-
2
-
-
0001877502
-
The Ah receptor signal transduction pathway
-
In; Denison, M. S. Helferich, W. G. Taylor and Francis: Bristol, PA
-
Denison, M. S.; Elferink, C. F.; Phelan, D. The Ah receptor signal transduction pathway. In Toxicant-Receptor Interactions in the Modulation of Signal Transduction and Gene Expression; Denison, M. S.; Helferich, W. G., Eds.; Taylor and Francis: Bristol, PA, 1998; pp 3-33.
-
(1998)
Toxicant-Receptor Interactions in the Modulation of Signal Transduction and Gene Expression
, pp. 3-33
-
-
Denison, M.S.1
Elferink, C.F.2
Phelan, D.3
-
3
-
-
0034969560
-
Induction of CYP1A1. The AhR/DRE paradigm: Transcription, receptor regulation, and expanding biological roles
-
DOI 10.2174/1389200013338603
-
Ma, Q. Induction of CYP1A1. The AhR/DRE paradigm: Transcription, receptor regulation, and expanding biological roles Curr. Drug Metab. 2001, 2, 149-164 (Pubitemid 32537000)
-
(2001)
Current Drug Metabolism
, vol.2
, Issue.2
, pp. 149-164
-
-
Ma, Q.1
-
4
-
-
0345708353
-
The mammalian basic helix-loop-helix/PAS family of transcriptional regulators
-
DOI 10.1016/S1357-2725(03)00211-5
-
Kewley, R. J.; Whitelaw, M. L.; Chapman-Smith, A. The mammalian basic helix-loop-helix/PAS family of transcriptional regulators Int. J. Biochem. Cell Biol. 2004, 36, 189-204 (Pubitemid 37487755)
-
(2004)
International Journal of Biochemistry and Cell Biology
, vol.36
, Issue.2
, pp. 189-204
-
-
Kewley, R.J.1
Whitelaw, M.L.2
Chapman-Smith, A.3
-
5
-
-
0020010617
-
2,3,7,8-Tetrachlorodibenzo-p-dioxin and related halogenated aromatic hydrocarbons: Examination of the mechanism of toxicity
-
Poland, A.; Knutson, J. C. 2,3,7,8-Tetrachlorodibenzo-p-dioxin and related halogenated aromatic hydrocarbons: examination of the mechanism of toxicity Annu. Rev. Pharmacol. Toxicol. 1982, 22, 517-542
-
(1982)
Annu. Rev. Pharmacol. Toxicol.
, vol.22
, pp. 517-542
-
-
Poland, A.1
Knutson, J.C.2
-
6
-
-
0024997614
-
Polychlorinated biphenyls (PCBs), dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs), and related compounds: Environmental and mechanistic considerations which support the development of toxic equivalency factors (TEFs)
-
Safe, S. Polychlorinated biphenyls (PCBs), dibenzo-p-dioxins (PCDDs), dibenzofurans (PCDFs), and related compounds: environmental and mechanistic considerations which support the development of toxic equivalency factors (TEFs) Crit. Rev. Toxicol. 1990, 21, 51-88 (Pubitemid 20283436)
-
(1990)
Critical Reviews in Toxicology
, vol.21
, Issue.1
, pp. 51-88
-
-
Safe, S.1
-
7
-
-
0001877503
-
Natural and synthetic ligands for the Ah receptor
-
In; Puga, A. Wallace, K. B. Taylor & Francis: Philadelphia, PA
-
Denison, M. S.; Seidel, S. D.; Rogers, W. J.; Ziccardi, M.; Winter, G. M.; Heath-Pagliuso, S. Natural and synthetic ligands for the Ah receptor. In Molecular Biology Approaches to Toxicology; Puga, A.; Wallace, K. B., Eds.; Taylor & Francis: Philadelphia, PA, 1998; pp 393-410.
-
(1998)
Molecular Biology Approaches to Toxicology
, pp. 393-410
-
-
Denison, M.S.1
Seidel, S.D.2
Rogers, W.J.3
Ziccardi, M.4
Winter, G.M.5
Heath-Pagliuso, S.6
-
8
-
-
0032406634
-
The Ah receptor: A regulator of the biochemical and toxicological actions of structurally diverse chemicals
-
DOI 10.1007/PL00002973
-
Denison, M. S.; Heath-Pagliuso, S. The Ah receptor: A regulator of the biochemical and toxicological actions of structurally diverse chemicals Bull. Environ. Contam. Toxicol. 1998, 61, 557-568 (Pubitemid 29010859)
-
(1998)
Bulletin of Environmental Contamination and Toxicology
, vol.61
, Issue.5
, pp. 557-568
-
-
Denison, M.S.1
Heath-Pagliuso, S.2
-
9
-
-
0037144119
-
Ligand binding and activation of the Ah receptor
-
DOI 10.1016/S0009-2797(02)00063-7, PII S0009279702000637
-
Denison, M. S.; Pandini, A.; Nagy, S. R.; Baldwin, E. P.; Bonati, L. Ligand binding and activation of the Ah receptor Chem. Biol. Interact. 2002, 141, 3-24 (Pubitemid 35229988)
-
(2002)
Chemico-Biological Interactions
, vol.141
, Issue.1-2
, pp. 3-24
-
-
Denison, M.S.1
Pandini, A.2
Nagy, S.R.3
Baldwin, E.P.4
Bonati, L.5
-
10
-
-
0038768712
-
Activation of the Aryl Hydrocarbon Receptor by Structurally Diverse Exogenous and Endogenous Chemicals
-
DOI 10.1146/annurev.pharmtox.43.100901.135828
-
Denison, M. S.; Nagy, S. R. Activation of the aryl hydrocarbon receptor by structurally diverse exogenous and endogenous chemicals Annu. Rev. Pharmacol. Toxicol. 2003, 43, 309-334 (Pubitemid 37372644)
-
(2003)
Annual Review of Pharmacology and Toxicology
, vol.43
, pp. 309-334
-
-
Denison, M.S.1
Nagy, S.R.2
-
11
-
-
38949097735
-
The search for endogenous activators of the aryl hydrocarbon receptor
-
Nguyen, L. P.; Bradfield, C. A. The search for endogenous activators of the aryl hydrocarbon receptor Chem. Res. Toxicol. 2008, 21, 102-106
-
(2008)
Chem. Res. Toxicol.
, vol.21
, pp. 102-106
-
-
Nguyen, L.P.1
Bradfield, C.A.2
-
12
-
-
57749090311
-
Role of the Per/Arnt/Sim domains in ligand-dependent transformation of the aryl hydrocarbon receptor
-
Soshilov, A. A.; Denison, M. S. Role of the Per/Arnt/Sim domains in ligand-dependent transformation of the aryl hydrocarbon receptor J. Biol. Chem. 2008, 283, 32995-32305
-
(2008)
J. Biol. Chem.
, vol.283
, pp. 32995-32305
-
-
Soshilov, A.A.1
Denison, M.S.2
-
13
-
-
0036153480
-
A model for recognition of polychlorinated dibenzo-p-dioxins by the aryl hydrocarbon receptor
-
DOI 10.1046/j.0014-2956.2002.02619.x
-
Procopio, M.; Lahm, A.; Tramontano, A.; Bonati, L.; Pitea, D. A model for recognition of polychlorinated dibenzo-p-dioxins by the aryl hydrocarbon receptor Eur. J. Biochem. 2002, 269, 13-18 (Pubitemid 34107334)
-
(2002)
European Journal of Biochemistry
, vol.269
, Issue.1
, pp. 13-18
-
-
Procopio, M.1
Lahm, A.2
Tramontano, A.3
Bonati, L.4
Pitea, D.5
-
14
-
-
33846337559
-
Structural and functional characterization of the aryl hydrocarbon receptor ligand binding domain by homology modeling and mutational analysis
-
DOI 10.1021/bi061460t
-
Pandini, A.; Denison, M. S.; Song, Y.; Soshilov, A. A.; Bonati, L. Structural and functional characterization of the aryl hydrocarbon receptor ligand binding domain by homology modeling and mutational analysis Biochemistry 2007, 46, 696-708 (Pubitemid 46133587)
-
(2007)
Biochemistry
, vol.46
, Issue.3
, pp. 696-708
-
-
Pandini, A.1
Denison, M.S.2
Song, Y.3
Soshilov, A.A.4
Bonati, L.5
-
15
-
-
0346734132
-
Structural basis for PAS domain heterodimerization in the basic helix-loop-helix-PAS transcription factor hypoxia-inducible factor
-
DOI 10.1073/pnas.2533374100
-
Erbel, P. J.; Card, P. B.; Karakuzu, O.; Bruick, R. K.; Gardner, K. H. Structural basis for PAS domain heterodimerization in the basic helix-loop-helix-PAS transcription factor hypoxia-inducible factor Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 15504-15509 (Pubitemid 38021019)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.26
, pp. 15504-15509
-
-
Erbel, P.J.A.1
Card, P.B.2
Karakuzu, O.3
Bruick, R.K.4
Gardner, K.H.5
-
16
-
-
26244466162
-
Structural basis of Arnt PAS-B dimerization: Use of a common beta-sheet interface for hetero- and homodimerization
-
Card, P. B.; Erbel, P. J.; Gardner, K. H. Structural basis of Arnt PAS-B dimerization: use of a common beta-sheet interface for hetero- and homodimerization J. Mol. Biol. 2005, 353, 664-678
-
(2005)
J. Mol. Biol.
, vol.353
, pp. 664-678
-
-
Card, P.B.1
Erbel, P.J.2
Gardner, K.H.3
-
17
-
-
67649612842
-
Detection of the TCDD binding-fingerprint within the Ah receptor ligand binding domain by structurally driven mutagenesis and functional analysis
-
Pandini, A.; Soshilov, A. A.; Song, Y.; Zhao, J.; Bonati, L.; Denison, M. S. Detection of the TCDD binding-fingerprint within the Ah receptor ligand binding domain by structurally driven mutagenesis and functional analysis Biochemistry 2009, 48, 5972-5983
-
(2009)
Biochemistry
, vol.48
, pp. 5972-5983
-
-
Pandini, A.1
Soshilov, A.A.2
Song, Y.3
Zhao, J.4
Bonati, L.5
Denison, M.S.6
-
18
-
-
70349194570
-
Modeling of the aryl hydrocarbon receptor (AhR) ligand binding domain and its utility in virtual ligand screening to predict new AhR ligands
-
Bisson, W. H.; Koch, D. C.; O'Donnell, E. F.; Khalil, S. M.; Kerkvliet, N. I.; Tanguay, R. L.; Abagyan, R.; Kolluri, S. K. Modeling of the aryl hydrocarbon receptor (AhR) ligand binding domain and its utility in virtual ligand screening to predict new AhR ligands J. Med. Chem. 2009, 52, 5635-5641
-
(2009)
J. Med. Chem.
, vol.52
, pp. 5635-5641
-
-
Bisson, W.H.1
Koch, D.C.2
O'Donnell, E.F.3
Khalil, S.M.4
Kerkvliet, N.I.5
Tanguay, R.L.6
Abagyan, R.7
Kolluri, S.K.8
-
19
-
-
70449519407
-
In silico predication of nuclear hormone receptors for organic pollutants by homology modeling and molecular docking
-
Wu, B.; Zhang, Y.; Kong, J.; Zhang, X.; Cheng, S. In silico predication of nuclear hormone receptors for organic pollutants by homology modeling and molecular docking Toxicol. Lett. 2009, 191, 69-73
-
(2009)
Toxicol. Lett.
, vol.191
, pp. 69-73
-
-
Wu, B.1
Zhang, Y.2
Kong, J.3
Zhang, X.4
Cheng, S.5
-
20
-
-
77956277333
-
Specific interactions between aryl hydrocarbon receptor and dioxin congeners: Ab initio fragment molecular orbital calculations
-
Yoshikawa, E.; Miyagi, S.; Dedachi, K.; Ishihara-Sugano, M.; Itoh, S.; Kurita, N. Specific interactions between aryl hydrocarbon receptor and dioxin congeners: Ab initio fragment molecular orbital calculations J. Mol. Graphics Modell. 2010, 29, 197-205
-
(2010)
J. Mol. Graphics Modell.
, vol.29
, pp. 197-205
-
-
Yoshikawa, E.1
Miyagi, S.2
Dedachi, K.3
Ishihara-Sugano, M.4
Itoh, S.5
Kurita, N.6
-
21
-
-
77958033879
-
Identification of optimum computational protocols for modeling the aryl hydrocarbon receptor (AhR) and its interaction with ligands
-
Jogalekar, A. S.; Reiling, S.; Vaz, R. J. Identification of optimum computational protocols for modeling the aryl hydrocarbon receptor (AhR) and its interaction with ligands Bioorg. Med. Chem. Lett. 2010, 20, 6616-9
-
(2010)
Bioorg. Med. Chem. Lett.
, vol.20
, pp. 6616-6619
-
-
Jogalekar, A.S.1
Reiling, S.2
Vaz, R.J.3
-
22
-
-
79951988195
-
Suppression of cytokine-mediated complement factor gene expression through selective activation of the Ah receptor with 3′,4′- dimethoxy-α-naphthoflavone
-
Murray, I. A.; Flaveny, C. A.; Chiaro, C. R.; Sharma, A. K.; Tanos, R. S.; Schroeder, J. C.; Amin, S. G.; Bisson, W. H.; Kolluri, S. K.; Perdew, G. H. Suppression of cytokine-mediated complement factor gene expression through selective activation of the Ah receptor with 3′,4′-dimethoxy- α-naphthoflavone Mol. Pharmacol. 2011, 79, 508-19
-
(2011)
Mol. Pharmacol.
, vol.79
, pp. 508-519
-
-
Murray, I.A.1
Flaveny, C.A.2
Chiaro, C.R.3
Sharma, A.K.4
Tanos, R.S.5
Schroeder, J.C.6
Amin, S.G.7
Bisson, W.H.8
Kolluri, S.K.9
Perdew, G.H.10
-
23
-
-
3242813635
-
Utility of homology models in the drug discovery process
-
DOI 10.1016/S1359-6446(04)03196-4, PII S1359644604031964
-
Hillisch, A.; Pineda, L. F.; Hilgenfeld, R. Utility of homology models in the drug discovery process Drug Discovery Today 2004, 9, 659-669 (Pubitemid 38981720)
-
(2004)
Drug Discovery Today
, vol.9
, Issue.15
, pp. 659-669
-
-
Hillisch, A.1
Pineda, L.F.2
Hilgenfeld, R.3
-
24
-
-
34447095430
-
Evaluation of the utility of homology models in high throughput docking
-
DOI 10.1007/s00894-007-0207-6
-
Ferrara, P.; Jacoby, E. Evaluation of the utility of homology models in high throughput docking J. Mol. Model. 2007, 8, 897-905 (Pubitemid 47028813)
-
(2007)
Journal of Molecular Modeling
, vol.13
, Issue.8
, pp. 897-905
-
-
Ferrara, P.1
Jacoby, E.2
-
25
-
-
67649518035
-
Homology modeling in drug discovery: Current trends and applications
-
Cavasotto, C. N.; Phatak, S. S. Homology modeling in drug discovery: current trends and applications Drug Discovery Today 2009, 14, 676-683
-
(2009)
Drug Discovery Today
, vol.14
, pp. 676-683
-
-
Cavasotto, C.N.1
Phatak, S.S.2
-
26
-
-
0038460858
-
Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes
-
DOI 10.1021/jm0300330
-
McGovern, S. L.; Shoichet, B. K. Information decay in molecular docking screens against holo, apo, and modeled conformations of enzymes J. Med. Chem. 2003, 46, 2895-2907 (Pubitemid 36775915)
-
(2003)
Journal of Medicinal Chemistry
, vol.46
, Issue.14
, pp. 2895-2907
-
-
McGovern, S.L.1
Shoichet, B.K.2
-
27
-
-
72949087796
-
Molecular docking screens using comparative models of proteins
-
Fan, H.; Irwin, J. J.; Webb, B. M.; Klebe, G.; Shoichet, B. K.; Sali, A. Molecular docking screens using comparative models of proteins J. Chem. Inf. Model. 2009, 49, 2512-2527
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 2512-2527
-
-
Fan, H.1
Irwin, J.J.2
Webb, B.M.3
Klebe, G.4
Shoichet, B.K.5
Sali, A.6
-
28
-
-
78649537557
-
Predicting the accuracy of protein-ligand docking on homology models
-
Bordogna, A.; Pandini, A.; Bonati, L. Predicting the accuracy of protein-ligand docking on homology models J. Comput. Chem. 2011, 32, 81-98
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 81-98
-
-
Bordogna, A.1
Pandini, A.2
Bonati, L.3
-
29
-
-
33646833091
-
Structure selection for protein kinase docking and virtual screening: Homology models or crystal structures?
-
DOI 10.2174/138920306778559368
-
Rockey, W. M.; Elcock, A. H. Structure selection for protein kinase docking and virtual screening: homology models or crystal structures? Curr. Protein Pept. Sci. 2006, 7, 437-457 (Pubitemid 44524492)
-
(2006)
Current Protein and Peptide Science
, vol.7
, Issue.5
, pp. 437-457
-
-
Rockey, W.M.1
Elcock, A.H.2
-
30
-
-
58849141619
-
Artificial ligand binding within the HIF2α transcription factor
-
Scheuermann, T. H.; Tomchick, D. R.; Machius, M.; Guo, Y.; Bruick, R. K.; Gardner, K. H. Artificial ligand binding within the HIF2α transcription factor Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 450-455
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 450-455
-
-
Scheuermann, T.H.1
Tomchick, D.R.2
MacHius, M.3
Guo, Y.4
Bruick, R.K.5
Gardner, K.H.6
-
31
-
-
72249095193
-
Principles of ligand binding within a completely buried cavity in HIF2α PAS-B
-
Key, J.; Scheuermann, T. H.; Anderson, P. C.; Daggett, V.; Gardner, K. H. Principles of ligand binding within a completely buried cavity in HIF2α PAS-B J. Am. Chem. Soc. 2009, 131, 17647-17654
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 17647-17654
-
-
Key, J.1
Scheuermann, T.H.2
Anderson, P.C.3
Daggett, V.4
Gardner, K.H.5
-
32
-
-
0036774056
-
Structure and interactions of PAS Kinase N-terminal PAS domain: Model for intramolecular kinase regulation
-
DOI 10.1016/S0969-2126(02)00857-2, PII S0969212602008572
-
Amezcua, C. A.; Harper, S. M.; Rutter, J.; Gardner, K. H. Structure and interactions of PAS kinase N-terminal PAS domain: Model for intramolecular kinase regulation Structure 2002, 10, 1349-1361 (Pubitemid 35232384)
-
(2002)
Structure
, vol.10
, Issue.10
, pp. 1349-1361
-
-
Amezcua, C.A.1
Harper, S.M.2
Rutter, J.3
Gardner, K.H.4
-
33
-
-
0028034621
-
Dioxin binding activities of polymorphic forms of mouse and human arylhydrocarbon receptors
-
Ema, M.; Ohe, N.; Suzuki, M.; Mimura, J.; Sogawa, K.; Ikawan, S.; Fujii-Kuriyama, Y. Dioxin binding activities of polymorphic forms of mouse and human arylhydrocarbon receptors J. Biol. Chem. 1994, 269, 27337-27343 (Pubitemid 24346556)
-
(1994)
Journal of Biological Chemistry
, vol.269
, Issue.44
, pp. 27337-27343
-
-
Ema, M.1
Ohe, N.2
Suzuki, M.3
Mimura, J.4
Sogawa, K.5
Ikawa, S.6
Fujii-Kuriyama, Y.7
-
34
-
-
0022921476
-
Polychlorinated dibenzo-p-dioxins: Quantitative in vitro and vivo structure-activity relationships
-
DOI 10.1016/0300-483X(86)90101-0
-
Mason, G.; Farrell, K.; Keys, B.; Piskorska-Pliszczynska, J.; Safe, L.; Safe, S. Polychlorinated dibenzo-p-dioxins: quantitative in vitro and in vivo structure-activity relationships Toxicology 1986, 41, 21-31 (Pubitemid 16044988)
-
(1986)
Toxicology
, vol.41
, Issue.1
, pp. 21-31
-
-
Mason, G.1
Farrell, K.2
Keys, B.3
-
35
-
-
0022555425
-
Comparative toxicology and mechanism of action of polychlorinated dibenzo-p-dioxins and dibenzofurans
-
Safe, S. H. Comparative toxicology and mechanism of action of polychlorinated dibenzo-p-dioxins and dibenzofurans Annu. Rev. Pharmacol. Toxicol. 1986, 26, 371-399 (Pubitemid 16090967)
-
(1986)
Annual Review of Pharmacology and Toxicology
, vol.26
, pp. 371-399
-
-
Safe, S.H.1
-
36
-
-
0010636992
-
Analysis of the Ah Receptor Signal Transduction Pathway
-
In; Maines, M. Costa, L. G. Reed, D. J. Sassa, S. Sipes, I. G. John Wiley and Sons: New York, NY
-
Denison, M. S.; Rogers, J. M.; Rushing, S. R.; Jones, C. L.; Tetangco, S. C.; Heath-Pagliuso, S. Analysis of the Ah Receptor Signal Transduction Pathway. In Current Protocols in Toxicology; Maines, M.; Costa, L. G.; Reed, D. J.; Sassa, S.; Sipes, I. G., Eds.; John Wiley and Sons: New York, NY, 2002; pp (4.8)1-(4.8)45.
-
(2002)
Current Protocols in Toxicology
, pp. 481-4845
-
-
Denison, M.S.1
Rogers, J.M.2
Rushing, S.R.3
Jones, C.L.4
Tetangco, S.C.5
Heath-Pagliuso, S.6
-
37
-
-
0017145975
-
Stereospecific, high affinity binding of 2,3,7,8-tetrachlorodibenzo-p- dioxin by hepatic cytosol. Evidence that the binding species is receptor for induction of aryl hydrocarbon hydroxylase
-
Poland, A.; Glover, E.; Kende, A. Stereospecific, high affinity binding of 2,3,7,8-tetrachlorodibenzo-p-dioxin by hepatic cytosol. Evidence that the binding species is receptor for induction of aryl hydrocarbon hydroxylase J. Biol. Chem. 1976, 251, 4936-4946
-
(1976)
J. Biol. Chem.
, vol.251
, pp. 4936-4946
-
-
Poland, A.1
Glover, E.2
Kende, A.3
-
38
-
-
0022907676
-
Ah receptor for 2,3,7,8-tetrachlorodibenzo-p-dioxin: Comparative studies in mammalian and nonmammalian species
-
DOI 10.1016/0045-6535(86)90452-2
-
Denison, M. S.; Wilkinson, C. F.; Okey, A. B. Ah receptor for 2,3,7,8-tetrachlorodibenzo-p-dioxin: comparative studies in mammalian and nonmammalian species Chemosphere 1986, 15, 1665-1672 (Pubitemid 17008412)
-
(1986)
Chemosphere
, vol.15
, Issue.9-12
, pp. 1665-1672
-
-
Denison, M.S.1
Wilkinson, C.F.2
Okey, A.B.3
-
39
-
-
2342489432
-
Comparison of recombinant cell bioassays for the detection of Ah receptor agonists
-
Han, D. H.; Nagy, S. R.; Denison, M. S. Comparison of recombinant cell bioassays for the detection of Ah receptor agonists Biofactors 2004, 20, 11-22 (Pubitemid 38586206)
-
(2004)
BioFactors
, vol.20
, Issue.1
, pp. 11-22
-
-
Han, D.1
Nagy, S.R.2
Denison, M.S.3
-
40
-
-
77951476466
-
Mechanism based common reactivity pattern (COREPA) modeling of AhR binding affinity
-
Petkov, P. I.; Rowlands, J. C.; Budinsky, R.; Zhao, B.; Denison, M. S.; Mekenyan, O. Mechanism based common reactivity pattern (COREPA) modeling of AhR binding affinity SAR QSAR Environ. Res. 2010, 21, 187-214
-
(2010)
SAR QSAR Environ. Res.
, vol.21
, pp. 187-214
-
-
Petkov, P.I.1
Rowlands, J.C.2
Budinsky, R.3
Zhao, B.4
Denison, M.S.5
Mekenyan, O.6
-
41
-
-
0036174712
-
Continuum secondary structure captures protein flexibility
-
DOI 10.1016/S0969-2126(02)00700-1, PII S0969212602007001
-
Andersen, C. A.; Palmer, A. G.; Brunak, S.; Rost, B. Continuum secondary structure captures protein flexibility Structure 2002, 10, 175-184 (Pubitemid 34164596)
-
(2002)
Structure
, vol.10
, Issue.2
, pp. 175-184
-
-
Andersen, C.A.F.1
Palmer, A.G.2
Brunak, S.3
Rost, B.4
-
42
-
-
0027136282
-
Comparative protein modelling by satisfaction of spatial restraints
-
DOI 10.1006/jmbi.1993.1626
-
Sali, A.; Blundell, T. L. Comparative protein modeling by satisfaction of spatial restraints J. Mol. Biol. 1993, 234, 779-815 (Pubitemid 24007801)
-
(1993)
Journal of Molecular Biology
, vol.234
, Issue.3
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
43
-
-
0033873929
-
Comparative protein structure modeling of genes and genomes
-
Marti-Renom, M. A.; Stuart, A.; Fiser, A.; Sanchez, R.; Melo, F.; Sali, A. Comparative protein structure modeling of genes and genomes Annu. Rev. Biophys. Biomol. Struct. 2002, 29, 291-325
-
(2002)
Annu. Rev. Biophys. Biomol. Struct.
, vol.29
, pp. 291-325
-
-
Marti-Renom, M.A.1
Stuart, A.2
Fiser, A.3
Sanchez, R.4
Melo, F.5
Sali, A.6
-
44
-
-
0033810049
-
Modeling of loops in protein structures
-
Fiser, A.; Do, R. K.; Sali, A. Modeling of loops in protein structures Protein Sci. 2000, 9, 1753-1773
-
(2000)
Protein Sci.
, vol.9
, pp. 1753-1773
-
-
Fiser, A.1
Do, R.K.2
Sali, A.3
-
46
-
-
33749578940
-
Statistical potential for assessment and prediction of protein structures
-
DOI 10.1110/ps.062416606
-
Shen, M.; Sali, A. Statistical potential for assessment and prediction of protein structures Protein Sci. 2006, 15, 2507-2524 (Pubitemid 44771688)
-
(2006)
Protein Science
, vol.15
, Issue.11
, pp. 2507-2524
-
-
Shen, M.-Y.1
Sali, A.2
-
47
-
-
0000243829
-
PROCHECK: A program to check the stereochemical quality of protein structures
-
Laskowski, R. A.; MacArthur, M. W.; Moss, D. S.; Thornton, J. M. PROCHECK: a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 1993, 26, 283-291
-
(1993)
J. Appl. Crystallogr.
, vol.26
, pp. 283-291
-
-
Laskowski, R.A.1
MacArthur, M.W.2
Moss, D.S.3
Thornton, J.M.4
-
48
-
-
0027490731
-
Recognition of errors in three-dimensional structures of proteins
-
DOI 10.1002/prot.340170404
-
Sippl, M. J. Recognition of errors in three-dimensional structures of proteins Proteins 1993, 17, 355-362 (Pubitemid 23358545)
-
(1993)
Proteins: Structure, Function and Genetics
, vol.17
, Issue.4
, pp. 355-362
-
-
Sippl, M.J.1
-
49
-
-
34547566446
-
ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins
-
Wiederstein, M.; Sippl, M. J. ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins Nucleic Acids Res. 2007, 35, W407-W410
-
(2007)
Nucleic Acids Res.
, vol.35
-
-
Wiederstein, M.1
Sippl, M.J.2
-
50
-
-
33747818007
-
CASTp: Computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues
-
Dundas, J.; Ouyang, Z.; Tseng, J.; Binkowski, A.; Turpaz, Y.; Liang, J. CASTp: Computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues Nucleic Acids Res. 2006, 34, W116-W118
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Dundas, J.1
Ouyang, Z.2
Tseng, J.3
Binkowski, A.4
Turpaz, Y.5
Liang, J.6
-
52
-
-
0000538815
-
Analytical molecular surface calculation
-
Connolly, M. L. Analytical molecular surface calculation J. Appl. Crystallogr. 1983, 16, 548-558
-
(1983)
J. Appl. Crystallogr.
, vol.16
, pp. 548-558
-
-
Connolly, M.L.1
-
53
-
-
33750124980
-
Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes
-
DOI 10.1021/jm051256o
-
Friesner, R. A.; Murphy, R. B.; Repasky, M. P.; Frye, L. L.; Greenwood, J. R.; Halgren, T. A.; Sanschagrin, P. C.; Mainz, D. T. 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
-
54
-
-
77957899529
-
Advances and challenges in protein-ligand docking
-
Huang, S. Y.; Zou, X. Advances and challenges in protein-ligand docking Int. J. Mol. Sci. 2010, 11, 3016-3034
-
(2010)
Int. J. Mol. Sci.
, vol.11
, pp. 3016-3034
-
-
Huang, S.Y.1
Zou, X.2
-
55
-
-
63149162777
-
Managing protein flexibility in docking and its applications
-
B-Rao, C.; Subramanian, J.; Sharma, S. D. Managing protein flexibility in docking and its applications Drug Discovery Today 2009, 14, 394-400
-
(2009)
Drug Discovery Today
, vol.14
, pp. 394-400
-
-
B-Rao, C.1
Subramanian, J.2
Sharma, S.D.3
-
56
-
-
77955574450
-
Ensemble docking from homology models
-
Novoa, E. M.; de Pouplana, L. R.; Barril, X.; Orozco, M. Ensemble docking from homology models J. Chem. Theory Comput. 2010, 6, 2547-2557
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 2547-2557
-
-
Novoa, E.M.1
De Pouplana, L.R.2
Barril, X.3
Orozco, M.4
-
57
-
-
12144289984
-
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 1. Method and Assessment of Docking Accuracy
-
DOI 10.1021/jm0306430
-
Friesner, R. A.; Banks, J. L.; Murphy, R. B.; Halgren, T. A.; Klicic, J. J.; Mainz, D. T.; Repasky, M. P.; Knoll, E. H.; Shaw, D. E.; Shelley, M.; Perry, J. K.; Francis, P.; Shenkin, P. S. Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy J. Med. Chem. 2004, 47, 1739-1749 (Pubitemid 38380917)
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.7
, pp. 1739-1749
-
-
Friesner, R.A.1
Banks, J.L.2
Murphy, R.B.3
Halgren, T.A.4
Klicic, J.J.5
Mainz, D.T.6
Repasky, M.P.7
Knoll, E.H.8
Shelley, M.9
Perry, J.K.10
Shaw, D.E.11
Francis, P.12
Shenkin, P.S.13
-
58
-
-
1642310340
-
Glide: A New Approach for Rapid, Accurate Docking and Scoring. 2. Enrichment Factors in Database Screening
-
DOI 10.1021/jm030644s
-
Halgren, T. A.; Murphy, R. B.; Friesner, R. A.; Beard, H. S.; Frye, L. L.; Pollard, W. T.; Banks, J. L. Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening J. Med. Chem. 2004, 47, 1750-1759 (Pubitemid 38380918)
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.7
, pp. 1750-1759
-
-
Halgren, T.A.1
Murphy, R.B.2
Friesner, R.A.3
Beard, H.S.4
Frye, L.L.5
Pollard, W.T.6
Banks, J.L.7
-
59
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
DOI 10.1021/jm050362n
-
Warren, G. L.; Andrews, C. W.; Capelli, A. M.; Clarke, B.; LaLonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Wall, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. A critical assessment of docking programs and scoring functions J. Med. Chem. 2006, 49, 5912-5931 (Pubitemid 44484938)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.20
, pp. 5912-5931
-
-
Warren, G.L.1
Andrews, C.W.2
Capelli, A.-M.3
Clarke, B.4
LaLonde, J.5
Lambert, M.H.6
Lindvall, M.7
Nevins, N.8
Semus, S.F.9
Senger, S.10
Tedesco, G.11
Wall, I.D.12
Woolven, J.M.13
Peishoff, C.E.14
Head, M.S.15
-
60
-
-
84973610749
-
A rapidly convergent simulation method: Mixed Monte Carlo/Stochastic Dynamics
-
Guarnieri, F.; Still, W. C. A rapidly convergent simulation method: Mixed Monte Carlo/Stochastic Dynamics J. Comput. Chem. 1994, 15, 1302-1310
-
(1994)
J. Comput. Chem.
, vol.15
, pp. 1302-1310
-
-
Guarnieri, F.1
Still, W.C.2
-
61
-
-
5744249209
-
Equation of state calculations by fast computing machines
-
Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. Equation of state calculations by fast computing machines J. Chem. Phys. 1953, 21, 1087-1093
-
(1953)
J. Chem. Phys.
, vol.21
, pp. 1087-1093
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.H.4
Teller, E.5
-
63
-
-
40949107666
-
Molecular determinants of species-specific agonist and antagonist activity of a substituted flavone towards the aryl hydrocarbon receptor
-
Henry, E. C.; Gasiewicz, T. A. Molecular determinants of species-specific agonist and antagonist activity of a substituted flavone towards the aryl hydrocarbon receptor Arch. Biochem. Biophys. 2008, 472, 77-88
-
(2008)
Arch. Biochem. Biophys.
, vol.472
, pp. 77-88
-
-
Henry, E.C.1
Gasiewicz, T.A.2
-
64
-
-
33846552502
-
Identification of amino acid residues in the Ah receptor involved in ligand binding
-
DOI 10.1016/j.bbrc.2006.12.227, PII S0006291X06028750
-
Goryo, K.; Suzuki, A.; Del Carpio, C. A.; Siizaki, K.; Kuriyama, E.; Mikami, Y.; Kinoshita, K.; Yasumoto, K.; Rannug, A.; Miyamoto, A.; Fujii-Kuriyama, Y.; Sogawa, K. Identification of amino acid residues in the Ah receptor involved in ligand binding Biochem. Biophys. Res. Commun. 2007, 354, 396-402 (Pubitemid 46161339)
-
(2007)
Biochemical and Biophysical Research Communications
, vol.354
, Issue.2
, pp. 396-402
-
-
Goryo, K.1
Suzuki, A.2
Carpio, C.A.D.3
Siizaki, K.4
Kuriyama, E.5
Mikami, Y.6
Kinoshita, K.7
Yasumoto, K.-i.8
Rannug, A.9
Miyamoto, A.10
Fujii-Kuriyama, Y.11
Sogawa, K.12
-
65
-
-
24944488902
-
Evidence that ligand binding is a key determinant of Ah receptor-mediated transcriptional activity
-
DOI 10.1016/j.abb.2005.07.014, PII S0003986105003073
-
Murray, I. A.; Reen, R. K.; Leathery, N.; Ramadoss, P.; Bonati, L.; Gonzalez, F. J.; Peters, J. M.; Perdew, G. H. Evidence that ligand binding is a key determinant of Ah receptor mediated transcriptional activity Arch. Biochem. Biophys. 2005, 442, 59-71 (Pubitemid 41330994)
-
(2005)
Archives of Biochemistry and Biophysics
, vol.442
, Issue.1
, pp. 59-71
-
-
Murray, I.A.1
Reen, R.K.2
Leathery, N.3
Ramadoss, P.4
Bonati, L.5
Gonzalez, F.J.6
Peters, J.M.7
Perdew, G.H.8
-
66
-
-
82355184186
-
-
Glide, version 5.5; Schrödinger, LLC: New York, NY.
-
Glide, version 5.5; Schrödinger, LLC: New York, NY, 2009.
-
(2009)
-
-
-
67
-
-
82355171557
-
-
Prime, version 2.2; Schrödinger, LLC: New York, NY.
-
Prime, version 2.2; Schrödinger, LLC: New York, NY, 2010.
-
(2010)
-
-
-
68
-
-
40649101151
-
Rescoring docking hit lists for model cavity sites: Predictions and experimental testing
-
Graves, A. P.; Shivakumar, D. M.; Boyce, S. E.; Jacobson, M. P.; Case, D. A.; Shoichet, B. K. Rescoring docking hit lists for model cavity sites: predictions and experimental testing J. Mol. Biol. 2008, 377, 914-934
-
(2008)
J. Mol. Biol.
, vol.377
, pp. 914-934
-
-
Graves, A.P.1
Shivakumar, D.M.2
Boyce, S.E.3
Jacobson, M.P.4
Case, D.A.5
Shoichet, B.K.6
-
69
-
-
45749138489
-
MM-GB/SA rescoring of docking poses in structure-based lead optimization
-
Guimarães, C. R.; Cardozo, M. MM-GB/SA rescoring of docking poses in structure-based lead optimization J. Chem. Inf. Model. 2008, 48, 958-970
-
(2008)
J. Chem. Inf. Model.
, vol.48
, pp. 958-970
-
-
Guimarães, C.R.1
Cardozo, M.2
-
70
-
-
82355163888
-
-
KNIME. (accessed Mar 14).
-
KNIME. http://www.knime.org/ (accessed Mar 14, 2011).
-
(2011)
-
-
-
71
-
-
0030040855
-
Identification of a novel domain in the aryl hydrocarbon receptor required for DNA binding
-
DOI 10.1074/jbc.271.7.3743
-
Fukunaga, B. N.; Hankinson, O. Identification of a novel domain in the aryl hydrocarbon receptor required for DNA binding J. Biol. Chem. 1996, 283, 3743-3749 (Pubitemid 26065693)
-
(1996)
Journal of Biological Chemistry
, vol.271
, Issue.7
, pp. 3743-3749
-
-
Fukunaga, B.N.1
Hankinson, O.2
-
72
-
-
82355184187
-
-
RCSB PDB. (accessed Oct 11).
-
RCSB PDB. http://www.rcsb.org/pdb/home/home.do (accessed Oct 11, 2010).
-
(2010)
-
-
-
73
-
-
82355171548
-
-
Maestro, version 9.0; Schrödinger, LLC: New York, NY.
-
Maestro, version 9.0; Schrödinger, LLC: New York, NY, 2009.
-
(2009)
-
-
-
74
-
-
82355163881
-
-
MacroModel, version 9.7; Schrödinger, LLC: New York, NY.
-
MacroModel, version 9.7; Schrödinger, LLC: New York, NY, 2009.
-
(2009)
-
-
-
75
-
-
0026620007
-
AMBER torsional parameters for the peptide backbone
-
DOI 10.1016/0040-4039(93)88034-G
-
McDonald, D. Q.; Still, W. C. AMBER torsional parameters for the peptide backbone Tetrahedron Lett. 1992, 33, 7743-7746 (Pubitemid 23002290)
-
(1992)
Tetrahedron Letters
, vol.33
, Issue.50
, pp. 7743-7746
-
-
McDonald, D.Q.1
Still, W.C.2
-
76
-
-
0344778061
-
General treatment of solvation for molecular mechanics
-
Still, W. C.; Tempczyk, A.; Hawlely, R. C.; Hendrickson, T. A. General treatment of solvation for molecular mechanics J. Am. Chem. Soc. 1990, 112, 6127-6129
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawlely, R.C.3
Hendrickson, T.A.4
|