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3242885550
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Predictive ADMET studies, the challenges and opportunities
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Davis AM, Riley RJ: Predictive ADMET studies, the challenges and opportunities. Curr Opin Chem Biol (2004) 8(4):378-386.
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Curr Opin Chem Biol
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Davis, A.M.1
Riley, R.J.2
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2942620237
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Building predictive ADMET models for early decisions in drug discovery
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Penzotti JE, Landrum GA, Putta S: Building predictive ADMET models for early decisions in drug discovery. Curr Opin Drug Discovery Dev (2004) 7(1):49-61.
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Curr Opin Drug Discovery Dev
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Penzotti, J.E.1
Landrum, G.A.2
Putta, S.3
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3
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0042416598
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In silico ADME/Tox: Why models fail
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Stouch TR, Kenyon JR, Johnson SR, Chen XQ, Doweyko A, Li Y: In silico ADME/Tox: Why models fail. J Comput Aided Mol Des (2003) 17(2-4):83-92.
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J Comput Aided Mol Des
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Stouch, T.R.1
Kenyon, J.R.2
Johnson, S.R.3
Chen, X.Q.4
Doweyko, A.5
Li, Y.6
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ADMET in silico modeling towards prediction paradise?
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Van de Waterbeemd H, Gifford E: ADMET in silico modeling towards prediction paradise? Nat Rev Drug Disc (2003) 2(3):192-204.
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Nat Rev Drug Disc
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Van De Waterbeemd, H.1
Gifford, E.2
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5
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0004100524
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Academic Press, San Diego, CA, USA
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Kier LB, Hall LH: Molecular Structure Description: The Electrotopological State. Academic Press, San Diego, CA, USA (1999). An excellent book for readers interested in Kier-Hall topological indices, which includes a CD-ROM giving many numerical examples of the different classes of topological indices and a small computer program to compute many of them.
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(1999)
Molecular Structure Description: The Electrotopological State
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Kier, L.B.1
Hall, L.H.2
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7
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0032841864
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The correlation and prediction of the solubility of compounds in water using an amended solvation energy relationship
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Abraham MH, Le J: The correlation and prediction of the solubility of compounds in water using an amended solvation energy relationship. J Pharm Sci (1999) 88(9):868-880.
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J Pharm Sci
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Abraham, M.H.1
Le, J.2
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8
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0028974572
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AQUAFAC 3: Aqueous functional group activity coefficients; application to the estimation of aqueous solubility
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Myrdal PB, Manka AM, Yalkowsky SH: AQUAFAC 3: Aqueous functional group activity coefficients; application to the estimation of aqueous solubility. Chemosphere (1995) 30:1619-1637.
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Chemosphere
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Myrdal, P.B.1
Manka, A.M.2
Yalkowsky, S.H.3
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9
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3042781869
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In silico ADME predictions: Data, models, facts and myths
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Lombardo F, Gifford E, Shalaeva MY: In silico ADME predictions: Data, models, facts and myths. Mini Rev Med Chem (2003) 3(8):861-875. A good review of ADME models covering the types and limitations of models, including comments on various published ADME models.
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Mini Rev Med Chem
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, pp. 861-875
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Lombardo, F.1
Gifford, E.2
Shalaeva, M.Y.3
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10
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0034320708
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Improving the odds in discriminating 'drug-like' from 'non drug-like' compounds
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Frimurer TM, Bywater R, Naerum L, Lauritsen LN, Brunak S: Improving the odds in discriminating 'drug-like' from 'non drug-like' compounds. J Chem Inf Comput Sci (2000) 40(6):1315-1324.
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J Chem Inf Comput Sci
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Frimurer, T.M.1
Bywater, R.2
Naerum, L.3
Lauritsen, L.N.4
Brunak, S.5
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11
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0041731599
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Prediction of aqueous solubility of a diverse set of compounds using quantitative structure-property relationships
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Cheng A, Merz KM Jr: Prediction of aqueous solubility of a diverse set of compounds using quantitative structure-property relationships. J Med Chem (2003) 46(17):3572-3580. Paper containing important topological indices that influence aqueous solubility, and provides a breakdown of the functional groups used and gives a comparison of predicted solubilities of drugs to drug-like compounds found in the Comprehensive Medical Chemistry (CMC) database.
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(2003)
J Med Chem
, vol.46
, Issue.17
, pp. 3572-3580
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Cheng, A.1
Merz Jr., K.M.2
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13
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6444225736
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Prediction of aqueous solubility based on large datasets using several QSPR models utilizing topological structure representation
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Votano JR, Parham M, Hall LH, Kier LB, Hall LM: Prediction of aqueous solubility based on large datasets using several QSPR models utilizing topological structure representation. Chem Biodivers (2004) 1(11):1829-1841. Paper providing a comprehensive breakdown of compound attributes, relating and describing important topological indices affecting the water solubility of a compound, and comparing results from various QSAR modeling algorithms.
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(2004)
Chem Biodivers
, vol.1
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, pp. 1829-1841
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Votano, J.R.1
Parham, M.2
Hall, L.H.3
Kier, L.B.4
Hall, L.M.5
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14
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4043112686
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Global and local computational models for aqueous solubility prediction of drug-like molecules
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Bergstrom CA, Wassvik CM, Norinder U, Luthman K, Artursson P: Global and local computational models for aqueous solubility prediction of drug-like molecules. J Chem Inf Comput Sci (2004) 44(4):1477-1488.
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J Chem Inf Comput Sci
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, pp. 1477-1488
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Bergstrom, C.A.1
Wassvik, C.M.2
Norinder, U.3
Luthman, K.4
Artursson, P.5
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15
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0037208305
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Using general regression and probabilistic neural networks to predict human intestinal absorption with topological descriptors derived from two-dimensional chemical structures
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2003
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Niwa T: Using general regression and probabilistic neural networks to predict human intestinal absorption with topological descriptors derived from two-dimensional chemical structures. (2003) J Chem Inf Comput Sci (2003) 43(1):113-119.
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J Chem Inf Comput Sci
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, pp. 113-119
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Niwa, T.1
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16
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Rapid calculation of polar molecular surface area and its application to the prediction of transport phenomena. 2. Prediction of blood-brain barrier penetration
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Clark DE: Rapid calculation of polar molecular surface area and its application to the prediction of transport phenomena. 2. Prediction of blood-brain barrier penetration. J Pharm Sci (1999) 88(8):815-821.
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J Pharm Sci
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Clark, D.E.1
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8544284073
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New predictors for several ADME/Tox properties: Aqueous solubility, human oral absorption and Ames genotoxicity using topological descriptors
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Votano JR, Parham M, Hall LH, Kier LB: New predictors for several ADME/Tox properties: Aqueous solubility, human oral absorption and Ames genotoxicity using topological descriptors. Mol Divers (2004) 8:385-397. In this study, the large number of compounds used and the trend analysis applied to important topological indices shed light on what types of functional groups enhance or diminish transcellular transport for drugs.
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Mol Divers
, vol.8
, pp. 385-397
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Votano, J.R.1
Parham, M.2
Hall, L.H.3
Kier, L.B.4
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18
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0030914681
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Polar molecular surface properties predict the intestinal absorption of drugs in humans
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Palm K, Stenberg P, Luthman K, Artursson P: Polar molecular surface properties predict the intestinal absorption of drugs in humans. Pharm Res (1997) 14(5):568-571.
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Pharm Res
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Palm, K.1
Stenberg, P.2
Luthman, K.3
Artursson, P.4
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19
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Experimental and computational screening models for the prediction of intestinal drug absorption
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Stenberg P, Norinder U, Luthman K, Artursson P: Experimental and computational screening models for the prediction of intestinal drug absorption. J Med Chem (2001) 44(12):1927-1937.
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J Med Chem
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Stenberg, P.1
Norinder, U.2
Luthman, K.3
Artursson, P.4
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21
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0036893593
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Evaluation of cytochrome P450 probe substrates commonly used by the pharmaceutical industry to study in vitro drug interactions
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Yuan R, Madani S, Wei XX, Reynolds K, Huang SM: Evaluation of cytochrome P450 probe substrates commonly used by the pharmaceutical industry to study in vitro drug interactions. Drug Metab Dispos (2002) 30(12):1311-1319.
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Drug Metab Dispos
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Yuan, R.1
Madani, S.2
Wei, X.X.3
Reynolds, K.4
Huang, S.M.5
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22
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0038121705
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Development and validation of k-nearest-neighbor QSPR models of metabolic stability of drug candidates
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Shen M, Xiao Y, Golbraikh A, Gombar VJ, Tropsha A: Development and validation of k-nearest-neighbor QSPR models of metabolic stability of drug candidates. J Med Chem (2003) 46(14):3013-3020. A well-documented explanation of the kNN-QSAR methodology employed with topological indices to treat a complex problem.
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(2003)
J Med Chem
, vol.46
, Issue.14
, pp. 3013-3020
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Shen, M.1
Xiao, Y.2
Golbraikh, A.3
Gombar, V.J.4
Tropsha, A.5
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23
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0141789965
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QSAR analysis of the inhibition of recombinant CYP 3A4 activity by structurally diverse compounds using partial least squares method
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Wanchanna S, Yamashita F, Hashida M: QSAR analysis of the inhibition of recombinant CYP 3A4 activity by structurally diverse compounds using partial least squares method. Pharm Res (2003) 20(9):1401-1408.
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Pharm Res
, vol.20
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, pp. 1401-1408
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Wanchanna, S.1
Yamashita, F.2
Hashida, M.3
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24
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0037325243
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Development of binary classification of structural chromosome aberrations for a diverse set of organic compounds from molecular structure
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Serra JR, Thompson ED, Jurs PC: Development of binary classification of structural chromosome aberrations for a diverse set of organic compounds from molecular structure. Chem Res Toxicol (2003) 16(2):153-163. Description of the use of two classification-based models, including a list of compounds. Of importance is the resulting small number of topological indices found to model clastogenicity.
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(2003)
Chem Res Toxicol
, vol.16
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, pp. 153-163
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Serra, J.R.1
Thompson, E.D.2
Jurs, P.C.3
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25
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A review of the genotoxicity of marketed pharmaceuticals
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Snyder RD, Green JW: A review of the genotoxicity of marketed pharmaceuticals. Mutat Res (2001) 488(2):151-169.
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Mutat Res
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, pp. 151-169
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Snyder, R.D.1
Green, J.W.2
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26
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2442548465
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Assessment of the sensitivity of the computational programs DEREK, TOPKAT and MCASE in the prediction of genotoxicity of pharmaceutical molecules
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Snyder RD, Pearl GS, Mandakas G, Choy WN, Goodsaid F, Rosenblum IY: Assessment of the sensitivity of the computational programs DEREK, TOPKAT and MCASE in the prediction of genotoxicity of pharmaceutical molecules. Environ Mol Mutagen (2004) 43(3):143-158. An important review delineating the lack of sensitivity of fragments/alerts to predict genotoxic drugs, and including topological indices used with a regression model.
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(2004)
Environ Mol Mutagen
, vol.43
, Issue.3
, pp. 143-158
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Snyder, R.D.1
Pearl, G.S.2
Mandakas, G.3
Choy, W.N.4
Goodsaid, F.5
Rosenblum, I.Y.6
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27
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6444224986
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Three new consensus QSAR models for the prediction of Ames genotoxicity
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Votano JR, Parham M, Hall LH, Kier LB, Oloff S, Tropsha A, Xie Q, Tong W: Three new consensus QSAR models for the prediction of Ames genotoxicity. Mutagenesis (2004) 19(5):365-377. An exhaustive study centered on three unique modeling algorithms, relating topological descriptors to known fragments/alerts and comparing results. An analysis of functional groups is provided, and on-line validation compounds are given with predicted results.
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(2004)
Mutagenesis
, vol.19
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, pp. 365-377
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Votano, J.R.1
Parham, M.2
Hall, L.H.3
Kier, L.B.4
Oloff, S.5
Tropsha, A.6
Xie, Q.7
Tong, W.8
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28
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0037365123
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Decision Forest: Combining the predictions of multiple independent decision tree models
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Tong W, Hong H, Fang H, Xie Q, Perkins R: Decision Forest: Combining the predictions of multiple independent decision tree models. J Chem Inf Comput Sci (2003) 43(2):525-531.
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J Chem Inf Comput Sci
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Tong, W.1
Hong, H.2
Fang, H.3
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Perkins, R.5
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29
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0000973407
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Definitive relationships among chemical structure, carcinogenicity and mutagenicity for 301 chemicals tested by the U. S. NTP
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Ashby J, Tennant RW: Definitive relationships among chemical structure, carcinogenicity and mutagenicity for 301 chemicals tested by the U. S. NTP. Mutat Res (1991) 257(3):229-306.
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Mutat Res
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Predicting the carcinogenic potential of pharmaceuticals in rodents using molecular structural similarity and E-state indices
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Contrera JF, Matthews EJ, Benz RD: Predicting the carcinogenic potential of pharmaceuticals in rodents using molecular structural similarity and E-state indices. Regul Toxicol Pharmcol (2003) 38(3):243-259.
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Regul Toxicol Pharmcol
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Contrera, J.F.1
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