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62. Bender A, Scheiber J, Glick M et al (2007) Analysis of pharmacology data and the prediction
of adverse drug reactions and off-target effects from chemical structure. ChemMedChem
2:861–873. doi:10.1002/cmdc.200700026
63. Scheiber J, Chen B, Milik M et al (2009) Gaining insight into off-target mediated effects of
drug candidates with a comprehensive systems chemical biology analysis. J Chem Inf Model
49:308–317. doi:10.1021/ci800344p
64. Subramanian A, Tamayo P, Mootha VK et al (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci
U S A 102:15545–15550. doi:10.1073/pnas.0506580102
65. Lamb J, Crawford ED, Peck D et al (2006) The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313:1929–1935.
doi:10.1126/science.1132939
66. Toyoshiba H, Sawada H, Naeshiro I, Horinouchi A (2009) Similar compounds searching system by using the gene expression microarray database. Toxicol Lett 186:52–57. doi:10.1016/j.
toxlet.2008.08.009
67. Minowa Y, Kondo C, Uehara T et al (2012) Toxicogenomic multigene biomarker for predicting the future onset of proximal tubular injury in rats. Toxicology 297:47–56. doi:10.1016/j.
tox.2012.03.014
68. Davis AP, Murphy CG, Johnson R et al (2013) The comparative toxicogenomics database:
update 2013. Nucleic Acids Res 41:D1104–1114. doi:10.1093/nar/gks994
69. Lagunin A, Ivanov S, Rudik A et al (2013) DIGEP-Pred: web-service for in silico prediction
of drug-induced gene expression profiles based on structural formula. Bioinforma Oxf Engl.
doi:10.1093/bioinformatics/btt322
70. Hardman JG, Limbird LE, Gilman AG (2001) Goodman & Gilman’s the pharmacological
basis of therapeutics, 10th edn. The McGraw-Hill, NY, USA
71. Manga N, Duffy JC, Rowe PH, Cronin MTD (2005) Structure-based methods for the prediction of the dominant P450 enzyme in human drug biotransformation: consideration of
CYP3A4, CYP2C9, CYP2D6. SAR QSAR Environ Res 16:43–61. doi:10.1080/1062936041
2331319871
72. Jonker DM, Visser SAG, van der Graaf PH et al (2005) Towards a mechanism-based
analysis of pharmacodynamic drug-drug interactions in vivo. Pharmacol Ther 106:1–18.
doi:10.1016/j.pharmthera.2004.10.014
73. Han H-K (2011) Role of transporters in drug interactions. Arch Pharm Res 34:1865–1877.
doi:10.1007/s12272–011-1107-y
74. Sedykh A, Fourches D, Duan J et al (2013) Human intestinal transporter database: QSAR
modeling and virtual profiling of drug uptake, efflux and interactions. Pharm Res 30:996–
1007. doi:10.1007/s11095-012-0935-x
75. Manzi SF, Shannon M (2005) Drug interactions—a review. Clin Pediatr Emerg Med 6:93–
102. doi:10.1016/j.cpem.2005.04.006
76. Hou T, Wang J (2008) Structure-ADME relationship: still a long way to go? Expert Opin
Drug Metab Toxicol 4:759–770. doi:10.1517/17425255.4.6.759
77. Metcalfe PD, Thomas S (2010) Challenges in the prediction and modeling of oral absorption
and bioavailability. Curr Opin Drug Discov Devel 13:104–110
78. Kirchmair J, Williamson MJ, Tyzack JD et al (2012) Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms. J Chem Inf Model
52:617–648. doi:10.1021/ci200542m
79. Deeks E, Perry C (2010) Efavirenz/emtricitabine/tenofovir disoproxil fumarate single-tablet
regimen (Atripla ® ): a review of its use in the management of HIV infection. Drugs 70:2315–
2338
80. Jacobs A (2005) Prediction of 2-year carcinogenicity study results for pharmaceutical products: how are we doing? Toxicol Sci Off J Soc Toxicol 88:18–23. doi:10.1093/toxsci/kfi248
81. Fourches D, Muratov E, Tropsha A (2010) Trust, but verify: on the importance of chemical structure curation in cheminformatics and QSAR modeling research. J Chem Inf Model
50:1189–1204. doi:10.1021/ci100176x
82. SYMMETRY
®
. http://www.prousresearch.com/Technology/SYMMETRY.aspx. Accessed 7
May 2013
A. Zakharov and A. Lagunin
62. Bender A, Scheiber J, Glick M et al (2007) Analysis of pharmacology data and the prediction
of adverse drug reactions and off-target effects from chemical structure. ChemMedChem
2:861–873. doi:10.1002/cmdc.200700026
63. Scheiber J, Chen B, Milik M et al (2009) Gaining insight into off-target mediated effects of
drug candidates with a comprehensive systems chemical biology analysis. J Chem Inf Model
49:308–317. doi:10.1021/ci800344p
64. Subramanian A, Tamayo P, Mootha VK et al (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci
U S A 102:15545–15550. doi:10.1073/pnas.0506580102
65. Lamb J, Crawford ED, Peck D et al (2006) The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science 313:1929–1935.
doi:10.1126/science.1132939
66. Toyoshiba H, Sawada H, Naeshiro I, Horinouchi A (2009) Similar compounds searching system by using the gene expression microarray database. Toxicol Lett 186:52–57. doi:10.1016/j.
toxlet.2008.08.009
67. Minowa Y, Kondo C, Uehara T et al (2012) Toxicogenomic multigene biomarker for predicting the future onset of proximal tubular injury in rats. Toxicology 297:47–56. doi:10.1016/j.
tox.2012.03.014
68. Davis AP, Murphy CG, Johnson R et al (2013) The comparative toxicogenomics database:
update 2013. Nucleic Acids Res 41:D1104–1114. doi:10.1093/nar/gks994
69. Lagunin A, Ivanov S, Rudik A et al (2013) DIGEP-Pred: web-service for in silico prediction
of drug-induced gene expression profiles based on structural formula. Bioinforma Oxf Engl.
doi:10.1093/bioinformatics/btt322
70. Hardman JG, Limbird LE, Gilman AG (2001) Goodman & Gilman’s the pharmacological
basis of therapeutics, 10th edn. The McGraw-Hill, NY, USA
71. Manga N, Duffy JC, Rowe PH, Cronin MTD (2005) Structure-based methods for the prediction of the dominant P450 enzyme in human drug biotransformation: consideration of
CYP3A4, CYP2C9, CYP2D6. SAR QSAR Environ Res 16:43–61. doi:10.1080/1062936041
2331319871
72. Jonker DM, Visser SAG, van der Graaf PH et al (2005) Towards a mechanism-based
analysis of pharmacodynamic drug-drug interactions in vivo. Pharmacol Ther 106:1–18.
doi:10.1016/j.pharmthera.2004.10.014
73. Han H-K (2011) Role of transporters in drug interactions. Arch Pharm Res 34:1865–1877.
doi:10.1007/s12272–011-1107-y
74. Sedykh A, Fourches D, Duan J et al (2013) Human intestinal transporter database: QSAR
modeling and virtual profiling of drug uptake, efflux and interactions. Pharm Res 30:996–
1007. doi:10.1007/s11095-012-0935-x
75. Manzi SF, Shannon M (2005) Drug interactions—a review. Clin Pediatr Emerg Med 6:93–
102. doi:10.1016/j.cpem.2005.04.006
76. Hou T, Wang J (2008) Structure-ADME relationship: still a long way to go? Expert Opin
Drug Metab Toxicol 4:759–770. doi:10.1517/17425255.4.6.759
77. Metcalfe PD, Thomas S (2010) Challenges in the prediction and modeling of oral absorption
and bioavailability. Curr Opin Drug Discov Devel 13:104–110
78. Kirchmair J, Williamson MJ, Tyzack JD et al (2012) Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms. J Chem Inf Model
52:617–648. doi:10.1021/ci200542m
79. Deeks E, Perry C (2010) Efavirenz/emtricitabine/tenofovir disoproxil fumarate single-tablet
regimen (Atripla ® ): a review of its use in the management of HIV infection. Drugs 70:2315–
2338
80. Jacobs A (2005) Prediction of 2-year carcinogenicity study results for pharmaceutical products: how are we doing? Toxicol Sci Off J Soc Toxicol 88:18–23. doi:10.1093/toxsci/kfi248
81. Fourches D, Muratov E, Tropsha A (2010) Trust, but verify: on the importance of chemical structure curation in cheminformatics and QSAR modeling research. J Chem Inf Model
50:1189–1204. doi:10.1021/ci100176x
82. SYMMETRY
®
. http://www.prousresearch.com/Technology/SYMMETRY.aspx. Accessed 7
May 2013