-
1
-
-
2542543615
-
SDOCKER: A method utilizing existing X-ray structures to improve docking accuracy
-
Wu, G.; Vieth, M. SDOCKER: A method utilizing existing X-ray structures to improve docking accuracy. J. Med. Chem. 2004, 47, 3142-3148.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 3142-3148
-
-
Wu, G.1
Vieth, M.2
-
2
-
-
4744365803
-
Soft docking and multiple receptor conformations in virtual screening
-
Ferrari, A. M.; Wei, B. Q.; Costantino, L.; Shoichet, B. K. Soft docking and multiple receptor conformations in virtual screening. J. Med. Chem. 2004, 47, 5076-5084.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 5076-5084
-
-
Ferrari, A.M.1
Wei, B.Q.2
Costantino, L.3
Shoichet, B.K.4
-
3
-
-
0036835460
-
Integration of virtual and high-throughput screening
-
Bajorath, J. Integration of virtual and high-throughput screening. Nat. Rev. Drug Discovery 2002, 1, 882-894.
-
(2002)
Nat. Rev. Drug Discovery
, vol.1
, pp. 882-894
-
-
Bajorath, J.1
-
4
-
-
0035957528
-
FlexE: Efficient molecular docking considering protein structure variations
-
Claussen, H.; Buning, C.; Rarey, M.; Lengauer, T. FlexE: Efficient molecular docking considering protein structure variations. J. Mol. Biol. 2001, 308, 377-395.
-
(2001)
J. Mol. Biol.
, vol.308
, pp. 377-395
-
-
Claussen, H.1
Buning, C.2
Rarey, M.3
Lengauer, T.4
-
5
-
-
13544249943
-
Genetic polymorphisms of cytochrome P450 2D6 (CYP2D6): Clinical consequences, evolutionary aspects and functional diversity
-
Ingelman-Sundberg, M. Genetic polymorphisms of cytochrome P450 2D6 (CYP2D6): Clinical consequences, evolutionary aspects and functional diversity. Pharmacogenomics J. 2005, 5, 6-13.
-
(2005)
Pharmacogenomics J.
, vol.5
, pp. 6-13
-
-
Ingelman-Sundberg, M.1
-
6
-
-
0036223831
-
Summary of information on human CYP enzymes: Human P450 metabolism data
-
Rendic S. Summary of information on human CYP enzymes: human P450 metabolism data. Drug Metab. Rev. 2002, 34, 83-448.
-
(2002)
Drug Metab. Rev.
, vol.34
, pp. 83-448
-
-
Rendic, S.1
-
7
-
-
0003653901
-
-
Wiley-VCH: Weinheim
-
Höltje, H.; Sippl, W.; Rognan, D.; Folkers, G. In Molecular Modeling: Basic Principles and Applications, 2nd ed.; Wiley-VCH: Weinheim, 2003; pp 18-19.
-
(2003)
Molecular Modeling: Basic Principles and Applications, 2nd ed.
, pp. 18-19
-
-
Höltje, H.1
Sippl, W.2
Rognan, D.3
Folkers, G.4
-
8
-
-
0029878720
-
VMD - Visual Molecular Dynamics
-
Humphrey, W.; Dalke, A.; Schulten, K. VMD - Visual Molecular Dynamics. J. Mol. Graphics Modell. 1996, 14, 33-38.
-
(1996)
J. Mol. Graphics Modell.
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
9
-
-
11644261806
-
Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function
-
Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated docking using a lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 1998, 19, 1639-1662.
-
(1998)
J. Comput. Chem.
, vol.19
, pp. 1639-1662
-
-
Morris, G.M.1
Goodsell, D.S.2
Halliday, R.S.3
Huey, R.4
Hart, W.E.5
Belew, R.K.6
Olson, A.J.7
-
10
-
-
0033397980
-
Python: A programming language for software integration and development
-
Sanner, M. F. Python: A programming language for software integration and development. J. Mol. Graphics Modell. 1999, 17, 51-61.
-
(1999)
J. Mol. Graphics Modell.
, vol.17
, pp. 51-61
-
-
Sanner, M.F.1
-
11
-
-
6044232040
-
Validation of model of cytochrome P450 2D6: An in silico tool for predicting metabolism and inhibition
-
Kemp, C. A.; Flanagan, J. U.; van Eldik, A. J.; Maréchal, J.; Wolf, C. R.; Roberts, G. C. K.; Paine, M. J. I.; Sutcliffe, M. J. Validation of model of cytochrome P450 2D6: An in silico tool for predicting metabolism and inhibition. J. Med. Chem. 2004, 47, 5340-5346.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 5340-5346
-
-
Kemp, C.A.1
Flanagan, J.U.2
Van Eldik, A.J.3
Maréchal, J.4
Wolf, C.R.5
Roberts, G.C.K.6
Paine, M.J.I.7
Sutcliffe, M.J.8
-
12
-
-
0032849040
-
Three and four dimensional-quantitative structure activity relationship (3D/4D-QSAR) analyses of CYP2D6 inhibitors
-
Ekins, S.; Bravi, G.; Binkley, S.; Gillespie, J. S.; Ring, B. J.; Wikel, J. H.; Wrighton, S. A. Three and four dimensional-quantitative structure activity relationship (3D/4D-QSAR) analyses of CYP2D6 inhibitors. Pharmacogenetics 1999, 9, 477-489.
-
(1999)
Pharmacogenetics
, vol.9
, 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
-
13
-
-
0027314831
-
Development of a pharmacophore for inhibition of human liver cytochrome P-450 2D6: Molecular modeling and inhibition studies
-
Strobl, G. R.; von Kruedener, S.; Stockigt, J.; Guengerich, F. P.; Wolff, T. 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.
-
(1993)
J. Med. Chem.
, vol.36
, pp. 1136-1145
-
-
Strobl, G.R.1
Von Kruedener, S.2
Stockigt, J.3
Guengerich, F.P.4
Wolff, T.5
-
14
-
-
33845778960
-
-
Developmental Therapeutics Program, http://dtp.nci.nih.gov/dtpstandard/ dwindex/index.jsp. (Accessed January 17, 2005)
-
Developmental Therapeutics Program, National Cancer Institute, http://dtp.nci.nih.gov/docs/idrugs/chemdata.html. For database searching, use the URL http://dtp.nci.nih.gov/dtpstandard/dwindex/index.jsp. (Accessed January 17, 2005).
-
-
-
-
15
-
-
0036022960
-
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
-
Wang, R.; Lai, L.; Wang, S. Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J. Comput.-Aided Mol. Des. 2002, 16, 11-26.
-
(2002)
J. Comput.-Aided Mol. Des.
, vol.16
, pp. 11-26
-
-
Wang, R.1
Lai, L.2
Wang, S.3
-
16
-
-
10044294023
-
An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes
-
Wang, R.; Lu, Y.; Fang, X.; Wang, S. An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes. J. Chem. Inf. Comput. Sci. 2004, 44, 2114-2125.
-
(2004)
J. Chem. Inf. Comput. Sci.
, vol.44
, pp. 2114-2125
-
-
Wang, R.1
Lu, Y.2
Fang, X.3
Wang, S.4
-
17
-
-
0037763817
-
Comparative evaluation of 11 scoring functions for molecular docking
-
Wang, R.; Lu, Y.; Wang, S. Comparative evaluation of 11 scoring functions for molecular docking. J. Med. Chem. 2003, 46, 2287-2303.
-
(2003)
J. Med. Chem.
, vol.46
, pp. 2287-2303
-
-
Wang, R.1
Lu, Y.2
Wang, S.3
-
18
-
-
5044245324
-
Phe120 contributes to the regiospecificity of cytochrome P450 2D6: Mutation leads to the formation of a novel dextromethorphan metabolite
-
Flanagan, J. U.; Marechal, J. D.; Ward, R.; Kemp, C. A.; McLaughlin, L. A.; Sutcliffe, M. J.; Roberts, G. C.; Paine, M. J.; Wolf, C. R. Phe120 contributes to the regiospecificity of cytochrome P450 2D6: mutation leads to the formation of a novel dextromethorphan metabolite. Biochem. J. 2004, 380, 353-360.
-
(2004)
Biochem. J.
, vol.380
, pp. 353-360
-
-
Flanagan, J.U.1
Marechal, J.D.2
Ward, R.3
Kemp, C.A.4
McLaughlin, L.A.5
Sutcliffe, M.J.6
Roberts, G.C.7
Paine, M.J.8
Wolf, C.R.9
-
19
-
-
0028832796
-
Evidence that aspartic acid 301 is a critical substrate-contact residue in the active site of cytochrome P450 2D6
-
Ellis, S. W.; Hayhurst, G. P.; Smith, G.; Lightfoot, T.; Wong, M. M.; Simula, A. P.; Ackland, M. J.; Sternberg, M. J.; Lennard, M. S.; Tucker, G. T.; Wolf, C. R. Evidence that aspartic acid 301 is a critical substrate-contact residue in the active site of cytochrome P450 2D6. J. Biol. Chem. 1995, 270, 29055-29058.
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 29055-29058
-
-
Ellis, S.W.1
Hayhurst, G.P.2
Smith, G.3
Lightfoot, T.4
Wong, M.M.5
Simula, A.P.6
Ackland, M.J.7
Sternberg, M.J.8
Lennard, M.S.9
Tucker, G.T.10
Wolf, C.R.11
-
20
-
-
0035870926
-
Influence of phenylalanine-481 substitutions on the catalytic activity of cytochrome P450 2D6
-
Hayhurst, G. P.; Harlow, J.; Chowdry, J.; Gross, E.; Hilton, E.; Lennard, M. S.; Tucker, G. T.; Ellis, S. W. Influence of phenylalanine-481 substitutions on the catalytic activity of cytochrome P450 2D6. Biochem. J. 2001, 355, 373-379.
-
(2001)
Biochem. J.
, vol.355
, pp. 373-379
-
-
Hayhurst, G.P.1
Harlow, J.2
Chowdry, J.3
Gross, E.4
Hilton, E.5
Lennard, M.S.6
Tucker, G.T.7
Ellis, S.W.8
-
21
-
-
24944497676
-
The role of phenylalanine 483 in cytochrome P450 2D6 is strongly substrate dependent
-
Lussenburg, B. M.; Keizers, P. H.; de Graaf, C.; Hidestrand, M.; Ingelman-Sundberg, M.; Vermeulen, N. P.; Commandeur, J. N. The role of phenylalanine 483 in cytochrome P450 2D6 is strongly substrate dependent. Biochem. Pharmacol. 2005, 70, 1253-1261.
-
(2005)
Biochem. Pharmacol.
, vol.70
, pp. 1253-1261
-
-
Lussenburg, B.M.1
Keizers, P.H.2
De Graaf, C.3
Hidestrand, M.4
Ingelman-Sundberg, M.5
Vermeulen, N.P.6
Commandeur, J.N.7
-
22
-
-
4043136505
-
Chemical proteomic tool for ligand mapping of CYP anti-targets: An NMR-compatible 3D QSAR descriptor in the heme-based coordinate system
-
Yao, H.; Costache, A. D.; Sem, D. S. Chemical proteomic tool for ligand mapping of CYP anti-targets: An NMR-compatible 3D QSAR descriptor in the heme-based coordinate system. J. Chem. Inf. Comput. Sci. 2004, 44, 1456-1465.
-
(2004)
J. Chem. Inf. Comput. Sci.
, vol.44
, pp. 1456-1465
-
-
Yao, H.1
Costache, A.D.2
Sem, D.S.3
-
23
-
-
0017411710
-
The protein data bank: A computer-based archival file for macromolecular structures
-
Bernstein, F. C.; Koetzle, T. F.; Williams, G. J.; Meyer, E. F.; Brice, M. D.; Rodgers, J. R.; Kennard, O.; Shimanouchi, T.; Tasumi, M. The protein data bank: a computer-based archival file for macromolecular structures. J. Mol Biol. 1977, 112, 535-542.
-
(1977)
J. Mol Biol.
, vol.112
, pp. 535-542
-
-
Bernstein, F.C.1
Koetzle, T.F.2
Williams, G.J.3
Meyer, E.F.4
Brice, M.D.5
Rodgers, J.R.6
Kennard, O.7
Shimanouchi, T.8
Tasumi, M.9
-
24
-
-
0031715982
-
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
-
Shindyalov, I. N.; Bourne, P. E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 1998, 11, 739-747.
-
(1998)
Protein Eng.
, vol.11
, pp. 739-747
-
-
Shindyalov, I.N.1
Bourne, P.E.2
-
25
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
26
-
-
0041784950
-
Allatom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A. D., Jr.; Bashford, D.; Bellot, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick. S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanbe, M.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. Allatom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B 1998, 102, 3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellot, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Iii, R.W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanbe, M.26
Wiórkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
27
-
-
0042415783
-
NAMD2: Greater scalability for parallel molecular dynamics
-
Kalé. L.; Skeel, R.; Bhandarkar. M.; Brunner. R.; Gursoy, A.; Krawetz, N.; Phillips. J.; Shinozaki, A.; Varadarajan, K.; Schulten, K. NAMD2: Greater scalability for parallel molecular dynamics. J. Comput. Phys. 1999, 151, 283-312.
-
(1999)
J. Comput. Phys.
, vol.151
, pp. 283-312
-
-
Kalé, L.1
Skeel, R.2
Bhandarkar, M.3
Brunner, R.4
Gursoy, A.5
Krawetz, N.6
Phillips, J.7
Shinozaki, A.8
Varadarajan, K.9
Schulten, K.10
-
28
-
-
85164392958
-
A Study of cross-validation and bootstrap for accuracy estimation and model selection
-
Kohavi, R. A Study of cross-validation and bootstrap for accuracy estimation and model selection. Int. Joint Conf. Artif. Intell. 1995, 14, 1137-1145.
-
(1995)
Int. Joint Conf. Artif. Intell.
, vol.14
, pp. 1137-1145
-
-
Kohavi, R.1
-
30
-
-
33646092472
-
Crystal structure of human cytochrome P450 2D6
-
Rowland, P.; Blaney, F. E.; Smyth, M. G.; Jones, J. J.; Leydon, V. R.; Oxbrow, A. K.; Lewis, C. J.; Tennant, M. G.; Modi, S.; Eggleston. D. S.; Chenery, R. J.; Bridges, A. M. Crystal structure of human cytochrome P450 2D6. J. Biol. Chem. 2006, 281, 7614-7622.
-
(2006)
J. Biol. Chem.
, vol.281
, pp. 7614-7622
-
-
Rowland, P.1
Blaney, F.E.2
Smyth, M.G.3
Jones, J.J.4
Leydon, V.R.5
Oxbrow, A.K.6
Lewis, C.J.7
Tennant, M.G.8
Modi, S.9
Eggleston, D.S.10
Chenery, R.J.11
Bridges, A.M.12
|