-
1
-
-
0034975654
-
IKr: The hERG Channel
-
Tseng, G.-N. IKr: The hERG Channel J. Mol. Cell. Cardiol. 2001, 33, 835-849
-
(2001)
J. Mol. Cell. Cardiol.
, vol.33
, pp. 835-849
-
-
Tseng, G.-N.1
-
2
-
-
33645317063
-
HERG potassium channels and cardiac arrhythmia
-
Sanguinetti, M. C.; Tristani-Firouzi, M. hERG potassium channels and cardiac arrhythmia Nature 2006, 440, 463-469
-
(2006)
Nature
, vol.440
, pp. 463-469
-
-
Sanguinetti, M.C.1
Tristani-Firouzi, M.2
-
3
-
-
14544268139
-
QT prolongation through hERG K+ channel blockade: Current knowledge and strategies for the early prediction during drug development
-
Recanatini, M.; Poluzzi, E.; Masetti, M.; Cavalli, A.; De Ponti, F. QT prolongation through hERG K+ channel blockade: Current knowledge and strategies for the early prediction during drug development Med. Res. Rev. 2005, 25, 133-166
-
(2005)
Med. Res. Rev.
, vol.25
, pp. 133-166
-
-
Recanatini, M.1
Poluzzi, E.2
Masetti, M.3
Cavalli, A.4
De Ponti, F.5
-
4
-
-
33745413284
-
Quantitative Structure-Activity Relationship Studies on Inhibition of HERG Potassium Channels
-
Yoshida, K.; Niwa, T. Quantitative Structure-Activity Relationship Studies on Inhibition of HERG Potassium Channels J. Chem. Inf. Model. 2006, 46, 1371-1378
-
(2006)
J. Chem. Inf. Model.
, vol.46
, pp. 1371-1378
-
-
Yoshida, K.1
Niwa, T.2
-
5
-
-
78049442434
-
In Silico Binary Classification QSAR Models Based on 4D-Fingerprints and MOE Descriptors for Prediction of hERG Blockage
-
Su, B.-H.; Shen, M.-y.; Esposito, E. X.; Hopfinger, A. J.; Tseng, Y. J. In Silico Binary Classification QSAR Models Based on 4D-Fingerprints and MOE Descriptors for Prediction of hERG Blockage J. Chem. Inf. Model. 2010, 50, 1304-1318
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 1304-1318
-
-
Su, B.-H.1
Shen, M.-Y.2
Esposito, E.X.3
Hopfinger, A.J.4
Tseng, Y.J.5
-
6
-
-
0038487659
-
Prediction of hERG potassium channel affinity by traditional and hologram qSAR methods
-
Keserü, G. Prediction of hERG potassium channel affinity by traditional and hologram qSAR methods Bioorg. Chem. Med. Lett. 2003, 13, 2773-2775
-
(2003)
Bioorg. Chem. Med. Lett.
, vol.13
, pp. 2773-2775
-
-
Keserü, G.1
-
7
-
-
33244474244
-
Development and Evaluation of an in Silico Model for hERG Binding
-
Song, M.; Clark, M. Development and Evaluation of an in Silico Model for hERG Binding J. Chem. Inf. Model. 2005, 46, 392-400
-
(2005)
J. Chem. Inf. Model.
, vol.46
, pp. 392-400
-
-
Song, M.1
Clark, M.2
-
8
-
-
33644971220
-
Prediction of hERG potassium channel affinity by the CODESSA approach
-
Coi, A.; Massarelli, I.; Murgia, L.; Saraceno, M.; Calderone, V.; Bianucci, A. M. Prediction of hERG potassium channel affinity by the CODESSA approach Bioorg. Med. Chem. 2006, 14, 3153-3159
-
(2006)
Bioorg. Med. Chem.
, vol.14
, pp. 3153-3159
-
-
Coi, A.1
Massarelli, I.2
Murgia, L.3
Saraceno, M.4
Calderone, V.5
Bianucci, A.M.6
-
9
-
-
82355160734
-
A Critical Assessment of Combined Ligand- and Structure-Based Approaches to hERG Channel Blocker Modeling
-
Du-Cuny, L.; Chen, L.; Zhang, S. A Critical Assessment of Combined Ligand- and Structure-Based Approaches to hERG Channel Blocker Modeling J. Chem. Inf. Model. 2011, 51, 2948-2960
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 2948-2960
-
-
Du-Cuny, L.1
Chen, L.2
Zhang, S.3
-
10
-
-
0037194634
-
Toward a Pharmacophore for Drugs Inducing the Long QT Syndrome: Insights from a CoMFA Study of HERG K+ Channel Blockers
-
Cavalli, A.; Poluzzi, E.; De Ponti, F.; Recanatini, M. Toward a Pharmacophore for Drugs Inducing the Long QT Syndrome: Insights from a CoMFA Study of HERG K+ Channel Blockers J. Med. Chem. 2002, 45, 3844-3853
-
(2002)
J. Med. Chem.
, vol.45
, pp. 3844-3853
-
-
Cavalli, A.1
Poluzzi, E.2
De Ponti, F.3
Recanatini, M.4
-
11
-
-
0036229805
-
Three-Dimensional Quantitative Structure-Activity Relationship for Inhibition of Human Ether-a-Go-Go-Related Gene Potassium Channel
-
Ekins, S.; Crumb, W. J.; Sarazan, R. D.; Wikel, J. H.; Wrighton, S. A. Three-Dimensional Quantitative Structure-Activity Relationship for Inhibition of Human Ether-a-Go-Go-Related Gene Potassium Channel J. Pharmacol. Exp. Ther. 2002, 301, 427-434
-
(2002)
J. Pharmacol. Exp. Ther.
, vol.301
, pp. 427-434
-
-
Ekins, S.1
Crumb, W.J.2
Sarazan, R.D.3
Wikel, J.H.4
Wrighton, S.A.5
-
12
-
-
1842686775
-
A model for identifying HERG K+ channel blockers
-
Aronov, A. M.; Goldman, B. B. A model for identifying HERG K+ channel blockers Bioorg. Med. Chem. 2004, 12, 2307-2315
-
(2004)
Bioorg. Med. Chem.
, vol.12
, pp. 2307-2315
-
-
Aronov, A.M.1
Goldman, B.B.2
-
13
-
-
33750998518
-
Common Pharmacophores for Uncharged Human Ether-a-go-go-Related Gene (hERG) Blockers
-
Aronov, A. M. Common Pharmacophores for Uncharged Human Ether-a-go-go-Related Gene (hERG) Blockers J. Med. Chem. 2006, 49, 6917-6921
-
(2006)
J. Med. Chem.
, vol.49
, pp. 6917-6921
-
-
Aronov, A.M.1
-
14
-
-
0038743107
-
Characterization of HERG potassium channel inhibition using CoMSiA 3D QSAR and homology modeling approaches
-
Pearlstein, R. A.; Vaz, R. J.; Kang, J.; Chen, X.-L.; Preobrazhenskaya, M.; Shchekotikhin, A. E.; Korolev, A. M.; Lysenkova, L. N.; Miroshnikova, O. V.; Hendrix, J.; Rampe, D. Characterization of HERG potassium channel inhibition using CoMSiA 3D QSAR and homology modeling approaches Bioorg. Chem. Med. Lett. 2003, 13, 1829-1835
-
(2003)
Bioorg. Chem. Med. Lett.
, vol.13
, pp. 1829-1835
-
-
Pearlstein, R.A.1
Vaz, R.J.2
Kang, J.3
Chen, X.-L.4
Preobrazhenskaya, M.5
Shchekotikhin, A.E.6
Korolev, A.M.7
Lysenkova, L.N.8
Miroshnikova, O.V.9
Hendrix, J.10
Rampe, D.11
-
15
-
-
79952124934
-
Combined Receptor and Ligand-Based Approach to the Universal Pharmacophore Model Development for Studies of Drug Blockade to the hERG1 Pore Domain
-
Durdagi, S.; Duff, H. J.; Noskov, S. Y. Combined Receptor and Ligand-Based Approach to the Universal Pharmacophore Model Development for Studies of Drug Blockade to the hERG1 Pore Domain J. Chem. Inf. Model. 2011, 51, 463-474
-
(2011)
J. Chem. Inf. Model.
, vol.51
, pp. 463-474
-
-
Durdagi, S.1
Duff, H.J.2
Noskov, S.Y.3
-
16
-
-
19444375852
-
Exploring blocker binding to a homology model of the open hERG K+ channel using docking and molecular dynamics methods
-
Österberg, F.; Åqvist, J. Exploring blocker binding to a homology model of the open hERG K+ channel using docking and molecular dynamics methods FEBS Lett. 2005, 579, 2939-2944
-
(2005)
FEBS Lett.
, vol.579
, pp. 2939-2944
-
-
Österberg, F.1
Åqvist, J.2
-
17
-
-
79959980468
-
Computer Simulations of Structure-Activity Relationships for hERG Channel Blockers
-
Boukharta, L.; Keränen, H.; Stary-Weinzinger, A.; Wallin, G.; de Groot, B. L.; Åqvist, J. Computer Simulations of Structure-Activity Relationships for hERG Channel Blockers Biochemistry 2011, 50, 6146-6156
-
(2011)
Biochemistry
, vol.50
, pp. 6146-6156
-
-
Boukharta, L.1
Keränen, H.2
Stary-Weinzinger, A.3
Wallin, G.4
De Groot, B.L.5
Åqvist, J.6
-
18
-
-
33644967111
-
New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies
-
Farid, R.; Day, T.; Friesner, R. A.; Pearlstein, R. A. New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies Bioorg. Med. Chem. 2006, 14, 3160-3173
-
(2006)
Bioorg. Med. Chem.
, vol.14
, pp. 3160-3173
-
-
Farid, R.1
Day, T.2
Friesner, R.A.3
Pearlstein, R.A.4
-
19
-
-
54149100153
-
Identification of a ″toxicophoric″ features for predicting drug-induced QT interval prolongation
-
Coi, A.; Massarelli, I.; Testai, L.; Calderone, V.; Bianucci, A. M. Identification of a ″toxicophoric″ features for predicting drug-induced QT interval prolongation Eur. J. Med. Chem. 2008, 43, 2479-2488
-
(2008)
Eur. J. Med. Chem.
, vol.43
, pp. 2479-2488
-
-
Coi, A.1
Massarelli, I.2
Testai, L.3
Calderone, V.4
Bianucci, A.M.5
-
20
-
-
14644392097
-
A two-state homology model of the hERG K+ channel: Application to ligand binding
-
Rajamani, R.; Tounge, B. A.; Li, J.; Reynolds, C. H. A two-state homology model of the hERG K+ channel: application to ligand binding Bioorg. Chem. Med. Lett. 2005, 15, 1737-1741
-
(2005)
Bioorg. Chem. Med. Lett.
, vol.15
, pp. 1737-1741
-
-
Rajamani, R.1
Tounge, B.A.2
Li, J.3
Reynolds, C.H.4
-
21
-
-
34250836484
-
Drug block of the hERG potassium channel: Insight from modeling
-
Stansfeld, P. J.; Gedeck, P.; Gosling, M.; Cox, B.; Mitcheson, J. S.; Sutcliffe, M. J. Drug block of the hERG potassium channel: Insight from modeling Proteins: Struct. Funct. Bioinf. 2007, 68, 568-580
-
(2007)
Proteins: Struct. Funct. Bioinf.
, vol.68
, pp. 568-580
-
-
Stansfeld, P.J.1
Gedeck, P.2
Gosling, M.3
Cox, B.4
Mitcheson, J.S.5
Sutcliffe, M.J.6
-
22
-
-
47249159421
-
Modeling hERG and its Interactions with Drugs: Recent Advances in Light of Current Potassium Channel Simulations
-
Recanatini, M.; Cavalli, A.; Masetti, M. Modeling hERG and its Interactions with Drugs: Recent Advances in Light of Current Potassium Channel Simulations Chem. Med. Chem. 2008, 3, 523-535
-
(2008)
Chem. Med. Chem.
, vol.3
, pp. 523-535
-
-
Recanatini, M.1
Cavalli, A.2
Masetti, M.3
-
23
-
-
0037157153
-
Computational Drug Design Accommodating Receptor Flexibility: The Relaxed Complex Scheme
-
Lin, J.-H.; Perryman, A. L.; Schames, J. R.; McCammon, J. A. Computational Drug Design Accommodating Receptor Flexibility: The Relaxed Complex Scheme J. Am. Chem. Soc. 2002, 124, 5632-5633
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 5632-5633
-
-
Lin, J.-H.1
Perryman, A.L.2
Schames, J.R.3
McCammon, J.A.4
-
24
-
-
40549090207
-
Modeling the hERG potassium channel in a phospholipid bilayer: Molecular dynamics and drug docking studies
-
Masetti, M.; Cavalli, A.; Recanatini, M. Modeling the hERG potassium channel in a phospholipid bilayer: Molecular dynamics and drug docking studies J. Comput. Chem. 2008, 29, 795-808
-
(2008)
J. Comput. Chem.
, vol.29
, pp. 795-808
-
-
Masetti, M.1
Cavalli, A.2
Recanatini, M.3
-
25
-
-
34247847889
-
Probing the Outer Mouth Structure of the hERG Channel with Peptide Toxin Footprinting and Molecular Modeling
-
Tseng, G.-N.; Sonawane, K. D.; Korolkova, Y. V.; Zhang, M.; Liu, J.; Grishin, E. V.; Guy, H. R. Probing the Outer Mouth Structure of the hERG Channel with Peptide Toxin Footprinting and Molecular Modeling Biophys. J. 2007, 92, 3524-3540
-
(2007)
Biophys. J.
, vol.92
, pp. 3524-3540
-
-
Tseng, G.-N.1
Sonawane, K.D.2
Korolkova, Y.V.3
Zhang, M.4
Liu, J.5
Grishin, E.V.6
Guy, H.R.7
-
26
-
-
0037188507
-
Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction
-
Xiang, Z.; Soto, C. S.; Honig, B. Evaluating conformational free energies: The colony energy and its application to the problem of loop prediction Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 7432-7437
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 7432-7437
-
-
Xiang, Z.1
Soto, C.S.2
Honig, B.3
-
27
-
-
38549178026
-
A statistical rescoring scheme for protein-ligand docking: Consideration of entropic effect
-
Lee, J.; Seok, C. A statistical rescoring scheme for protein-ligand docking: Consideration of entropic effect Proteins: Struct. Funct. Bioinf. 2008, 70, 1074-1083
-
(2008)
Proteins: Struct. Funct. Bioinf.
, vol.70
, pp. 1074-1083
-
-
Lee, J.1
Seok, C.2
-
28
-
-
41949132916
-
Flexible ligand docking to multiple receptor conformations: A practical alternative
-
Totrov, M.; Abagyan, R. Flexible ligand docking to multiple receptor conformations: a practical alternative Curr. Opin. Struct. Biol. 2008, 18, 178-184
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 178-184
-
-
Totrov, M.1
Abagyan, R.2
-
29
-
-
0034521981
-
Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models
-
Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E. Calculating Structures and Free Energies of Complex Molecules: Combining Molecular Mechanics and Continuum Models Acc. Chem. Res. 2000, 33, 889-897
-
(2000)
Acc. Chem. Res.
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
Donini, O.11
Cieplak, P.12
Srinivasan, J.13
Case, D.A.14
Cheatham, T.E.15
-
30
-
-
0034811498
-
Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA
-
Wang, J.; Morin, P.; Wang, W.; Kollman, P. A. Use of MM-PBSA in Reproducing the Binding Free Energies to HIV-1 RT of TIBO Derivatives and Predicting the Binding Mode to HIV-1 RT of Efavirenz by Docking and MM-PBSA J. Am. Chem. Soc. 2001, 123, 5221-5230
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 5221-5230
-
-
Wang, J.1
Morin, P.2
Wang, W.3
Kollman, P.A.4
-
31
-
-
1642370447
-
Physicochemical Features of the hERG Channel Drug Binding Site
-
Fernandez, D.; Ghanta, A.; Kauffman, G. W.; Sanguinetti, M. C. Physicochemical Features of the hERG Channel Drug Binding Site J. Biol. Chem. 2004, 279, 10120-10127
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 10120-10127
-
-
Fernandez, D.1
Ghanta, A.2
Kauffman, G.W.3
Sanguinetti, M.C.4
-
32
-
-
83455205897
-
In silico Analysis of Conformational Changes Induced by Mutation of Aromatic Binding Residues: Consequences for Drug Binding in the hERG K+ Channel
-
Knape, K.; Linder, T.; Wolschann, P.; Beyer, A.; Stary-Weinzinger, A. In silico Analysis of Conformational Changes Induced by Mutation of Aromatic Binding Residues: Consequences for Drug Binding in the hERG K+ Channel PLoS ONE 2011, 6, e28778
-
(2011)
PLoS ONE
, vol.6
, pp. 28778
-
-
Knape, K.1
Linder, T.2
Wolschann, P.3
Beyer, A.4
Stary-Weinzinger, A.5
-
33
-
-
70349932423
-
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
-
Morris, G. M.; Huey, R.; Lindstrom, W.; Sanner, M. F.; Belew, R. K.; Goodsell, D. S.; Olson, A. J. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility J. Comput. Chem. 2009, 30, 2785-2791
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 2785-2791
-
-
Morris, G.M.1
Huey, R.2
Lindstrom, W.3
Sanner, M.F.4
Belew, R.K.5
Goodsell, D.S.6
Olson, A.J.7
-
34
-
-
77951992987
-
Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments
-
Craig, I. R.; Essex, J. W.; Spiegel, K. Ensemble Docking into Multiple Crystallographically Derived Protein Structures: An Evaluation Based on the Statistical Analysis of Enrichments J. Chem. Inf. Model. 2010, 50, 511-524
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 511-524
-
-
Craig, I.R.1
Essex, J.W.2
Spiegel, K.3
-
35
-
-
1542741046
-
Identification of a Minimal Subset of Receptor Conformations for Improved Multiple Conformation Docking and Two-Step Scoring
-
Yoon, S.; Welsh, W. J. Identification of a Minimal Subset of Receptor Conformations for Improved Multiple Conformation Docking and Two-Step Scoring J. Chem. Inf. Comput. Sci. 2003, 44, 88-96
-
(2003)
J. Chem. Inf. Comput. Sci.
, vol.44
, pp. 88-96
-
-
Yoon, S.1
Welsh, W.J.2
-
36
-
-
0035846166
-
Are Free Energy Calculations Useful in Practice? A Comparison with Rapid Scoring Functions for the p38 MAP Kinase Protein System
-
Pearlman, D. A.; Charifson, P. S. Are Free Energy Calculations Useful in Practice? A Comparison with Rapid Scoring Functions for the p38 MAP Kinase Protein System J. Med. Chem. 2001, 44, 3417-3423
-
(2001)
J. Med. Chem.
, vol.44
, pp. 3417-3423
-
-
Pearlman, D.A.1
Charifson, P.S.2
-
37
-
-
67650759939
-
Side Chain Flexibilities in the Human Ether-a-go-go Related Gene Potassium Channel (hERG) Together with Matched-Pair Binding Studies Suggest a New Binding Mode for Channel Blockers
-
Zachariae, U.; Giordanetto, F.; Leach, A. G. Side Chain Flexibilities in the Human Ether-a-go-go Related Gene Potassium Channel (hERG) Together with Matched-Pair Binding Studies Suggest a New Binding Mode for Channel Blockers J. Med. Chem. 2009, 52, 4266-4276
-
(2009)
J. Med. Chem.
, vol.52
, pp. 4266-4276
-
-
Zachariae, U.1
Giordanetto, F.2
Leach, A.G.3
-
38
-
-
84860310064
-
Computational Design and Discovery of ″minimally Structured″ hERG Blockers
-
Cavalli, A.; Buonfiglio, R.; Ianni, C.; Masetti, M.; Ceccarini, L.; Caves, R.; Chang, M. W. Y.; Mitcheson, J. S.; Roberti, M.; Recanatini, M. Computational Design and Discovery of ″Minimally Structured″ hERG Blockers J. Med. Chem. 2012, 55, 4010-4014
-
(2012)
J. Med. Chem.
, vol.55
, pp. 4010-4014
-
-
Cavalli, A.1
Buonfiglio, R.2
Ianni, C.3
Masetti, M.4
Ceccarini, L.5
Caves, R.6
Chang, M.W.Y.7
Mitcheson, J.S.8
Roberti, M.9
Recanatini, M.10
-
39
-
-
0028871814
-
Evaluation of comparative protein modelling by MODELLER
-
Sali, A.; Potterton, L.; Yuan, F.; van Vlijmen, H.; Karplus, M. Evaluation of comparative protein modelling by MODELLER Proteins 1995, 23, 318-326
-
(1995)
Proteins
, vol.23
, pp. 318-326
-
-
Sali, A.1
Potterton, L.2
Yuan, F.3
Van Vlijmen, H.4
Karplus, M.5
-
40
-
-
0026655361
-
Stereochemical quality of protein structure coordinates
-
Morris, A. L.; MacArthur, M. W.; Hutchinson, E. G.; Thornton, J. M. Stereochemical quality of protein structure coordinates Proteins: Struct. Funct. Bioinf. 1992, 12, 345-364
-
(1992)
Proteins: Struct. Funct. Bioinf.
, vol.12
, pp. 345-364
-
-
Morris, A.L.1
MacArthur, M.W.2
Hutchinson, E.G.3
Thornton, J.M.4
-
41
-
-
79952608525
-
Accurate bond and angle parameters for X-ray protein structure refinement
-
Engh, R. A.; Huber, R. Accurate bond and angle parameters for X-ray protein structure refinement Acta Cryst. A 1991, 47, 392-400
-
(1991)
Acta Cryst. A
, vol.47
, pp. 392-400
-
-
Engh, R.A.1
Huber, R.2
-
42
-
-
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
-
43
-
-
0030404988
-
HOLE: A program for the analysis of the pore dimensions of ion channel structural models
-
Smart, O. S.; Neduvelil, J. G.; Wang, X.; Wallace, B. A.; Sansom, M. S. HOLE: a program for the analysis of the pore dimensions of ion channel structural models. J. Mol. Graph. Model. 1996, 14.
-
(1996)
J. Mol. Graph. Model.
, vol.14
-
-
Smart, O.S.1
Neduvelil, J.G.2
Wang, X.3
Wallace, B.A.4
Sansom, M.S.5
-
44
-
-
0030305457
-
R: A Language for Data Analysis and Graphics
-
Ihaka, R.; Gentleman, R. R: A Language for Data Analysis and Graphics J. Comput. Graph. Stat. 1996, 5, 299-314
-
(1996)
J. Comput. Graph. Stat.
, vol.5
, pp. 299-314
-
-
Ihaka, R.1
Gentleman, R.2
-
45
-
-
0003578015
-
-
Fourth ed. Arnold: London, UK.
-
Everitt, B. S.; Landau, S.; Leese, M. Cluster Analysis, Fourth ed.; Arnold: London, UK, 2001.
-
(2001)
Cluster Analysis
-
-
Everitt, B.S.1
Landau, S.2
Leese, M.3
-
46
-
-
49149147973
-
Iterative partial equalization of orbital electronegativity: A rapid access to atomic charges
-
Gasteiger, J.; Marsili, M. Iterative partial equalization of orbital electronegativity: a rapid access to atomic charges Tetrahedron 1980, 36, 3219-3228
-
(1980)
Tetrahedron
, vol.36
, pp. 3219-3228
-
-
Gasteiger, J.1
Marsili, M.2
-
47
-
-
0021757436
-
A new force field for molecular mechanical simulation of nucleic acids and proteins
-
Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S.; Weiner, P. A new force field for molecular mechanical simulation of nucleic acids and proteins J. Am. Chem. Soc. 1984, 106, 765-784
-
(1984)
J. Am. Chem. Soc.
, vol.106
, pp. 765-784
-
-
Weiner, S.J.1
Kollman, P.A.2
Case, D.A.3
Singh, U.C.4
Ghio, C.5
Alagona, G.6
Profeta, S.7
Weiner, P.8
-
48
-
-
15244349255
-
Application of MM/PBSA colony free energy to loop decoy discrimination: Toward correlation between energy and root mean square deviation
-
Fogolari, F.; Tosatto, S. C. E. Application of MM/PBSA colony free energy to loop decoy discrimination: Toward correlation between energy and root mean square deviation Protein Sci. 2005, 14, 889-901
-
(2005)
Protein Sci.
, vol.14
, pp. 889-901
-
-
Fogolari, F.1
Tosatto, S.C.E.2
-
49
-
-
73349111930
-
Scoring Ensembles of Docked Protein:Ligand Interactions for Virtual Lead Optimization
-
Paulsen, J. L.; Anderson, A. C. Scoring Ensembles of Docked Protein:Ligand Interactions for Virtual Lead Optimization J. Chem. Inf. Model. 2009, 49, 2813-2819
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 2813-2819
-
-
Paulsen, J.L.1
Anderson, A.C.2
-
50
-
-
35348864558
-
Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors
-
Ferrari, A. M.; Degliesposti, G.; Sgobba, M.; Rastelli, G. Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors Bioorg. Med. Chem. 2007, 15, 7865-7877
-
(2007)
Bioorg. Med. Chem.
, vol.15
, pp. 7865-7877
-
-
Ferrari, A.M.1
Degliesposti, G.2
Sgobba, M.3
Rastelli, G.4
-
51
-
-
33750467966
-
Ligand Affinities Predicted with the MM/PBSA Method: Dependence on the Simulation Method and the Force Field
-
Weis, A.; Katebzadeh, K.; Söderhjelm, P.; Nilsson, I.; Ryde, U. Ligand Affinities Predicted with the MM/PBSA Method: Dependence on the Simulation Method and the Force Field J. Med. Chem. 2006, 49, 6596-6606
-
(2006)
J. Med. Chem.
, vol.49
, pp. 6596-6606
-
-
Weis, A.1
Katebzadeh, K.2
Söderhjelm, P.3
Nilsson, I.4
Ryde, U.5
-
52
-
-
78049265751
-
-
University of California: San Francisco, CA.
-
Case, D. A.; Darden, T. A.; Cheatham, I., T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; Roberts, B.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, A.; Kolossváry, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Liu, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Cai, Q.; Ye, X.; Wang, J.; Hsieh, M.-J.; Cui, G.; Roe, D. R.; Mathews, D. H.; Seetin, M. G.; Sagui, C.; Babin, V.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Kollman, P. A. AMBER 11; University of California: San Francisco, CA, 2010.
-
(2010)
AMBER 11
-
-
Case, D.A.1
Darden, T.A.2
Cheatham, I..T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Walker, R.C.8
Zhang, W.9
Merz, K.M.10
Roberts, B.11
Wang, B.12
Hayik, S.13
Roitberg, A.14
Seabra, A.15
Kolossváry, I.16
Wong, K.F.17
Paesani, F.18
Vanicek, J.19
Liu, J.20
Wu, X.21
Brozell, S.R.22
Steinbrecher, T.23
Gohlke, H.24
Cai, Q.25
Ye, X.26
Wang, J.27
Hsieh, M.-J.28
Cui, G.29
Roe, D.R.30
Mathews, D.H.31
Seetin, M.G.32
Sagui, C.33
Babin, V.34
Luchko, T.35
Gusarov, S.36
Kovalenko, A.37
Kollman, P.A.38
more..
-
53
-
-
0002636134
-
Pairwise solute descreening of solute charges from a dielectric medium
-
Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. Pairwise solute descreening of solute charges from a dielectric medium Chem. Phys. Lett. 1995, 246, 122-129
-
(1995)
Chem. Phys. Lett.
, vol.246
, pp. 122-129
-
-
Hawkins, G.D.1
Cramer, C.J.2
Truhlar, D.G.3
-
54
-
-
33748390341
-
Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium
-
Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium J. Phys. Chem. 1996, 100, 19824-19839
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 19824-19839
-
-
Hawkins, G.D.1
Cramer, C.J.2
Truhlar, D.G.3
-
55
-
-
77953513118
-
Improved side-chain torsion potentials for the Amber ff99SB protein force field
-
Lindorff-Larsen, K.; Piana, S.; Palmo, K.; Maragakis, P.; Klepeis, J. L.; Dror, R. O.; Shaw, D. E. Improved side-chain torsion potentials for the Amber ff99SB protein force field Proteins: Struct. Funct. Bioinf. 2010, 78, 1950-1958
-
(2010)
Proteins: Struct. Funct. Bioinf.
, vol.78
, pp. 1950-1958
-
-
Lindorff-Larsen, K.1
Piana, S.2
Palmo, K.3
Maragakis, P.4
Klepeis, J.L.5
Dror, R.O.6
Shaw, D.E.7
-
56
-
-
2942532422
-
Development and testing of a general amber force field
-
Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and testing of a general amber force field J. Comput. Chem. 2004, 25, 1157-1174
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1157-1174
-
-
Wang, J.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
57
-
-
3042524904
-
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
-
Bayly, C. I.; Cieplak, P.; Cornell, W.; Kollman, P. A. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model J. Phys. Chem. 1993, 97, 10269-10280
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.3
Kollman, P.A.4
-
58
-
-
0000667030
-
Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation
-
Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Kollmann, P. A. Application of RESP charges to calculate conformational energies, hydrogen bond energies, and free energies of solvation J. Am. Chem. Soc. 1993, 115, 9620-9631
-
(1993)
J. Am. Chem. Soc.
, vol.115
, pp. 9620-9631
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Kollmann, P.A.4
-
59
-
-
70450206724
-
-
revision B.01; Gaussian, Inc. Wallingford, CT.
-
Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery, J. A.; Peralta, J. E.; Ogliaro, F.; Bearpark, M.; Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V. N.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, J. M.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J. Gaussian 09, revision B.01; Gaussian, Inc.: Wallingford, CT, 2009.
-
(2009)
Gaussian 09
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
Scalmani, G.7
Barone, V.8
Mennucci, B.9
Petersson, G.A.10
Nakatsuji, H.11
Caricato, M.12
Li, X.13
Hratchian, H.P.14
Izmaylov, A.F.15
Bloino, J.16
Zheng, G.17
Sonnenberg, J.L.18
Hada, M.19
Ehara, M.20
Toyota, K.21
Fukuda, R.22
Hasegawa, J.23
Ishida, M.24
Nakajima, T.25
Honda, Y.26
Kitao, O.27
Nakai, H.28
Vreven, T.29
Montgomery, J.A.30
Peralta, J.E.31
Ogliaro, F.32
Bearpark, M.33
Heyd, J.J.34
Brothers, E.35
Kudin, K.N.36
Staroverov, V.N.37
Kobayashi, R.38
Normand, J.39
Raghavachari, K.40
Rendell, A.41
Burant, J.C.42
Iyengar, S.S.43
Tomasi, J.44
Cossi, M.45
Rega, N.46
Millam, J.M.47
Klene, M.48
Knox, J.E.49
Cross, J.B.50
Bakken, V.51
Adamo, C.52
Jaramillo, J.53
Gomperts, R.54
Stratmann, R.E.55
Yazyev, O.56
Austin, A.J.57
Cammi, R.58
Pomelli, C.59
Ochterski, J.W.60
Martin, R.L.61
Morokuma, K.62
Zakrzewski, V.G.63
Voth, G.A.64
Salvador, P.65
Dannenberg, J.J.66
Dapprich, S.67
Daniels, A.D.68
Farkas69
Foresman, J.B.70
Ortiz, J.V.71
Cioslowski, J.72
Fox, D.J.73
more..
-
60
-
-
0035964342
-
Electrostatics of nanosystems: Application to microtubules and the ribosome
-
Baker, N. A.; Sept, D.; Joseph, S.; Holst, M. J.; McCammon, J. A. Electrostatics of nanosystems: Application to microtubules and the ribosome Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 10037-10041
-
(2001)
Proc. Natl. Acad. Sci. U.S.A.
, vol.98
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
61
-
-
32844457567
-
Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models
-
Sitkoff, D.; Sharp, K. A.; Honig, B. Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models J. Phys. Chem. 1994, 98, 1978-1988
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
62
-
-
20444377245
-
Validation and Use of the MM-PBSA Approach for Drug Discovery
-
Kuhn, B.; Gerber, P.; Schulz-Gasch, T.; Stahl, M. Validation and Use of the MM-PBSA Approach for Drug Discovery J. Med. Chem. 2005, 48, 4040-4048
-
(2005)
J. Med. Chem.
, vol.48
, pp. 4040-4048
-
-
Kuhn, B.1
Gerber, P.2
Schulz-Gasch, T.3
Stahl, M.4
|