zinke, G. Graetschel and E. Schlede, Alt. Lab. Anim., 2000, 28, 665.
106. www.bfr.bund.de
107. H. S. Rosenkranz, Y. P. Zhang and G. Klopman, Alt. Lab. Anim., 1998, 26, 779.
108. www.insilicofirst.com
109. E. Benfenati and G. Gini, Toxicology, 1997, 119, 213.
110. R. Benigni, Mutat. Res., 1997, 387, 35.
111. A. M. Richard and R. Benigni, SAR QSAR Environ. Res., 2002, 13, 1.
112. R. Benigni, Drug Discov. Today: Technologies, 2004, 1, 457.
113. www.mdli.com
114. E. J. Matthews, N. L. Kruhlak, R. D. Benz and J. F. Contrera, Toxicol. Mech. Meth., 2008, 18, 189.
115. www.prousresearch.com
116. N. F. Cariello, J. D. Wilson, B. H. Britt, D. J. Wedd, B. Burlinson and V. Gombar, Mutagenesis, 2002, 17, 321.
117. R. D. Snyder, G. S. Pearl, G. Mandakas, W. N. Choy, F. Goodsaid and L. Y. Rosenblum, Environ. Mol. Mutagen., 2004, 43, 143.
118. D. F. V. Lewis, M. G. Bird and M. N. Jacobs, Hum. Exp. Toxicol., 2002, 21, 115.
119. M. Ganguly, N. Brown, A. Schuffenhauer, P. Ertl, V. J. Gillet and P. A. Greenidge, J. Chem. Inf. Model., 2006, 46, 2110.
120. M. Hewitt, M. T. D. Cronin, J. C. Madden, P. H. Rowe, C. Johnson, A. Obi and S. J. Enoch, J. Chem. Inf. Model., 2007, 47, 1460.
121. J. R. Votano, M. Parham, L. H. Hall, L. B. Kier, S. Oloff, A. Tropsha, Q. Xie and W. Tong, Mutagenesis, 2004, 19, 365.
122. P. Gramatica, E. Giani and E. Papa, J. Mol. Graph. Model., 2007, 25, 755.
123. W. Tong, Q. Xie, H. Hong, L. Shi, H. Fang and R. Perkins, Environ. Health Perspect., 2004, 112, 1249.
124. Q. Liao, J. H. Yao, F. Li, S. G. Yuan, J. P. Doucet, A. Panaye and B. T. Fan, SAR QSAR Environ. Res., 2004, 15, 217.
125. S. J. Enoch, M. T. D. Cronin, T. W. Schultz and J. C. Madden, Chemosphere, 2008, 71, 1225.
126. C. M. Ellison, M. T. D. Cronin, J. C. Madden and T. W. Schultz, SAR QSAR Environ. Res., 2008, 19, 751.
127. G. F. Gerberick, C. A. Ryan, P. S. Kern, H. Schlatter, R. J. Dearman, I. Kimber, G. Y. Patlewicz and D. A. Basketter, Dermatitis, 2005, 16, 157.