-
1
-
-
0037364162
-
ADMET in silico modelling: Towards prediction paradise?
-
•• Good introduction to the field of predictive ADMET modeling, together with a critical assessment of current limitations
-
Van De Waterbeemd H, Gifford E. ADMET in silico modelling: towards prediction paradise? Nat Rev Drug Discov 2003;2:192-204 •• Good introduction to the field of predictive ADMET modeling, together with a critical assessment of current limitations.
-
(2003)
Nat Rev Drug Discov
, vol.2
, pp. 192-204
-
-
Van De Waterbeemd, H.1
Gifford, E.2
-
2
-
-
1542362349
-
Automated high throughput ADME assays for metabolic stability and cytochrome P450 inhibition profiling of combinatorial libraries
-
DOI 10.1016/j.jpba.2003.08.001, PII S0731708503006678
-
Jenkins KM, Angeles R, Quintos MT, et al. Automated high throughput ADME assays for metabolic stability and cytochrome P450 inhibition profiling of combinatorial libraries. J Pharm Biomed Anal 2004;34:989-1004 (Pubitemid 38296402)
-
(2004)
Journal of Pharmaceutical and Biomedical Analysis
, vol.34
, Issue.5
, pp. 989-1004
-
-
Jenkins, K.M.1
Angeles, R.2
Quintos, M.T.3
Xu, R.4
Kassel, D.B.5
Rourick, R.A.6
-
3
-
-
0842332512
-
High-Throughput Screening for Stability and Inhibitory Activity of Compounds toward Cytochrome P450-Mediated Metabolism
-
DOI 10.1002/jps.10545
-
Ansede JH, Thakker DR. High-throughput screening for stability and inhibitory activity of compounds toward cytochrome P450-mediated metabolism. J Pharm Sci 2004;93:239-255 (Pubitemid 38174247)
-
(2004)
Journal of Pharmaceutical Sciences
, vol.93
, Issue.2
, pp. 239-255
-
-
Ansede, J.H.1
Thakker, D.R.2
-
4
-
-
26944495704
-
High throughput P450 inhibition screens in early drug discovery
-
DOI 10.1016/S1359-6446(05)03580-4, PII S1359644605035804
-
Zlokarnik G, Grootenhuis PD, Watson JB. High throughput P450 inhibition screens in early drug discovery. Drug Discov Today 2005;10:1443-1450 (Pubitemid 41483873)
-
(2005)
Drug Discovery Today
, vol.10
, Issue.21
, pp. 1443-1450
-
-
Zlokarnik, G.1
Grootenhuis, P.D.J.2
Watson, J.B.3
-
5
-
-
33846380861
-
Clinical implications of pharmacogenetics of cytochrome P450 drug metabolizing enzymes
-
DOI 10.1016/j.bbagen.2006.09.019, PII S0304416506002959
-
Kirchheiner J, Seeringer A. Clinical implications of pharmacogenetics of cytochrome P450 drug metabolizing enzymes. Biochim Biophys Acta 2007;1770:489-494 (Pubitemid 46136751)
-
(2007)
Biochimica et Biophysica Acta - General Subjects
, vol.1770
, Issue.3
, pp. 489-494
-
-
Kirchheiner, J.1
Seeringer, A.2
-
6
-
-
0033569516
-
Pharmacogenomics: Translating functional genomics into rational therapeutics
-
Evans WE, Relling MV. Pharmacogenomics: translating functional genomics into rational therapeutics. Science 1999;286:487-491
-
(1999)
Science
, vol.286
, pp. 487-491
-
-
Evans, W.E.1
Relling, M.V.2
-
7
-
-
0036891062
-
In silico prediction of ADME and pharmacokinetics. Report of an expert meeting organised by COST B15
-
Boobis A, Gundert-Remy U, Kremers P, et al. In silico prediction of ADME and pharmacokinetics. Report of an expert meeting organised by COST B15. Eur J Pharm Sci 2002;17:183-193
-
(2002)
Eur J Pharm Sci
, vol.17
, pp. 183-193
-
-
Boobis, A.1
Gundert-Remy, U.2
Kremers, P.3
-
9
-
-
0034885012
-
Role of drug metabolism in drug discovery and development
-
• Overview of drug metabolism in the human body and its investigation in drug discovery projects
-
Kumar GN, Surapaneni S. Role of drug metabolism in drug discovery and development. Med Res Rev 2001;21:397-411 • Overview of drug metabolism in the human body and its investigation in drug discovery projects.
-
(2001)
Med Res Rev
, vol.21
, pp. 397-411
-
-
Kumar, G.N.1
Surapaneni, S.2
-
13
-
-
45949107967
-
Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450
-
DOI 10.1517/17425255.4.5.513
-
Stjernschantz E, Vermeulen NP, Oostenbrink C. Computational prediction of drug binding and rationalisation of selectivity towards cytochromes P450. Expert Opin Drug Metab Toxicol 2008;4:513-527 (Pubitemid 351890736)
-
(2008)
Expert Opinion on Drug Metabolism and Toxicology
, vol.4
, Issue.5
, pp. 513-527
-
-
Stjernschantz, E.1
Vermeulen, N.P.E.2
Oostenbrink, C.3
-
14
-
-
39149111256
-
Improvement in the handling of drug-drug interactions
-
Fuhr U. Improvement in the handling of drug-drug interactions. Eur J Clin Pharmacol 2008;64:167-171
-
(2008)
Eur J Clin Pharmacol
, vol.64
, pp. 167-171
-
-
Fuhr, U.1
-
15
-
-
8544224973
-
The UDP glycosyltransferase gene superfamily: Rcommended nomenclature update based on evolutionary divergence
-
DOI 10.1097/00008571-199708000-00001
-
Mackenzie PI, Owens IS, Burchell B, et al. The UDP glycosyltransferase gene superfamily: recommended nomenclature update based on evolutionary divergence. Pharmacogenet 1997;7:255-269 (Pubitemid 27358064)
-
(1997)
Pharmacogenetics
, vol.7
, Issue.4
, pp. 255-269
-
-
Mackenzie, P.I.1
Owens, I.S.2
Burchell, B.3
Bock, K.W.4
Bairoch, A.5
Belanger, A.6
Fournel-Gigleux, S.7
Green, M.8
Hum, D.W.9
Iyanagi, T.10
Lancet, D.11
Louisot, P.12
Magdalou, J.13
Chowdhury, J.R.14
Ritter, J.K.15
Schachter, H.16
Tephly, T.R.17
Tipton, K.F.18
Nebert, D.W.19
-
16
-
-
0037707638
-
Metabolic stability for drug discovery and development: Pharmacokinetic and biochemical challenges
-
Masimirembwa CM, Bredberg U, Andersson TB. Metabolic stability for drug discovery and development: pharmacokinetic and biochemical challenges. Clin Pharmacokinet 2003;42:515-528 (Pubitemid 36801870)
-
(2003)
Clinical Pharmacokinetics
, vol.42
, Issue.6
, pp. 515-528
-
-
Masimirembwa, C.M.1
Bredberg, U.2
Andersson, T.B.3
-
17
-
-
24944492194
-
Utility of recombinant cytochrome P450 enzymes: A drug metabolism perspective
-
DOI 10.2174/138920005774330602
-
Tang W, Wang RW, Lu AY. Utility of recombinant cytochrome p450 enzymes: a drug metabolism perspective. Curr Drug Metab 2005;6:503-517 (Pubitemid 41300795)
-
(2005)
Current Drug Metabolism
, vol.6
, Issue.5
, pp. 503-517
-
-
Tang, W.1
Wang, R.W.2
Lu, A.Y.H.3
-
18
-
-
4644341747
-
Human hepatocytes in primary culture: The choice to investigate drug metabolism in man
-
DOI 10.2174/1389200043335414
-
Gomez-Lechon MJ, Donato MT, Castell JV, et al. Human hepatocytes in primary culture: the choice to investigate drug metabolism in man. Curr Drug Metab 2004;5:443-462 (Pubitemid 39276606)
-
(2004)
Current Drug Metabolism
, vol.5
, Issue.5
, pp. 443-462
-
-
Gomez-Lechon, M.J.1
Donato, M.T.2
Castell, J.V.3
Jover, R.4
-
19
-
-
0036319482
-
Comparison of the computer programs DEREK and TOPKAT to predict bacterial mutagenicity. Deductive estimate of risk from existing knowledge. Toxicity prediction by komputer assisted technology
-
Cariello NF, Wilson JD, Britt BH, et al. Comparison of the computer programs DEREK and TOPKAT to predict bacterial mutagenicity. Deductive estimate of risk from existing knowledge. Toxicity prediction by komputer assisted technology. Mutagenesis 2002;17:321-329
-
(2002)
Mutagenesis
, vol.17
, pp. 321-329
-
-
Cariello, N.F.1
Wilson, J.D.2
Britt, B.H.3
-
20
-
-
0032619762
-
Knowledge-based expert systems for toxicity and metabolism prediction: DEREK, STAR and METEOR
-
Greene N, Judson PN, Langowski JJ, et al. Knowledge-based expert systems for toxicity and metabolism prediction: DEREK, STAR and METEOR. SAR QSAR Environ Res 1999;10:299-314
-
(1999)
SAR QSAR Environ Res
, vol.10
, pp. 299-314
-
-
Greene, N.1
Judson, P.N.2
Langowski, J.J.3
-
21
-
-
0000353230
-
The characterization of chemical structures using molecular properties. A survey
-
Livingstone DJ. The characterization of chemical structures using molecular properties. A survey. J Chem Inf Comput Sci 2000;40:195-209
-
(2000)
J Chem Inf Comput Sci
, vol.40
, pp. 195-209
-
-
Livingstone, D.J.1
-
23
-
-
10644249977
-
In silico methods for predicting ligand binding determinants of cytochromes P450
-
De Groot MJ, Kirton SB, Sutcliffe MJ. In silico methods for predicting ligand binding determinants of cytochromes P450. Curr Top Med Chem 2004;4:1803-1824
-
(2004)
Curr Top Med Chem
, vol.4
, pp. 1803-1824
-
-
De Groot, M.J.1
Kirton, S.B.2
Sutcliffe, M.J.3
-
24
-
-
0034962557
-
Pharmacophore and three-dimensional quantitative structure activity relationship methods for modeling cytochrome p450 active sites
-
Ekins S, De Groot MJ, Jones JP. Pharmacophore and three-dimensional quantitative structure activity relationship methods for modeling cytochrome p450 active sites. Drug Metab Dispos 2001;29:936-944 (Pubitemid 32605906)
-
(2001)
Drug Metabolism and Disposition
, vol.29
, Issue.7
, pp. 936-944
-
-
Ekins, S.1
De Groot, M.J.2
Jones, J.P.3
-
25
-
-
33748124863
-
Machine learning techniques for in silico modeling of drug metabolism
-
DOI 10.2174/156802606778108915
-
Fox T, Kriegl JM. Machine learning techniques for in silico modeling of drug metabolism. Curr Top Med Chem 2006;6:1579-1591 (Pubitemid 44304616)
-
(2006)
Current Topics in Medicinal Chemistry
, vol.6
, Issue.15
, pp. 1579-1591
-
-
Fox, T.1
Kriegl, J.M.2
-
27
-
-
3242740497
-
Prediction of drug-like molecular properties: Modeling cytochrome p450 interactions
-
• Comprehensive survey of different statistical learning methods that can be applied to model ADMET end points
-
Jalaie M, Arimoto R, Gifford E, et al. Prediction of drug-like molecular properties: modeling cytochrome p450 interactions. Methods Mol Biol 2004;275:449-520 • Comprehensive survey of different statistical learning methods that can be applied to model ADMET end points.
-
(2004)
Methods Mol Biol
, vol.275
, pp. 449-520
-
-
Jalaie, M.1
Arimoto, R.2
Gifford, E.3
-
29
-
-
67649217287
-
-
Catalyst, Accelrys Software Inc, San Diego, CA, USA
-
Catalyst, Accelrys Software Inc, San Diego, CA, USA
-
-
-
-
31
-
-
0043132440
-
Methods for reliability and uncertainty assessment and for applicability evaluations of classification- and regression-based QSARs
-
•• Good overview of different approaches to assess the confidence of classification and regression models
-
Eriksson L, Jaworska J, Worth AP, et al. Methods for reliability and uncertainty assessment and for applicability evaluations of classification- and regression-based QSARs. Environ Health Perspect 2003;111:1361-75 •• Good overview of different approaches to assess the confidence of classification and regression models.
-
(2003)
Environ Health Perspect
, vol.111
, pp. 1361-1375
-
-
Eriksson, L.1
Jaworska, J.2
Worth, A.P.3
-
33
-
-
0038724207
-
The importance of being earnest: Validation is the absolute essential for successful application and interpretation of QSPR models
-
Tropsha A, Gramatica P, Gombar VK. The importance of being earnest: Validation is the absolute essential for successful application and interpretation of QSPR models. QSAR Comb Sci 2003;22:69-77 •• Description of best practices in establishing reliable and predictive QSAR models. (Pubitemid 36717473)
-
(2003)
QSAR and Combinatorial Science
, vol.22
, Issue.1
, pp. 69-77
-
-
Tropsha, A.1
Gramatica, P.2
Gombar, V.K.3
-
34
-
-
20444404916
-
Assessing the reliability of a QSAR model's predictions
-
DOI 10.1016/j.jmgm.2005.03.003, PII S1093326305000173
-
He L, Jurs PC. Assessing the reliability of a QSAR model's predictions. J Mol Graph Model 2005;23:503-523 (Pubitemid 40803520)
-
(2005)
Journal of Molecular Graphics and Modelling
, vol.23
, Issue.6
, pp. 503-523
-
-
He, L.1
Jurs, P.C.2
-
35
-
-
13944260141
-
Prediction of binding modes for ligands in the cytochromes P450 and other heme-containing proteins
-
DOI 10.1002/prot.20389
-
Kirton SB, Murray CW, Verdonk ML, et al. Prediction of binding modes for ligands in the cytochromes P450 and other heme-containing proteins. Proteins 2005;58:836-844 (Pubitemid 40271248)
-
(2005)
Proteins: Structure, Function and Genetics
, vol.58
, Issue.4
, pp. 836-844
-
-
Kirton, S.B.1
Murray, C.W.2
Verdonk, M.L.3
Taylor, R.D.4
-
36
-
-
0037008160
-
Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors
-
DOI 10.1002/1521-3773(20020802)41:15<2644::AID-ANIE2644>3.0.CO;2-O
-
Gohlke H, Klebe G. Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. Angew Chem Int Ed Engl 2002;41:2644-2676 (Pubitemid 34893207)
-
(2002)
Angewandte Chemie - International Edition
, vol.41
, Issue.15
, pp. 2644-2676
-
-
Gohlke, H.1
Klebe, G.2
-
37
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
DOI 10.1006/jmbi.1996.0897
-
Jones G, Willett P, Glen RC, et al. Development and validation of a genetic algorithm for flexible docking. J Mol Biol 1997;267:727-748 (Pubitemid 27170693)
-
(1997)
Journal of Molecular Biology
, vol.267
, Issue.3
, pp. 727-748
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
Leach, A.R.4
Taylor, R.5
-
38
-
-
33750124980
-
Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes
-
DOI 10.1021/jm051256o
-
Friesner RA, Murphy RB, Repasky MP, et al. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem 2006;49:6177-6196 (Pubitemid 44595196)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.21
, pp. 6177-6196
-
-
Friesner, R.A.1
Murphy, R.B.2
Repasky, M.P.3
Frye, L.L.4
Greenwood, J.R.5
Halgren, T.A.6
Sanschagrin, P.C.7
Mainz, D.T.8
-
39
-
-
52249113723
-
SFCscore: Scoring functions for affinity prediction of protein-ligand complexes
-
Sotriffer CA, Sanschagrin P, Matter H, et al. SFCscore: Scoring functions for affinity prediction of protein-ligand complexes. Proteins 2008;73:395-419
-
(2008)
Proteins
, vol.73
, pp. 395-419
-
-
Sotriffer, C.A.1
Sanschagrin, P.2
Matter, H.3
-
40
-
-
33748608826
-
Computational approaches: Reaction trajectories, structures, and atomic motions. Enzyme reactions and proficiency
-
Bruice TC. Computational approaches: reaction trajectories, structures, and atomic motions. Enzyme reactions and proficiency. Chem Rev 2006;106:3119-3139
-
(2006)
Chem Rev
, vol.106
, pp. 3119-3139
-
-
Bruice, T.C.1
-
41
-
-
0343725680
-
Critical assessment of the performance of the semiempirical divide and conquer method for single point calculations and geometry optimizations of large chemical systems
-
DOI 10.1063/1.1323257
-
Van Der Vaart A, Rez D, Merz J. Critical assessment of the performance of the semiempirical divide and conquer method for single point calculations and geometry optimizations of large chemical systems. J Chem Phys 2000;113:10512-10523 (Pubitemid 32076950)
-
(2000)
Journal of Chemical Physics
, vol.113
, Issue.23
, pp. 10512-10523
-
-
Van Der Vaart, A.1
Suarez, D.2
Merz Jr., K.M.3
-
42
-
-
33747461412
-
Novel structural features of CDK inhibition revealed by an ab initio computational method combined with dynamic simulations
-
DOI 10.1021/jm060190+
-
Heady L, Fernandez-Serra M, Mancera RL, et al. Novel structural features of CDK inhibition revealed by an ab initio computational method combined with dynamic simulations. J Med Chem 2006;49:5141-5153 (Pubitemid 44260210)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.17
, pp. 5141-5153
-
-
Heady, L.1
Fernandez-Serra, M.2
Mancera, R.L.3
Joyce, S.4
Venkitaraman, A.R.5
Attacho, E.6
Skylaris, C.-K.7
Ciacchi, L.C.8
Payne, M.C.9
-
43
-
-
34047191046
-
QM/MM studies of enzymes
-
DOI 10.1016/j.cbpa.2007.01.684, PII S136759310700021X
-
Senn HM, Thiel W. QM/MM studies of enzymes. Curr Opin Chem Biol 2007;11:182-187 (Pubitemid 46528365)
-
(2007)
Current Opinion in Chemical Biology
, vol.11
, Issue.2
, pp. 182-187
-
-
Senn, H.M.1
Thiel, W.2
-
44
-
-
58149161538
-
QM/MM modeling of benzene hydroxylation in human cytochrome P450 2C9
-
In press
-
Bathelt CM, Mulholland AJ, Harvey JN. QM/MM modeling of benzene hydroxylation in human cytochrome P450 2C9. J Phys Chem A 2008; In press
-
(2008)
J Phys Chem A
-
-
Bathelt, C.M.1
Mulholland, A.J.2
Harvey, J.N.3
-
45
-
-
1942539332
-
Prediction of in vitro metabolic stability of calcitriol analogs by QSAR
-
DOI 10.1023/B:JCAM.0000021861.31978.da
-
Jensen BF, Sorensen MD, Kissmeyer AM, et al. Prediction of in vitro metabolic stability of calcitriol analogs by QSAR. J Comput Aided Mol Des 2003;17:849-859 (Pubitemid 38519141)
-
(2003)
Journal of Computer-Aided Molecular Design
, vol.17
, Issue.12
, pp. 849-859
-
-
Jensen, B.F.1
Sorensen, M.D.2
Kissmeyer, A.-M.3
Bjorkling, F.4
Sonne, K.5
Engelsen, S.B.6
Norgaard, L.7
-
46
-
-
37749023039
-
Development of in silico models for human liver microsomal stability
-
Lee PH, Cucurull-Sanchez L, Lu J, et al. Development of in silico models for human liver microsomal stability. J Comput Aided Mol Des 2007;21:665-673
-
(2007)
J Comput Aided Mol des
, vol.21
, pp. 665-673
-
-
Lee, P.H.1
Cucurull-Sanchez, L.2
Lu, J.3
-
47
-
-
37349114485
-
Predicting human liver microsomal stability with machine learning techniques
-
DOI 10.1016/j.jmgm.2007.06.005, PII S1093326307001015
-
Sakiyama Y, Yuki H, Moriya T, et al. Predicting human liver microsomal stability with machine learning techniques. J Mol Graph Model 2008;26:907-915 (Pubitemid 350298011)
-
(2008)
Journal of Molecular Graphics and Modelling
, vol.26
, Issue.6
, pp. 907-915
-
-
Sakiyama, Y.1
Yuki, H.2
Moriya, T.3
Hattori, K.4
Suzuki, M.5
Shimada, K.6
Honma, T.7
-
48
-
-
44449142895
-
A probabilistic approach to classifying metabolic stability
-
• Application of Gaussian processes and their intrinsic confidence estimator in predictive modeling
-
Schwaighofer A, Schroeter T, Mika S, et al. A probabilistic approach to classifying metabolic stability. J Chem Inf Model 2008;48:785-96 • Application of Gaussian processes and their intrinsic confidence estimator in predictive modeling.
-
(2008)
J Chem Inf Model
, vol.48
, pp. 785-796
-
-
Schwaighofer, A.1
Schroeter, T.2
Mika, S.3
-
50
-
-
0002628667
-
Regression and classification using Gaussian process priors
-
Neal RM. Regression and classification using Gaussian process priors. Bayesian Statistics 1999;6:475-501
-
(1999)
Bayesian Statistics
, vol.6
, pp. 475-501
-
-
Neal, R.M.1
-
52
-
-
42749092988
-
The importance of the domain of applicability in QSAR modeling
-
Weaver S, Gleeson MP. The importance of the domain of applicability in QSAR modeling. J Mol Graph Model 2008;26:1315-1326
-
(2008)
J Mol Graph Model
, vol.26
, pp. 1315-1326
-
-
Weaver, S.1
Gleeson, M.P.2
-
53
-
-
0043031339
-
Predicting ADME properties and side effects: The BioPrint approach
-
Krejsa CM, Horvath D, Rogalski SL, et al. Predicting ADME properties and side effects: the BioPrint approach. Curr Opin Drug Discov Devel 2003;6:470-480 (Pubitemid 36975350)
-
(2003)
Current Opinion in Drug Discovery and Development
, vol.6
, Issue.4
, pp. 470-480
-
-
Krejsa, C.M.1
Horvath, D.2
Rogalski, S.L.3
Penzotti, J.E.4
Mao, B.5
Barbosa, F.6
Migeon, J.C.7
-
54
-
-
33344473208
-
A combined approach to drug metabolism and toxicity assessment
-
DOI 10.1124/dmd.105.008458
-
Ekins S, Andreyev S, Ryabov A, et al. A combined approach to drug metabolism and toxicity assessment. Drug Metab Dispos 2006;34:495-503 (Pubitemid 43290909)
-
(2006)
Drug Metabolism and Disposition
, vol.34
, Issue.3
, pp. 495-503
-
-
Ekins, S.1
Andreyev, S.2
Ryabov, A.3
Kirillov, E.4
Rakhmatulin, E.A.5
Sorokina, S.6
Bugrim, A.7
Nikolskaya, T.8
-
55
-
-
15944425080
-
Techniques: Application of systems biology to absorption, distribution, metabolism, excretion and toxicity
-
DOI 10.1016/j.tips.2005.02.006
-
Ekins S, Nikolsky Y, Nikolskaya T. Techniques: application of systems biology to absorption, distribution, metabolism, excretion and toxicity. Trends Pharmacol Sci 2005;26:202-209 (Pubitemid 40432655)
-
(2005)
Trends in Pharmacological Sciences
, vol.26
, Issue.4
, pp. 202-209
-
-
Ekins, S.1
Nikolsky, Y.2
Nikolskaya, T.3
-
56
-
-
33847395360
-
Classification of metabolites with kernel-partial least squares (K-PLS)
-
DOI 10.1124/dmd.106.013185
-
Embrechts MJ, Ekins S. Classification of metabolites with kernel-partial least squares (K-PLS). Drug Metab Dispos 2007;35:325-327 (Pubitemid 46333915)
-
(2007)
Drug Metabolism and Disposition
, vol.35
, Issue.3
, pp. 325-327
-
-
Embrechts, M.J.1
Ekins, S.2
-
57
-
-
0142061139
-
A human drug metabolism database: Potential roles in the quantitative predictions of drug metabolism and metabolism-related drug-drug interactions
-
DOI 10.2174/1389200033489299
-
Erhardt PW. A human drug metabolism database: potential roles in the quantitative predictions of drug metabolism and metabolism-related drug-drug interactions. Curr Drug Metab 2003;4:411-422 (Pubitemid 37287555)
-
(2003)
Current Drug Metabolism
, vol.4
, Issue.5
, pp. 411-422
-
-
Erhardt, P.W.1
-
58
-
-
67649195886
-
-
Accelrys Software Inc., San Diego, CA, USA
-
Metabolism Database, Accelrys Software Inc., San Diego, CA, USA
-
Metabolism Database
-
-
-
59
-
-
52849122979
-
-
MDL Information Systems Inc., San Ramon, CA, USA
-
Metabolite Database, MDL Information Systems Inc., San Ramon, CA, USA
-
Metabolite Database
-
-
-
60
-
-
0141925274
-
Using absolute and relative reasoning in the prediction of the potential metabolism of xenobiotics
-
Button WG, Judson PN, Long A, et al. Using absolute and relative reasoning in the prediction of the potential metabolism of xenobiotics. J Chem Inf Comput Sci 2003;43:1371-1377
-
(2003)
J Chem Inf Comput Sci
, vol.43
, pp. 1371-1377
-
-
Button, W.G.1
Judson, P.N.2
Long, A.3
-
61
-
-
23044488827
-
Predicting drug metabolism - An evaluation of the expert system METEOR
-
DOI 10.1002/cbdv.200590064
-
Testa B, Balmat AL, Long A, et al. Predicting drug metabolism - an evaluation of the expert system METEOR. Chem Biodivers 2005;2:872-885 (Pubitemid 41064996)
-
(2005)
Chemistry and Biodiversity
, vol.2
, Issue.7
, pp. 872-885
-
-
Testa, B.1
Balmat, A.-L.2
Long, A.3
Judson, P.4
-
62
-
-
0028534521
-
META. 1. A program for the evaluation of metabolic transformation of chemicals
-
Klopman G, Dimayuga M, Talafous J. META. 1. A program for the evaluation of metabolic transformation of chemicals. J Chem Inf Comput Sci 1994;34:1320-1325
-
(1994)
J Chem Inf Comput Sci
, vol.34
, pp. 1320-1325
-
-
Klopman, G.1
Dimayuga, M.2
Talafous, J.3
-
63
-
-
0028534522
-
META. 2. A dictionary model of mammalian xenobiotic metabolism
-
Talafous J, Sayre LM, Mieyal JJ, et al. META. 2. A dictionary model of mammalian xenobiotic metabolism. J Chem Inf Comput Sci 1994;34:1326-1333
-
(1994)
J Chem Inf Comput Sci
, vol.34
, pp. 1326-1333
-
-
Talafous, J.1
Sayre, L.M.2
Mieyal, J.J.3
-
65
-
-
0024027564
-
Predicting metabolic pathways by logic programming
-
Darvas F. Predicting metabolic pathways by logic programming. J Mol Graph 1988;6:80-86
-
(1988)
J Mol Graph
, vol.6
, pp. 80-86
-
-
Darvas, F.1
-
66
-
-
0043234176
-
Modeling of human cytochrome P450-mediated drug metabolism using unsupervised machine learning approach
-
DOI 10.1021/jm030102a
-
Korolev D, Balakin KV, Nikolsky Y, et al. Modeling of human cytochrome p450-mediated drug metabolism using unsupervised machine learning approach. J Med Chem 2003;46:3631-3643 (Pubitemid 36988650)
-
(2003)
Journal of Medicinal Chemistry
, vol.46
, Issue.17
, pp. 3631-3643
-
-
Korolev, D.1
Balakin, K.V.2
Nikolsky, Y.3
Kirillov, E.4
Ivanenkov, Y.A.5
Savchuk, N.P.6
Ivashchenko, A.A.7
Nikolskaya, T.8
-
68
-
-
4444222623
-
In silico ADME-Tox prediction: The more, the merrier
-
Banik GM. In silico ADME-Tox prediction: The more, the merrier. Curr Drug Disc 2004;31-34
-
(2004)
Curr Drug Disc
, pp. 31-34
-
-
Banik, G.M.1
-
69
-
-
34247265434
-
Reaction site mapping of xenobiotic biotransformations
-
DOI 10.1021/ci600376q
-
Boyer S, Arnby CH, Carlsson L, et al. Reaction site mapping of xenobiotic biotransformations. J Chem Inf Model 2007;47:583-590 (Pubitemid 46615959)
-
(2007)
Journal of Chemical Information and Modeling
, vol.47
, Issue.2
, pp. 583-590
-
-
Boyer, S.1
Arnby, C.H.2
Carlsson, L.3
Smith, J.4
Stein, V.5
Glen, R.C.6
-
70
-
-
47649092672
-
SyGMa: Combining expert knowledge and empirical scoring in the prediction of metabolites
-
Ridder L, Wagener M. SyGMa: combining expert knowledge and empirical scoring in the prediction of metabolites. Chem Med Chem 2008;3:821-832
-
(2008)
Chem Med Chem
, vol.3
, pp. 821-832
-
-
Ridder, L.1
Wagener, M.2
-
71
-
-
27444434892
-
MetaSite: Understanding metabolism in human cytochromes from the perspective of the chemist
-
DOI 10.1021/jm050529c
-
Cruciani G, Carosati E, De Boeck B, et al. MetaSite: understanding metabolism in human cytochromes from the perspective of the chemist. J Med Chem 2005;48:6970-6979 (Pubitemid 41533118)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.22
, pp. 6970-6979
-
-
Cruciani, G.1
Carosati, E.2
De Boeck, B.3
Ethirajulu, K.4
Mackie, C.5
Howe, T.6
Vianello, R.7
-
72
-
-
0021871375
-
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
-
DOI 10.1021/jm00145a002
-
Goodford PJ. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem 1985;28:849-857 (Pubitemid 15012490)
-
(1985)
Journal of Medicinal Chemistry
, vol.28
, Issue.7
, pp. 849-857
-
-
Goodford, P.J.1
-
73
-
-
35949002128
-
CYP2C9 structure-metabolism relationships: Substrates, inhibitors, and metabolites
-
DOI 10.1021/jm070745g
-
Ahlström MM, Ridderström M, Zamora I. CYP2C9 structure-metabolism relationships: substrates, inhibitors, and metabolites. J Med Chem 2007;50:5382-5391 (Pubitemid 350064000)
-
(2007)
Journal of Medicinal Chemistry
, vol.50
, Issue.22
, pp. 5382-5391
-
-
Ahlstrom, M.M.1
Ridderstrom, M.2
Zamora, I.3
-
74
-
-
34548501268
-
CYP2C9 structure-metabolism relationships: Optimizing the metabolic stability of COX-2 inhibitors
-
DOI 10.1021/jm0705096
-
Ahlström MM, Ridderström M, Zamora I, et al. CYP2C9 structure-metabolism relationships: optimizing the metabolic stability of COX-2 inhibitors. J Med Chem 2007;50:4444-4452 (Pubitemid 47378841)
-
(2007)
Journal of Medicinal Chemistry
, vol.50
, Issue.18
, pp. 4444-4452
-
-
Ahlstrom, M.M.1
Ridderstrom, M.2
Zamora, I.3
Luthman, K.4
-
75
-
-
33847099636
-
Predicting the oxidative metabolism of statins: An application of the MetaSite algorithm
-
DOI 10.1007/s11095-006-9199-7
-
Caron G, Ermondi G, Testa B. Predicting the oxidative metabolism of statins: an application of the MetaSite algorithm. Pharm Res 2007;24:480-501 (Pubitemid 46295168)
-
(2007)
Pharmaceutical Research
, vol.24
, Issue.3
, pp. 480-501
-
-
Caron, G.1
Ermondi, G.2
Testa, B.3
-
76
-
-
33646764551
-
Comparison of methods for the prediction of the metabolic sites for CYP3A4-mediated metabolic reactions
-
DOI 10.1124/dmd.105.008631
-
Zhou D, Afzelius L, Grimm SW, et al. Comparison of methods for the prediction of the metabolic sites for CYP3A4-mediated metabolic reactions. Drug Metab Dispos 2006;34:976-983 (Pubitemid 43763754)
-
(2006)
Drug Metabolism and Disposition
, vol.34
, Issue.6
, pp. 976-983
-
-
Zhou, D.1
Afzelius, L.2
Grimm, S.W.3
Andersson, T.B.4
Zauhar, R.J.5
Zamora, I.6
-
77
-
-
34250901033
-
Exploration of enzyme-ligand interactions in CYP2D6 & 3A4 homology models and crystal structures using a novel computational approach
-
DOI 10.1021/ci600561v
-
Kjellander B, Masimirembwa CM, Zamora I. Exploration of enzyme-ligand interactions in CYP2D6 & 3A4 homology models and crystal structures using a novel computational approach. J Chem Inf Model 2007;47:1234-1247 (Pubitemid 46973737)
-
(2007)
Journal of Chemical Information and Modeling
, vol.47
, Issue.3
, pp. 1234-1247
-
-
Kjellander, B.1
Masimirembwa, C.M.2
Zamora, I.3
-
80
-
-
0037431382
-
A model for predicting likely sites of CYP3A4-mediated metabolism on drug-like molecules
-
DOI 10.1021/jm020400s
-
Singh SB, Shen LQ, Walker MJ, et al. A model for predicting likely sites of CYP3A4-mediated metabolism on drug-like molecules. J Med Chem 2003;46:1330-1336 (Pubitemid 36512698)
-
(2003)
Journal of Medicinal Chemistry
, vol.46
, Issue.8
, pp. 1330-1336
-
-
Singh, S.B.1
Shen, L.Q.2
Walker, M.J.3
Sheridan, R.P.4
-
81
-
-
33744803155
-
Multiple molecular dynamics simulations of human P450 monooxygenase CYP2C9: The molecular basis of substrate binding and regioselectivity toward warfarin
-
DOI 10.1002/prot.20951
-
Seifert A, Tatzel S, Schmid RD, et al. Multiple molecular dynamics simulations of human p450 monooxygenase CYP2C9: the molecular basis of substrate binding and regioselectivity toward warfarin. Proteins 2006;64:147-155 (Pubitemid 43830993)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.64
, Issue.1
, pp. 147-155
-
-
Seifert, A.1
Tatzel, S.2
Schmid, R.B.3
Pleiss, J.4
-
82
-
-
0042265520
-
Crystal structure of human cytochrome P450 2C9 with bound warfarin
-
DOI 10.1038/nature01862
-
Williams PA, Cosme J, Ward A, et al. Crystal structure of human cytochrome P450 2C9 with bound warfarin. Nature 2003;424:464-468 (Pubitemid 36917499)
-
(2003)
Nature
, vol.424
, Issue.6947
, pp. 464-468
-
-
Williams, P.A.1
Cosme, J.2
Ward, A.3
Angove, H.C.4
Vinkovic, D.M.5
Jhoti, H.6
-
83
-
-
39749093726
-
Prediction of metabolism by cytochrome P450 2C9: Alignment and docking studies of a validated database of substrates
-
DOI 10.1021/jm7009793
-
Sykes MJ, McKinnon RA, Miners JO. Prediction of metabolism by cytochrome P450 2C 9: alignment and docking studies of a validated database of substrates. J Med Chem 2008;51:780-91 • An investigation of the performance of shape-based molecular alignments to predict potential sites of metabolism. (Pubitemid 351304687)
-
(2008)
Journal of Medicinal Chemistry
, vol.51
, Issue.4
, pp. 780-791
-
-
Sykes, M.J.1
McKinnon, R.A.2
Miners, J.O.3
-
85
-
-
0742288622
-
The "Rebound Controversy": An overview and theoretical modeling of the rebound step in C-H hydroxylation by cytochrome P450
-
Shaik S, Cohen S, De Visser SP, et al. The "Rebound Controversy": an overview and theoretical modeling of the rebound step in C-H hydroxylation by cytochrome P450. Eur J Med Chem 2004;207-226
-
(2004)
Eur J Med Chem
, pp. 207-226
-
-
Shaik, S.1
Cohen, S.2
De Visser, S.P.3
-
86
-
-
0034692380
-
A model 'rebound' mechanism of hydroxylation by cytochrome P450: Stepwise and effectively concerted pathways, and their reactivity patterns
-
Ogliaro F, Harris N, Cohen S, et al. A model 'rebound' mechanism of hydroxylation by cytochrome P450: stepwise and effectively concerted pathways, and their reactivity patterns. J Am Chem Soc 2000;122:8977-8989
-
(2000)
J Am Chem Soc
, vol.122
, pp. 8977-8989
-
-
Ogliaro, F.1
Harris, N.2
Cohen, S.3
-
87
-
-
0023865160
-
Theoretical study of the product specificity in the hydroxylation of camphor, norcamphor, 5,5-difluorocamphor, and pericyclocamphanone by cytochrome P-450cam
-
Collins JR, Loew GH. Theoretical study of the product specificity in the hydroxylation of camphor, norcamphor, 5,5-difluorocamphor, and pericyclocamphanone by cytochrome P-450cam. J Biol Chem 1988;263:3164-3170
-
(1988)
J Biol Chem
, vol.263
, pp. 3164-3170
-
-
Collins, J.R.1
Loew, G.H.2
-
88
-
-
0029774123
-
Predicting the rates and regioselectivity of reactions mediated by the P450 superfamily
-
Jones JP, Korzekwa KR. Predicting the rates and regioselectivity of reactions mediated by the P450 superfamily. Methods Enzymol 1996;272:326-335 (Pubitemid 26299897)
-
(1996)
Methods in Enzymology
, vol.272
, pp. 326-335
-
-
Jones, J.P.1
Korzekwa, K.R.2
-
89
-
-
0025150366
-
Theoretical studies on cytochrome P-450 mediated hydroxylation: A predictive model for hydrogen atom abstractions
-
Korzekwa KR, Jones JP, Gillette JR. Theoretical studies on cytochrome P-450 mediated hydroxylation: A predictive model for hydrogen atom abstractions. J Am Chem Soc 1990;112:7042-7046 (Pubitemid 20319136)
-
(1990)
Journal of the American Chemical Society
, vol.112
, Issue.19
, pp. 7042-7046
-
-
Korzekwa, K.R.1
Jones, J.P.2
Gillette, J.R.3
-
90
-
-
0036136527
-
Computational models for cytochrome P450: A predictive electronic model for aromatic oxidation and hydrogen atom abstraction
-
DOI 10.1124/dmd.30.1.7
-
Jones JP, Mysinger M, Korzekwa KR. Computational models for cytochrome P450: a predictive electronic model for aromatic oxidation and hydrogen atom abstraction. Drug Metab Dispos 2002;30:7-12 (Pubitemid 34016934)
-
(2002)
Drug Metabolism and Disposition
, vol.30
, Issue.1
, pp. 7-12
-
-
Jones, J.P.1
Mysinger, M.2
Korzekwa, K.R.3
-
91
-
-
18344376209
-
Do Fukui function maxima relate to sites of metabolism? A critical case study
-
Beck ME. Do Fukui function maxima relate to sites of metabolism? A critical case study. J Chem Inf Model 2005;45:273-282
-
(2005)
J Chem Inf Model
, vol.45
, pp. 273-282
-
-
Beck, M.E.1
-
92
-
-
0028962083
-
Metabolite predictions for para-substituted anisoles based on ab initio complete active space self-consistent field calculations
-
De Groot MJ, Donne-Op Den Kelder GM, Commandeur JN, et al. Metabolite predictions for para-substituted anisoles based on ab initio complete active space self-consistent field calculations. Chem Res Toxicol 1995;8:437-443
-
(1995)
Chem Res Toxicol
, vol.8
, pp. 437-443
-
-
De Groot, M.J.1
Donne-Op Den Kelder, G.M.2
Commandeur, J.N.3
-
93
-
-
0006059357
-
Quantum-chemical studies of model cytochrome P450 hydrocarbon oxidation mechanisms. 1. A MINDO/3 study of hydroxylation and epoxidation pathways for methane and ethylene
-
Pudzianowski AT, Loew GH. Quantum-chemical studies of model cytochrome P450 hydrocarbon oxidation mechanisms. 1. A MINDO/3 study of hydroxylation and epoxidation pathways for methane and ethylene. J Am Chem Soc 1980;102:5443-5449
-
(1980)
J Am Chem Soc
, vol.102
, pp. 5443-5449
-
-
Pudzianowski, A.T.1
Loew, G.H.2
-
94
-
-
0034779948
-
An assessment of the reaction energetics for cytochrome P450-mediated reactions
-
DOI 10.1006/abbi.2000.2147
-
Higgins L, Korzekwa KR, Rao S, et al. An assessment of the reaction energetics for cytochrome P450-mediated reactions. Arch Biochem Biophys 2001;385:220-230 (Pubitemid 32989001)
-
(2001)
Archives of Biochemistry and Biophysics
, vol.385
, Issue.1
, pp. 220-230
-
-
Higgins, L.1
Korzekwa, K.R.2
Rao, S.3
Shou, M.4
Jones, J.P.5
-
95
-
-
1342323500
-
An analysis, of the regioselectivity of aromatic hydroxylation and N-oxygenation by cytochrome P450 enzymes
-
DOI 10.1124/dmd.32.3.328
-
Dowers TS, Rock DA, Rock DA, et al. An analysis of the regioselectivity of aromatic hydroxylation and N-oxygenation by cytochrome P450 enzymes. Drug Metab Dispos 2004;32:328-332 (Pubitemid 38263891)
-
(2004)
Drug Metabolism and Disposition
, vol.32
, Issue.3
, pp. 328-332
-
-
Dowers, T.S.1
Rock, D.A.2
Rock, D.A.3
Perkins, B.N.S.4
Jones, J.P.5
-
96
-
-
0037464481
-
Construction and assessment of models of CYP2E1: Predictions of metabolism from docking, molecular dynamics, and density functional theoretical calculations
-
DOI 10.1021/jm020538a
-
Park JY, Harris D. Construction and assessment of models of CYP2E1: predictions of metabolism from docking, molecular dynamics, and density functional theoretical calculations. J Med Chem 2003;46:1645-1660 (Pubitemid 36444218)
-
(2003)
Journal of Medicinal Chemistry
, vol.46
, Issue.9
, pp. 1645-1660
-
-
Park, J.-Y.1
Harris, D.2
-
98
-
-
21944432511
-
Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes
-
DOI 10.1021/cr030722j
-
Shaik S, Kumar D, De Visser SP, et al. Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes. Chem Rev 2005;105:2279-2328 (Pubitemid 40947949)
-
(2005)
Chemical Reviews
, vol.105
, Issue.6
, pp. 2279-2328
-
-
Shaik, S.1
Kumar, D.2
De Visser, S.P.3
Altun, A.4
Thiel, W.5
-
99
-
-
33750486521
-
Prediction of activation energies for hydrogen abstraction by cytochrome P450
-
DOI 10.1021/jm060551l
-
Olsen L, Rydberg P, Rod TH, et al. Prediction of activation energies for hydrogen abstraction by cytochrome p450. J Med Chem 2006;49:6489-6499 (Pubitemid 44657443)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.22
, pp. 6489-6499
-
-
Olsen, L.1
Rydberg, P.2
Rod, T.H.3
Ryde, U.4
-
100
-
-
84962377244
-
A theoretical study on the mechanism of camphor hydroxylation by compound I of cytochrome p450
-
DOI 10.1021/ja0208862
-
Kamachi T, Yoshizawa K. A theoretical study on the mechanism of camphor hydroxylation by compound I of cytochrome p450. J Am Chem Soc 2003;125:4652-4661 (Pubitemid 36418711)
-
(2003)
Journal of the American Chemical Society
, vol.125
, Issue.15
, pp. 4652-4661
-
-
Kamachi, T.1
Yoshizawa, K.2
-
101
-
-
12144287949
-
cam: Theory Supports a Two-State Rebound Mechanism
-
DOI 10.1021/ja039847w
-
Schöneboom JC, Cohen S, Lin H, et al. Quantum mechanical/molecular mechanical investigation of the mechanism of C-H hydroxylation of camphor by cytochrome P450cam: theory supports a two-state rebound mechanism. J Am Chem Soc 2004;126:4017-4034 (Pubitemid 38391894)
-
(2004)
Journal of the American Chemical Society
, vol.126
, Issue.12
, pp. 4017-4034
-
-
Schoneboom, J.C.1
Cohen, S.2
Lin, H.3
Shaik, S.4
Thiel, W.5
-
102
-
-
25144520939
-
Electronic structure of compound I in human isoforms of cytochrome P450 from QM/MM modeling
-
DOI 10.1021/ja0520924
-
Bathelt CM, Zurek J, Mulholland AJ, et al. Electronic structure of compound I in human isoforms of cytochrome P450 from QM/MM modeling. J Am Chem Soc 2005;127:12900-12908 (Pubitemid 41339174)
-
(2005)
Journal of the American Chemical Society
, vol.127
, Issue.37
, pp. 12900-12908
-
-
Bathelt, C.M.1
Zurek, J.2
Mulholland, A.J.3
Harvey, J.N.4
-
103
-
-
33845379303
-
Atom pairs as molecular features in structure-activity studies: Definition and applications
-
Carhart RE, Smith DH, Venkataraghavan R. Atom pairs as molecular features in structure-activity studies: definition and applications. J Chem Inf Comput Sci 1985;25:64-73
-
(1985)
J Chem Inf Comput Sci
, vol.25
, pp. 64-73
-
-
Carhart, R.E.1
Smith, D.H.2
Venkataraghavan, R.3
-
104
-
-
0028454829
-
Extending the trend vector: The trend matrix and sample-based partial least squares
-
Sheridan RP, Nachbar RB, Bush BL. Extending the trend vector: the trend matrix and sample-based partial least squares. J Comput Aided Mol Des 1994;8:323-340
-
(1994)
J Comput Aided Mol des
, vol.8
, pp. 323-340
-
-
Sheridan, R.P.1
Nachbar, R.B.2
Bush, B.L.3
-
105
-
-
42149138057
-
New combined model for the prediction of regioselectivity in cytochrome P450/3A4 mediated metabolism
-
Oh WS, Kim DN, Jung J, et al. New combined model for the prediction of regioselectivity in cytochrome P450/3A4 mediated metabolism. J Chem Inf Model 2008;48:591-601
-
(2008)
J Chem Inf Model
, vol.48
, pp. 591-601
-
-
Oh, W.S.1
Kim, D.N.2
Jung, J.3
-
106
-
-
4644322438
-
Quantitative structure-metabolism relationship modeling of metabolic N-dealkylation reaction rates
-
DOI 10.1124/dmd.104.000364
-
Balakin KV, Ekins S, Bugrim A, et al. Quantitative structure-metabolism relationship modeling of metabolic N-dealkylation reaction rates. Drug Metab Dispos 2004;32:1111-1120 (Pubitemid 39287585)
-
(2004)
Drug Metabolism and Disposition
, vol.32
, Issue.10
, pp. 1111-1120
-
-
Balakin, K.V.1
Ekins, S.2
Bugrim, A.3
Ivanenkov, V.A.4
Korolev, D.5
Nikolsky, Y.V.6
Ivashchenko, A.A.7
Savchuk, N.P.8
Nikolskaya, T.9
-
107
-
-
34447515639
-
Empirical regioselectivity models for human cytochromes P450 3A4, 2D6, and 2C9
-
DOI 10.1021/jm0613471
-
Sheridan RP, Korzekwa KR, Torres RA, et al. Empirical regioselectivity models for human cytochromes P450 3A4, 2D6, and 2C9. J Med Chem 2007;50:3173-3184 (Pubitemid 47065966)
-
(2007)
Journal of Medicinal Chemistry
, vol.50
, Issue.14
, pp. 3173-3184
-
-
Sheridan, R.P.1
Korzekwa, K.R.2
Torres, R.A.3
Walker, M.J.4
-
108
-
-
0002641548
-
Quantitative relationships between lipophilic character and drug metabolism
-
Hansch C. Quantitative relationships between lipophilic character and drug metabolism. Drug Metab Rev 1972;1:1-13
-
(1972)
Drug Metab Rev
, vol.1
, pp. 1-13
-
-
Hansch, C.1
-
109
-
-
34548684996
-
Linear quantitative structure-activity relationships for the interaction of small molecules with human cytochrome P450 isoenzymes
-
Fox T, Kriegl JM. Linear quantitative structure-activity relationships for the interaction of small molecules with human cytochrome P450 isoenzymes. Ann Rev Comp Chem 2007;3:63-81
-
(2007)
Ann Rev Comp Chem
, vol.3
, pp. 63-81
-
-
Fox, T.1
Kriegl, J.M.2
-
110
-
-
0037281964
-
Baseline lipophilicity relationships in human cytochromes P450 associated with drug metabolism
-
DOI 10.1081/DMR-120018245
-
Lewis DF, Dickins M. Baseline lipophilicity relationships in human cytochromes P450 associated with drug metabolism. Drug Metab Rev 2003;35:1-18 (Pubitemid 36249783)
-
(2003)
Drug Metabolism Reviews
, vol.35
, Issue.1
, pp. 1-18
-
-
Lewis, D.F.V.1
Dickins, M.2
-
111
-
-
0034950245
-
Development of a generalized, quantitative physicochemical model of CYP3A4 inhibition for use in early drug discovery
-
DOI 10.1023/A:1011085411050
-
Riley RJ, Parker AJ, Trigg S, et al. Development of a generalized, quantitative physicochemical model of CYP3A4 inhibition for use in early drug discovery. Pharm Res 2001;18:652-655 (Pubitemid 32595794)
-
(2001)
Pharmaceutical Research
, vol.18
, Issue.5
, pp. 652-655
-
-
Riley, R.J.1
Parker, A.J.2
Trigg, S.3
Manners, C.N.4
-
112
-
-
33745741280
-
Computational approaches for predicting CYP-related metabolism properties in the screening of new drugs
-
•• Nice overview of different in silico approaches to predict CYP interactions
-
Crivori P, Poggesi I. Computational approaches for predicting CYP-related metabolism properties in the screening of new drugs. Eur J Med Chem 2006;41:795-808 •• Nice overview of different in silico approaches to predict CYP interactions.
-
(2006)
Eur J Med Chem
, vol.41
, pp. 795-808
-
-
Crivori, P.1
Poggesi, I.2
-
113
-
-
54249099193
-
Generalized proteochemometric model of multiple cytochrome P450 enzymes and their inhibitors
-
Kontijevskis A, Komorowski J, Wikberg JE. Generalized proteochemometric model of multiple cytochrome P450 enzymes and their inhibitors. J Chem Inf Model 2008;48:1840-1850
-
(2008)
J Chem Inf Model
, vol.48
, pp. 1840-1850
-
-
Kontijevskis, A.1
Komorowski, J.2
Wikberg, J.E.3
-
114
-
-
0032849040
-
Three and four dimensional-quantitative structure activity relationship (3D/4D-QSAR) analyses of CYP2D6 inhibitors
-
Ekins S, Bravi G, Binkley S, et al. Three and four dimensional- quantitative structure activity relationship (3D/4D-QSAR) analyses of CYP2D6 inhibitors. Pharmacogenet 1999;9:477-489 (Pubitemid 29419566)
-
(1999)
Pharmacogenetics
, vol.9
, Issue.4
, pp. 477-489
-
-
Ekins, S.1
Bravi, G.2
Binkley, S.3
Gillespie, J.S.4
Ring, B.J.5
Wikel, J.H.6
Wrighton, S.A.7
-
115
-
-
0033011395
-
Three- And four-dimensional quantitative structure activity relationship analyses of cytochrome P-450 3A4 inhibitors
-
Ekins S, Bravi G, Binkley S, et al. Three-and four-dimensional quantitative structure activity relationship analyses of cytochrome P-450 3A4 inhibitors. J Pharmacol Exp Ther 1999;290:429-438 (Pubitemid 29302353)
-
(1999)
Journal of Pharmacology and Experimental Therapeutics
, vol.290
, Issue.1
, pp. 429-438
-
-
Ekins, S.1
Bravi, G.2
Binkley, S.3
Gillespie, J.S.4
Ring, B.J.5
Wikel, J.H.6
Wrighton, S.A.7
-
116
-
-
0032822383
-
Three-dimensional-quantitative structure activity relationship analysis of cytochrome P-450 3A4 substrates
-
Ekins S, Bravi G, Wikel JH, et al. Three-dimensional-quantitative structure activity relationship analysis of cytochrome P-450 3A4 substrates. J Pharmacol Exp Ther 1999;291:424-433 (Pubitemid 29451619)
-
(1999)
Journal of Pharmacology and Experimental Therapeutics
, vol.291
, Issue.1
, pp. 424-433
-
-
Ekins, S.1
Bravi, G.2
Wikel, J.H.3
Wrighton, S.A.4
-
117
-
-
0027314831
-
Development of a pharmacophore for inhibition of human liver cytochrome P- 450 2D6: Molecular modeling and inhibition studies
-
DOI 10.1021/jm00061a004
-
Strobl GR, Von Kruedener S, Stockigt J, et al. Development of a pharmacophore for inhibition of human liver cytochrome P-450 2D6: molecular modeling and inhibition studies. J Med Chem 1993;36:1136-1145 (Pubitemid 23159287)
-
(1993)
Journal of Medicinal Chemistry
, vol.36
, Issue.9
, pp. 1136-1145
-
-
Strobl, G.R.1
Von Kruedener, S.2
Stockigt, J.3
Guengerich, F.P.4
Wolff, T.5
-
119
-
-
33645822986
-
Development and validation of an in silico P450 profiler based on pharmacophore models
-
Schuster D, Laggner C, Steindl TM, et al. Development and validation of an in silico P450 profiler based on pharmacophore models. Curr Drug Discov Technol 2006;3:1-48
-
(2006)
Curr Drug Discov Technol
, vol.3
, pp. 1-48
-
-
Schuster, D.1
Laggner, C.2
Steindl, T.M.3
-
120
-
-
53249095707
-
Considerations and recent advances in QSAR models for cytochrome P450-mediated drug metabolism prediction
-
Li H, Sun J, Fan X, et al. Considerations and recent advances in QSAR models for cytochrome P450-mediated drug metabolism prediction. J Comput Aided Mol Des 2008;22:843-855
-
(2008)
J Comput Aided Mol des
, vol.22
, pp. 843-855
-
-
Li, H.1
Sun, J.2
Fan, X.3
-
121
-
-
33748104432
-
Application of support vector machines to in silico prediction of cytochrome P450 enzyme substrates and inhibitors
-
DOI 10.2174/156802606778108942
-
Yap CW, Xue Y, Li ZR, et al. Application of support vector machines to in silico prediction of cytochrome p450 enzyme substrates and inhibitors. Curr Top Med Chem 2006;6:1593-1607 (Pubitemid 44304617)
-
(2006)
Current Topics in Medicinal Chemistry
, vol.6
, Issue.15
, pp. 1593-1607
-
-
Yap, C.W.1
Xue, Y.2
Li, Z.R.3
Chen, Y.Z.4
-
122
-
-
33846864233
-
Classification of highly unbalanced CYP450 data of drugs using cost sensitive machine learning techniques
-
• An interesting study on the generation of stable classification models from unbalanced training sets
-
Eitrich T, Kless A, Druska C, et al. Classification of highly unbalanced CYP450 data of drugs using cost sensitive machine learning techniques. J Chem Inf Model 2007;47:92-103 • An interesting study on the generation of stable classification models from unbalanced training sets.
-
(2007)
J Chem Inf Model
, vol.47
, pp. 92-103
-
-
Eitrich, T.1
Kless, A.2
Druska, C.3
-
123
-
-
36949009228
-
Generation of in-silico cytochrome P450 1A2, 2C9, 2C19, 2D6, and 3A4 inhibition QSAR models
-
DOI 10.1007/s10822-007-9139-6
-
Gleeson MP, Davis AM, Chohan KK, et al. Generation of in silico cytochrome P450 1A2, 2C9, 2C19, 2D6, and 3A4 inhibition QSAR models. J Comput Aided Mol Des 2007;21:559-573 (Pubitemid 50005007)
-
(2007)
Journal of Computer-Aided Molecular Design
, vol.21
, Issue.10-11
, pp. 559-573
-
-
Gleeson, M.P.1
Davis, A.M.2
Chohan, K.K.3
Paine, S.W.4
Boyer, S.5
Gavaghan, C.L.6
Arnby, C.H.7
Kankkonen, C.8
Albertson, N.9
-
124
-
-
33846923287
-
In silico prediction of cytochrome P450 2D6 and 3A4 inhibition using Gaussian kernel weighted k-nearest neighbor and extended connectivity fingerprints, including structural fragment analysis of inhibitors versus noninhibitors
-
Jensen BF, Vind C, Padkjaer SB, et al. In silico prediction of cytochrome P450 2D6 and 3A4 inhibition using Gaussian kernel weighted k-nearest neighbor and extended connectivity fingerprints, including structural fragment analysis of inhibitors versus noninhibitors. J Med Chem 2007;50:501-511
-
(2007)
J Med Chem
, vol.50
, pp. 501-511
-
-
Jensen, B.F.1
Vind, C.2
Padkjaer, S.B.3
-
125
-
-
34250690497
-
A virtual screening filter for identification of cytochrome P450 2C9 (CYP2C9) inhibitors
-
DOI 10.1002/qsar.200630143
-
Byvatov E, Baringhaus KH, Schneider G, et al. A virtual screening filter for identification of cytochrome P450 2C9 (CYP2C9) inhibitors. QSAR Comb Sci 2007;26:618-628 (Pubitemid 46932851)
-
(2007)
QSAR and Combinatorial Science
, vol.26
, Issue.5
, pp. 618-628
-
-
Byvatov, E.1
Baringhaus, K.-H.2
Schneider, G.3
Matter, H.4
-
126
-
-
20544460560
-
Prediction of human cytochrome P450 inhibition using support vector machines
-
DOI 10.1002/qsar.200430925
-
Kriegl JM, Arnhold T, Beck B, et al. Prediction of human cytochrome P450 inhibition using support vector machines. QSAR Comb Sci 2005;24:491-502 (Pubitemid 40839677)
-
(2005)
QSAR and Combinatorial Science
, vol.24
, Issue.4
, pp. 491-502
-
-
Kriegl, J.M.1
Arnhold, T.2
Beck, B.3
Fox, T.4
-
127
-
-
48249154237
-
Predictive QSAR models for polyspecific drug targets: The importance of feature selection
-
Demel MA, Janecek AGK, Thai KM, et al. Predictive QSAR models for polyspecific drug targets: The importance of feature selection. Curr Comput Aided Drug Des 2008;4:91-110
-
(2008)
Curr Comput Aided Drug des
, vol.4
, pp. 91-110
-
-
Demel, M.A.1
Janecek, A.G.K.2
Thai, K.M.3
-
128
-
-
10044263240
-
Similarity to molecules in the training set is a good discriminator for prediction accuracy in QSAR
-
Sheridan RP, Feuston BP, Maiorov VN, et al. Similarity to molecules in the training set is a good discriminator for prediction accuracy in QSAR. J Chem Inf Comput Sci 2004;44:1912-1928
-
(2004)
J Chem Inf Comput Sci
, vol.44
, pp. 1912-1928
-
-
Sheridan, R.P.1
Feuston, B.P.2
Maiorov, V.N.3
-
129
-
-
0038443423
-
Dimension related distance and its application in QSAR/QSPR model error estimation
-
Xu YJ, Gao H. Dimension related distance and its application in QSAR/QSPR model error estimation. QSAR Comb Sci 2003;22:422-429 (Pubitemid 36875080)
-
(2003)
QSAR and Combinatorial Science
, vol.22
, Issue.4
, pp. 422-429
-
-
Xu, Y.-J.1
Gao, H.2
-
130
-
-
13944268698
-
Greater than the sum of its parts: Combining models for useful ADMET prediction
-
• A study on how to combine different models with great relevance for practical application in the drug discovery process
-
O'Brien SE, De Groot MJ. Greater than the sum of its parts: combining models for useful ADMET prediction. J Med Chem 2005;48:1287-91 • A study on how to combine different models with great relevance for practical application in the drug discovery process.
-
(2005)
J Med Chem
, vol.48
, pp. 1287-1291
-
-
O'Brien, S.E.1
De Groot, M.J.2
-
132
-
-
39149140400
-
High confidence predictions of drug-drug interactions: Predicting affinities for cytochrome P450 2C9 with multiple computational methods
-
DOI 10.1021/jm701130z
-
Hudelson MG, Ketkar NS, Holder LB, et al. High confidence predictions of drug-drug interactions: predicting affinities for cytochrome P450 2C9 with multiple computational methods. J Med Chem 2008;51:648-654 (Pubitemid 351252292)
-
(2008)
Journal of Medicinal Chemistry
, vol.51
, Issue.3
, pp. 648-654
-
-
Hudelson, M.G.1
Ketkar, N.S.2
Holder, L.B.3
Carlson, T.J.4
Peng, C.-C.5
Waldher, B.J.6
Jones, J.P.7
-
133
-
-
34547679825
-
Ligand-based models for the isoform specificity of cytochrome P450 3A4, 2D6, and 2C9 substrates
-
DOI 10.1021/ci700010t
-
Terfloth L, Bienfait B, Gasteiger J. Ligand-based models for the isoform specificity of cytochrome P450 3A4, 2D6, and 2C9 substrates. J Chem Inf Model 2007;47:1688-1701 (Pubitemid 47210071)
-
(2007)
Journal of Chemical Information and Modeling
, vol.47
, Issue.4
, pp. 1688-1701
-
-
Terfloth, L.1
Bienfait, B.2
Gasteiger, J.3
-
134
-
-
17444411955
-
Cytochrome p450 in silico: An integrative modeling approach
-
•• A comprehensive survey on computational methods to model interactions between small molecules and CYP isoenzymes, with a focus on structure-based methods
-
De Graaf C, Vermeulen NP, Feenstra, KA. Cytochrome p450 in silico: an integrative modeling approach. J Med Chem 2005;48:2725-55 •• A comprehensive survey on computational methods to model interactions between small molecules and CYP isoenzymes, with a focus on structure-based methods.
-
(2005)
J Med Chem
, vol.48
, pp. 2725-2755
-
-
De Graaf, C.1
Vermeulen, N.P.2
Feenstra, K.A.3
-
135
-
-
33646107162
-
Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking
-
De Graaf C, Oostenbrink C, Keizers PH, et al. Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking. J Med Chem 2006;49:2417-2430
-
(2006)
J Med Chem
, vol.49
, pp. 2417-2430
-
-
De Graaf, C.1
Oostenbrink, C.2
Keizers, P.H.3
-
136
-
-
33845772311
-
Synergistic use of compound properties and docking scores in neural network modeling of CYP2D6 binding: Predicting affinity and conformational sampling
-
DOI 10.1021/ci600267k
-
Bazeley PS, Prithivi S, Struble CA, et al. Synergistic use of compound properties and docking scores in neural network modeling of CYP2D6 binding: predicting affinity and conformational sampling. J Chem Inf Model 2006;46:2698-2708 (Pubitemid 46008139)
-
(2006)
Journal of Chemical Information and Modeling
, vol.46
, Issue.6
, pp. 2698-2708
-
-
Bazeley, P.S.1
Prithivi, S.2
Struble, C.A.3
Povinelli, R.J.4
Sem, D.S.5
-
137
-
-
67649209010
-
-
GOLD, Cambridge Crystallographic Data Centre, Cambrigde, UK
-
GOLD, Cambridge Crystallographic Data Centre, Cambrigde, UK
-
-
-
-
138
-
-
38849122616
-
Recent advances in the in silico modelling of UDP glucuronosyltransferase substrates
-
DOI 10.2174/138920008783331167
-
Sorich MJ, Smith PA, Miners JO, et al. Recent advances in the in silico modelling of UDP glucuronosyltransferase substrates. Curr Drug Metab 2008;9:60-69 (Pubitemid 351201671)
-
(2008)
Current Drug Metabolism
, vol.9
, Issue.1
, pp. 60-69
-
-
Sorich, M.J.1
Smith, P.A.2
Miners, J.O.3
Mackenzie, P.I.4
McKinnon, R.A.5
-
139
-
-
0033621476
-
X-ray crystal structure of human dopamine sulfotransferase, SULT1A3. Molecular modeling and quantitative structure-activity relationship analysis demonstrate a molecular basis for sulfotransferase substrate specificity
-
DOI 10.1074/jbc.274.53.37862
-
Dajani R, Cleasby A, Neu M, et al. X-ray crystal structure of human dopamine sulfotransferase, SULT1A3. Molecular modeling and quantitative structure-activity relationship analysis demonstrate a molecular basis for sulfotransferase substrate specificity. J Biol Chem 1999;274:37862-37868 (Pubitemid 30026852)
-
(1999)
Journal of Biological Chemistry
, vol.274
, Issue.53
, pp. 37862-37868
-
-
Dajani, R.1
Cleasby, A.2
Margarete, N.3
Wonacott, A.J.4
Jhoti, H.5
Hood, A.M.6
Modi, S.7
Hersey, A.8
Taskinen, J.9
Cooke, R.M.10
Manchee, G.R.11
Coughtrie, M.W.H.12
-
140
-
-
0141959679
-
CoMFA modeling of enzyme kinetics: K(m) values for sulfation of diverse phenolic substrates by human catecholamine sulfotransferase SULT1A3
-
Sipila J, Hood AM, Coughtrie MW, et al. CoMFA modeling of enzyme kinetics: K(m) values for sulfation of diverse phenolic substrates by human catecholamine sulfotransferase SULT1A3. J Chem Inf Comput Sci 2003;43:1563-1569
-
(2003)
J Chem Inf Comput Sci
, vol.43
, pp. 1563-1569
-
-
Sipila, J.1
Hood, A.M.2
Coughtrie, M.W.3
-
141
-
-
13144260727
-
Identification of a human nuclear receptor defines a new signaling pathway for CYP3A induction
-
DOI 10.1073/pnas.95.21.12208
-
Bertilsson G, Heidrich J, Svensson K, et al. Identification of a human nuclear receptor defines a new signaling pathway for CYP3A induction. Proc Natl Acad Sci USA 1998;95:12208-12213 (Pubitemid 28483744)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.21
, pp. 12208-12213
-
-
Bertilsson, G.1
Heidrich, J.2
Svensson, K.3
Asman, M.4
Jendeberg, L.5
Sydow-Backman, M.6
Ohlsson, R.7
Postlind, H.8
Blomquist, P.9
Berkenstam, A.10
-
142
-
-
47949085749
-
A comprehensive in vitro and in silico analysis of antibiotics that activate pregnane X receptor and induce CYP3A4 in liver and intestine
-
Yasuda K, Ranade A, Venkataramanan R, et al. A comprehensive in vitro and in silico analysis of antibiotics that activate pregnane X receptor and induce CYP3A4 in liver and intestine. Drug Metab Dispos 2008;36:1689-1697
-
(2008)
Drug Metab Dispos
, vol.36
, pp. 1689-1697
-
-
Yasuda, K.1
Ranade, A.2
Venkataramanan, R.3
-
143
-
-
47949086965
-
Machine learning methods and docking for predicting human pregnane X receptor activation
-
Khandelwal A, Krasowski MD, Reschly EJ, et al. Machine learning methods and docking for predicting human pregnane X receptor activation. Chem Res Toxicol 2008;21:1457-1467
-
(2008)
Chem Res Toxicol
, vol.21
, pp. 1457-1467
-
-
Khandelwal, A.1
Krasowski, M.D.2
Reschly, E.J.3
-
144
-
-
30144443169
-
Systems-ADME/Tox: Resources and network approaches
-
DOI 10.1016/j.vascn.2005.05.005, PII S1056871905000729
-
Ekins S. Systems-ADME/Tox: resources and network approaches. J Pharmacol Toxicol Methods 2006;53:38-66 (Pubitemid 43054914)
-
(2006)
Journal of Pharmacological and Toxicological Methods
, vol.53
, Issue.1
, pp. 38-66
-
-
Ekins, S.1
-
145
-
-
1042302103
-
Early prediction of drug metabolism and toxicity: Systems biology approach and modeling
-
DOI 10.1016/S1359-6446(03)02971-4, PII S1359644603029714
-
Bugrim A, Nikolskaya T, Nikolsky Y. Early prediction of drug metabolism and toxicity: systems biology approach and modeling. Drug Discov Today 2004;9:127-135 (Pubitemid 38198311)
-
(2004)
Drug Discovery Today
, vol.9
, Issue.3
, pp. 127-135
-
-
Bugrim, A.1
Nikolskaya, T.2
Nikolsky, Y.3
|