-
1
-
-
0032977399
-
Energetic Dissection of Specificity in Serine Proteases
-
Vindigni, A. Energetic Dissection of Specificity in Serine Proteases Comb. Chem. High Throughput Screening 1999, 2, 139-153
-
(1999)
Comb. Chem. High Throughput Screening
, vol.2
, pp. 139-153
-
-
Vindigni, A.1
-
2
-
-
0035424616
-
Design of RNA-Binding Proteins and Ligands
-
Cheng, A. C.; Calabro, V.; Frankel, A. D. Design of RNA-Binding Proteins and Ligands Curr. Opin. Struct. Biol. 2001, 11, 478-484
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 478-484
-
-
Cheng, A.C.1
Calabro, V.2
Frankel, A.D.3
-
3
-
-
84871960256
-
Perspective: Alchemical Free Energy Calculations for Drug Discovery
-
Mobley, D. L.; Klimovich, P. V. Perspective: Alchemical Free Energy Calculations for Drug Discovery J. Chem. Phys. 2012, 137, 230901
-
(2012)
J. Chem. Phys.
, vol.137
, pp. 230901
-
-
Mobley, D.L.1
Klimovich, P.V.2
-
4
-
-
33748538349
-
Automatic Atom Type and Bond Type Perception in Molecular Mechanical Calculations
-
Wang, J.; Wang, W.; Kollman, P. A.; Case, D. A. Automatic Atom Type and Bond Type Perception in Molecular Mechanical Calculations J. Mol. Graphics Modell. 2006, 25, 247-260
-
(2006)
J. Mol. Graphics Modell.
, vol.25
, pp. 247-260
-
-
Wang, J.1
Wang, W.2
Kollman, P.A.3
Case, D.A.4
-
5
-
-
84871545594
-
Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing
-
Vanommeslaeghe, K.; MacKerell, A. D. Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing J. Chem. Inf. Model. 2012, 52, 3144-3154
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 3144-3154
-
-
Vanommeslaeghe, K.1
Mackerell, A.D.2
-
6
-
-
84871544678
-
Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges
-
Vanommeslaeghe, K.; Raman, E. P.; MacKerell, A. D. Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges J. Chem. Inf. Model. 2012, 52, 3155-3168
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 3155-3168
-
-
Vanommeslaeghe, K.1
Raman, E.P.2
Mackerell, A.D.3
-
7
-
-
70450206724
-
-
Revision D.01; Gaussian: Wallingford, CT, USA
-
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.; Gaussian 09, Revision D.01; Gaussian: Wallingford, CT, USA, 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
-
8
-
-
0037008160
-
Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors
-
Gohlke, H.; Klebe, K. Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors Angew. Chem., Int. Ed. 2002, 41, 2644-2676
-
(2002)
Angew. Chem., Int. Ed.
, vol.41
, pp. 2644-2676
-
-
Gohlke, H.1
Klebe, K.2
-
9
-
-
33749260698
-
A Critical Assessment of Docking Programs and Scoring Functions
-
Warren, G. L.; Andrews, C. W.; Capelli, A. M.; Clarke, B.; LaLonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semis, S. F.; Senger, S. A Critical Assessment of Docking Programs and Scoring Functions J. Med. Chem. 2006, 49, 5912-5931
-
(2006)
J. Med. Chem.
, vol.49
, 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
Semis, S.F.9
Senger, S.10
-
10
-
-
0031058541
-
The Statistical-Thermodynamic Basis for Computation of Binding Affinities: A Critical Review
-
Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. The Statistical-Thermodynamic Basis for Computation of Binding Affinities: A Critical Review Biophys. J. 1997, 72, 1047-1069
-
(1997)
Biophys. J.
, vol.72
, pp. 1047-1069
-
-
Gilson, M.K.1
Given, J.A.2
Bush, B.L.3
McCammon, J.A.4
-
11
-
-
0141682863
-
Absolute Binding Free Energies: A Quantitative Approach for Their Calculation
-
Boresch, S.; Tettinger, F.; Leitgeb, M.; Karplus, M. Absolute Binding Free Energies: A Quantitative Approach for Their Calculation J. Phys. Chem. B 2003, 107, 9535-9551
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 9535-9551
-
-
Boresch, S.1
Tettinger, F.2
Leitgeb, M.3
Karplus, M.4
-
13
-
-
65249124122
-
Computations of Standard Binding Free Energies with Molecular Dynamics Simulations
-
Deng, Y.; Roux, B. Computations of Standard Binding Free Energies with Molecular Dynamics Simulations J. Phys. Chem. B 2009, 113, 2234-2246
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 2234-2246
-
-
Deng, Y.1
Roux, B.2
-
14
-
-
77952390528
-
Basic Ingredients of Free Energy Calculations
-
Christ, C. D.; Mark, A. E.; van Gunsteren, W. F. Basic Ingredients of Free Energy Calculations J. Comput. Chem. 2010, 31, 1569-1582
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 1569-1582
-
-
Christ, C.D.1
Mark, A.E.2
Van Gunsteren, W.F.3
-
17
-
-
84890794190
-
Frontiers in Free-Energy Calculations of Biological Systems
-
Chipot, C. Frontiers in Free-Energy Calculations of Biological Systems Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2013, 4, 71-89
-
(2013)
Wiley Interdiscip. Rev.: Comput. Mol. Sci.
, vol.4
, pp. 71-89
-
-
Chipot, C.1
-
18
-
-
0141990949
-
Extremely Precise Free Energy Calculations of Amino Acid Side Chain Analogs: Comparison of Common Molecular Mechanics Force Fields for Proteins
-
Shirts, M. R.; Pitera, J. W.; Swope, W. C.; Pande, V. S. Extremely Precise Free Energy Calculations of Amino Acid Side Chain Analogs: Comparison of Common Molecular Mechanics Force Fields for Proteins J. Chem. Phys. 2003, 119, 5740-5761
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 5740-5761
-
-
Shirts, M.R.1
Pitera, J.W.2
Swope, W.C.3
Pande, V.S.4
-
19
-
-
7544232432
-
Hydration of Amino Acid Side Chains: Nonpolar and Electrostatic Contributions Calculated from Staged Molecular Dynamics Free Energy Simulations with Explicit Water Molecules
-
Deng, Y.; Roux, B. Hydration of Amino Acid Side Chains: Nonpolar and Electrostatic Contributions Calculated from Staged Molecular Dynamics Free Energy Simulations with Explicit Water Molecules J. Phys. Chem. B 2004, 108, 16567-16576
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 16567-16576
-
-
Deng, Y.1
Roux, B.2
-
20
-
-
0034730366
-
Modeling Protein-Small Molecule Interactions: Structure and Thermodynamics of Noble Gases Binding in a Cavity in Mutant Phage T4 Lysozyme L99A
-
Mann, G.; Hermans, J. Modeling Protein-Small Molecule Interactions: Structure and Thermodynamics of Noble Gases Binding in a Cavity in Mutant Phage T4 Lysozyme L99A J. Mol. Biol. 2000, 302, 979-989
-
(2000)
J. Mol. Biol.
, vol.302
, pp. 979-989
-
-
Mann, G.1
Hermans, J.2
-
21
-
-
33646415982
-
Direct Calculation of the Binding Free Energies of FKBP Ligands
-
Fujitani, H.; Tanida, Y.; Ito, M.; Jayachandran, G.; Snow, C. D.; Shirts, M. R.; Sorin, E. J.; Pande, V. S. Direct Calculation of the Binding Free Energies of FKBP Ligands J. Chem. Phys. 2005, 123, 084108
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 084108
-
-
Fujitani, H.1
Tanida, Y.2
Ito, M.3
Jayachandran, G.4
Snow, C.D.5
Shirts, M.R.6
Sorin, E.J.7
Pande, V.S.8
-
22
-
-
18744411546
-
Free Energies of Ligand Binding for Structurally Diverse Compounds
-
Oostenbrink, C.; van Gunsteren, W. F. Free Energies of Ligand Binding for Structurally Diverse Compounds Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 6750-6754
-
(2005)
Proc. Natl. Acad. Sci. U. S. A.
, vol.102
, pp. 6750-6754
-
-
Oostenbrink, C.1
Van Gunsteren, W.F.2
-
23
-
-
33748252631
-
On the Use of Orientational Restraints and Symmetry Corrections in Alchemical Free Energy Calculations
-
Mobley, D. L.; Chodera, J. D.; Dill, K. A. On the Use of Orientational Restraints and Symmetry Corrections in Alchemical Free Energy Calculations J. Chem. Phys. 2006, 125, 084902
-
(2006)
J. Chem. Phys.
, vol.125
, pp. 084902
-
-
Mobley, D.L.1
Chodera, J.D.2
Dill, K.A.3
-
24
-
-
33749238080
-
Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant
-
Deng, Y.; Roux, B. Calculation of Standard Binding Free Energies: Aromatic Molecules in the T4 Lysozyme L99A Mutant J. Chem. Theory Comput. 2006, 2, 1255-1273
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 1255-1273
-
-
Deng, Y.1
Roux, B.2
-
25
-
-
33749532284
-
Absolute Binding Free Energy Calculations Using Molecular Dynamics Simulations with Restraining Potentials
-
Wang, J.; Deng, Y.; Roux, B. Absolute Binding Free Energy Calculations Using Molecular Dynamics Simulations with Restraining Potentials Biophys. J. 2006, 91, 2798-2814
-
(2006)
Biophys. J.
, vol.91
, pp. 2798-2814
-
-
Wang, J.1
Deng, Y.2
Roux, B.3
-
26
-
-
33947397110
-
Comparison of Charge Models for Fixed-Charge Force Fields: Small-Molecule Hydration Free Energies in Explicit Solvent
-
Mobley, D.; Dumont, E.; Chodera, J.; Dill, K. Comparison of Charge Models for Fixed-Charge Force Fields: Small-Molecule Hydration Free Energies in Explicit Solvent J. Phys. Chem. B 2007, 111, 2242-2254
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 2242-2254
-
-
Mobley, D.1
Dumont, E.2
Chodera, J.3
Dill, K.4
-
27
-
-
34547110591
-
Predicting Absolute Ligand Binding Free Energies to a Simple Model Site
-
Mobley, D. L.; Graves, A. P.; Chodera, J. D.; McReynolds, A. C.; Shoichet, B. K.; Dill, K. A. Predicting Absolute Ligand Binding Free Energies to a Simple Model Site J. Mol. Biol. 2007, 371, 1118-1134
-
(2007)
J. Mol. Biol.
, vol.371
, pp. 1118-1134
-
-
Mobley, D.L.1
Graves, A.P.2
Chodera, J.D.3
McReynolds, A.C.4
Shoichet, B.K.5
Dill, K.A.6
-
28
-
-
0000127140
-
Methods for Estimating the Configuratonal Entropy of Macromolecules
-
Karplus, M.; Kushick, J. N. Methods for Estimating the Configuratonal Entropy of Macromolecules Macromolecules 1981, 14, 325-332
-
(1981)
Macromolecules
, vol.14
, pp. 325-332
-
-
Karplus, M.1
Kushick, J.N.2
-
29
-
-
0030887944
-
Inclusion of Loss of Translational and Rotational Freedom in Theoretical Estimates of Free Energies of Binding. Application to a Complex of Benzene and Mutant T4 Lysozyme
-
Hermans, J.; Wang, L. Inclusion of Loss of Translational and Rotational Freedom in Theoretical Estimates of Free Energies of Binding. Application to a Complex of Benzene and Mutant T4 Lysozyme J. Am. Chem. Soc. 1997, 119, 2707-2714
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 2707-2714
-
-
Hermans, J.1
Wang, L.2
-
30
-
-
0036677555
-
On the Calculation of Absolute Macromolecular Binding Free Energies
-
Luo, H.; Sharp, K. On the Calculation of Absolute Macromolecular Binding Free Energies Proc. Natl. Acad. Sci. U. S. A. 2002, 99, 10399-10404
-
(2002)
Proc. Natl. Acad. Sci. U. S. A.
, vol.99
, pp. 10399-10404
-
-
Luo, H.1
Sharp, K.2
-
31
-
-
17044372385
-
Absolute and Relative Entropies from Computer Simulation with Applications to Ligand Binding
-
Carlson, J.; Aqvist, J. Absolute and Relative Entropies from Computer Simulation with Applications to Ligand Binding J. Phys. Chem. B 2005, 109, 6448-6456
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 6448-6456
-
-
Carlson, J.1
Aqvist, J.2
-
32
-
-
25844507555
-
The Entropic Cost of Protein-Protein Association
-
Minh, D. D. L.; Bui, J. M.; Chang, C.; Jain, T.; Swanson, J. M. J.; McCammon, J. A. The Entropic Cost of Protein-Protein Association Biophys. J. 2005, 89, L25-L27
-
(2005)
Biophys. J.
, vol.89
-
-
Minh, D.D.L.1
Bui, J.M.2
Chang, C.3
Jain, T.4
Swanson, J.M.J.5
McCammon, J.A.6
-
33
-
-
33846822002
-
Ligand Configurational Entropy and Protein Binding
-
Chang, C. A.; Chen, W.; Gilson, M. K. Ligand Configurational Entropy and Protein Binding Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 1534-1539
-
(2007)
Proc. Natl. Acad. Sci. U. S. A.
, vol.104
, pp. 1534-1539
-
-
Chang, C.A.1
Chen, W.2
Gilson, M.K.3
-
34
-
-
84872165531
-
Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?
-
Gumbart, J. C.; Roux, B.; Chipot, C. Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy? J. Chem. Theory Comput. 2013, 9, 794-802
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 794-802
-
-
Gumbart, J.C.1
Roux, B.2
Chipot, C.3
-
35
-
-
18744372751
-
Calculation of Absolute Protein-Ligand Binding Free Energy from Computer Simulations
-
Woo, H.; Roux, B. Calculation of Absolute Protein-Ligand Binding Free Energy from Computer Simulations Proc. Natl. Acad. Sci. U. S. A. 2005, 102, 6825-6830
-
(2005)
Proc. Natl. Acad. Sci. U. S. A.
, vol.102
, pp. 6825-6830
-
-
Woo, H.1
Roux, B.2
-
36
-
-
42449129769
-
Potential of Mean Force Calculations of Ligand Binding to Ion Channels from Jarzynski's Equality and Umbrella Sampling
-
Bastug, T.; Chen, P. C.; Patra, S. M.; Kuyucak, S. Potential of Mean Force Calculations of Ligand Binding to Ion Channels from Jarzynski's Equality and Umbrella Sampling J. Chem. Phys. 2008, 128, 155104
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 155104
-
-
Bastug, T.1
Chen, P.C.2
Patra, S.M.3
Kuyucak, S.4
-
37
-
-
67649386435
-
Mechanism and Energetics of Charybdotoxin Unbinding from a Potassium Channel from Molecular Dynamics Simulations
-
Chen, P. C.; Kuyucak, S. Mechanism and Energetics of Charybdotoxin Unbinding from a Potassium Channel from Molecular Dynamics Simulations Biophys. J. 2009, 96, 2577-2588
-
(2009)
Biophys. J.
, vol.96
, pp. 2577-2588
-
-
Chen, P.C.1
Kuyucak, S.2
-
38
-
-
65249154272
-
Standard Free Energy of Binding form a One-Dimensional Potential of Mean Force
-
Doudou, S.; Burton, N. A.; Henchman, R. H. Standard Free Energy of Binding form a One-Dimensional Potential of Mean Force J. Chem. Theory Comput. 2009, 5, 909-918
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 909-918
-
-
Doudou, S.1
Burton, N.A.2
Henchman, R.H.3
-
39
-
-
79959663208
-
Accurate Determination of the Binding Free Energy for KcsA-Charybdotoxin Complex from the Potential of Mean Force Calculations with Restraints
-
Chen, P. C.; Kuyucak, S. Accurate Determination of the Binding Free Energy for KcsA-Charybdotoxin Complex from the Potential of Mean Force Calculations with Restraints Biophys. J. 2011, 100, 2466-2474
-
(2011)
Biophys. J.
, vol.100
, pp. 2466-2474
-
-
Chen, P.C.1
Kuyucak, S.2
-
40
-
-
79959190343
-
Optimized Potential of Mean Force Calculations for Standard Binding Free Energies
-
Buch, I.; Sadiq, S. K.; De Fabritiis, G. Optimized Potential of Mean Force Calculations for Standard Binding Free Energies J. Chem. Theory Comput. 2011, 7, 1765-1772
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 1765-1772
-
-
Buch, I.1
Sadiq, S.K.2
De Fabritiis, G.3
-
41
-
-
84867391072
-
Structural Basis of the Selective Block of Kv1.2 by Maurotoxin from Computer Simulations
-
Chen, R.; Chung, S. H. Structural Basis of the Selective Block of Kv1.2 by Maurotoxin from Computer Simulations PLoS One 2012, 7 e47253
-
(2012)
PLoS One
, vol.7
-
-
Chen, R.1
Chung, S.H.2
-
42
-
-
84860307772
-
Affinity and Selectivity of ShK Toxin for the Kv1 Potassium Channels from Free Energy Simulations
-
Rashid, M. H.; Kuyucak, S. Affinity and Selectivity of ShK Toxin for the Kv1 Potassium Channels from Free Energy Simulations J. Phys. Chem. B 2012, 116, 4812-4822
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 4812-4822
-
-
Rashid, M.H.1
Kuyucak, S.2
-
43
-
-
84882330872
-
Efficient Determination of Protein-Protein Standard Binding Free Energies from First Principles
-
Gumbart, J. C.; Roux, B.; Chipot, C. Efficient Determination of Protein-Protein Standard Binding Free Energies from First Principles J. Chem. Theory Comput. 2013, 9, 3789-3798
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 3789-3798
-
-
Gumbart, J.C.1
Roux, B.2
Chipot, C.3
-
44
-
-
79952354508
-
The Hidden Energetics of Ligand Binding and Activation in a Glutamate Receptor
-
Lau, A. Y.; Roux, B. The Hidden Energetics of Ligand Binding and Activation in a Glutamate Receptor Nat. Struct. Mol. Biol. 2011, 18, 283-287
-
(2011)
Nat. Struct. Mol. Biol.
, vol.18
, pp. 283-287
-
-
Lau, A.Y.1
Roux, B.2
-
45
-
-
0035950796
-
Can Absolute Free Energies of Association Be Estimated from Molecular Mechanical Simulations? the Biotin-Streptavidin System Revisited
-
Dixit, S. B; Chipot, C. Can Absolute Free Energies of Association Be Estimated from Molecular Mechanical Simulations? The Biotin-Streptavidin System Revisited J. Phys. Chem. A 2001, 105, 9795-9799
-
(2001)
J. Phys. Chem. A
, vol.105
, pp. 9795-9799
-
-
Dixit, S.B.1
Chipot, C.2
-
46
-
-
84886717690
-
Blind Prediction of Charged Ligand Binding Affinities in a Model Binding Site
-
Rocklin, G. J.; Boyce, S. E.; Fischer, M.; Fish, I.; Mobley, D. L.; Shoichet, B. K.; Dill, K. A. Blind Prediction of Charged Ligand Binding Affinities in a Model Binding Site J. Mol. Biol. 2013, 425, 4569-4583
-
(2013)
J. Mol. Biol.
, vol.425
, pp. 4569-4583
-
-
Rocklin, G.J.1
Boyce, S.E.2
Fischer, M.3
Fish, I.4
Mobley, D.L.5
Shoichet, B.K.6
Dill, K.A.7
-
49
-
-
84892388463
-
A Potent and Selective Peptide Blocker of the Kv1.3 Channel: Prediction from Free-Energy Simulations and Experimental Confirmation
-
Rashid, M. H.; Heinzelmann, G.; Huq, R.; Tajhya, R. B.; Chang, S. C.; Chhabra, S.; Pennington, M. W.; Beeton, C.; Norton, R. S.; Kuyucak, S. A Potent and Selective Peptide Blocker of the Kv1.3 Channel: Prediction from Free-Energy Simulations and Experimental Confirmation PLoS One 2013, 8 e78712
-
(2013)
PLoS One
, vol.8
-
-
Rashid, M.H.1
Heinzelmann, G.2
Huq, R.3
Tajhya, R.B.4
Chang, S.C.5
Chhabra, S.6
Pennington, M.W.7
Beeton, C.8
Norton, R.S.9
Kuyucak, S.10
-
50
-
-
85007947085
-
Effects of Sodium Glutamate on the Nervous System
-
Hayashi, T. Effects of Sodium Glutamate on the Nervous System Keio J. Med. 1954, 3, 183-192
-
(1954)
Keio J. Med.
, vol.3
, pp. 183-192
-
-
Hayashi, T.1
-
51
-
-
0037832971
-
Ligands for Glutamate Receptors: Design and Therapeutic Prospects
-
Brauner-Osborne, H.; Egebjerg, J.; Nielsen, E. O.; Madsen, U.; Krogsgaard-Larsen, P. Ligands for Glutamate Receptors: Design and Therapeutic Prospects J. Med. Chem. 2000, 43, 2609-2645
-
(2000)
J. Med. Chem.
, vol.43
, pp. 2609-2645
-
-
Brauner-Osborne, H.1
Egebjerg, J.2
Nielsen, E.O.3
Madsen, U.4
Krogsgaard-Larsen, P.5
-
52
-
-
34249098796
-
AMPA Receptor Potentiators: Application for Depression and Parkinson's Disease
-
O'Neill, M. J.; Witkin, J. M. AMPA Receptor Potentiators: Application for Depression and Parkinson's Disease Curr. Drug Targets 2007, 8, 603-620
-
(2007)
Curr. Drug Targets
, vol.8
, pp. 603-620
-
-
O'Neill, M.J.1
Witkin, J.M.2
-
53
-
-
66149128065
-
Mechanisms of Antagonism of the GluR2 AMPA Receptor: Structure and Dynamics of the Complex of Two Willardiine Antagonists with the Glutamate Binding Domain
-
Ahmed, A. H.; Thompson, M. D.; Fenwick, M. K.; Romero, B.; Loh, A. P.; Jane, D. E.; Sondermann, H.; Oswald, R. E. Mechanisms of Antagonism of the GluR2 AMPA Receptor: Structure and Dynamics of the Complex of Two Willardiine Antagonists with the Glutamate Binding Domain Biochemistry 2009, 48, 3894-3903
-
(2009)
Biochemistry
, vol.48
, pp. 3894-3903
-
-
Ahmed, A.H.1
Thompson, M.D.2
Fenwick, M.K.3
Romero, B.4
Loh, A.P.5
Jane, D.E.6
Sondermann, H.7
Oswald, R.E.8
-
54
-
-
0033636314
-
Mechanisms for Activation and Antagonism of an AMPA-Sensitive Glutamate Receptor: Crystal Structures of the GluR2 Ligand Binding Core
-
Armstrong, N.; Gouaux, E. Mechanisms for Activation and Antagonism of an AMPA-Sensitive Glutamate Receptor: Crystal Structures of the GluR2 Ligand Binding Core Neuron 2000, 28, 165-181
-
(2000)
Neuron
, vol.28
, pp. 165-181
-
-
Armstrong, N.1
Gouaux, E.2
-
55
-
-
0036968894
-
Structural Basis for AMPA Receptor Activation and Ligand Selectivity: Crystal Structures of Five Agonist Complexes with the GluR2 Ligand-Binding Core
-
Hogner, A.; Kastrup, J. S.; Jin, R.; Liljefors, T.; Mayer, M. L.; Egebjerg, J.; Larsen, I. K.; Gouaux, E. Structural Basis for AMPA Receptor Activation and Ligand Selectivity: Crystal Structures of Five Agonist Complexes with the GluR2 Ligand-Binding Core J. Mol. Biol. 2002, 322, 93-109
-
(2002)
J. Mol. Biol.
, vol.322
, pp. 93-109
-
-
Hogner, A.1
Kastrup, J.S.2
Jin, R.3
Liljefors, T.4
Mayer, M.L.5
Egebjerg, J.6
Larsen, I.K.7
Gouaux, E.8
-
56
-
-
38449097102
-
TARP Auxiliary Subunits Switch AMPA Receptor Antagonists into Partial Agonists
-
Menuz, K.; Stroud, R. M.; Nicoll, R. A.; Hays, F. A. TARP Auxiliary Subunits Switch AMPA Receptor Antagonists into Partial Agonists Science 2007, 318, 815-817
-
(2007)
Science
, vol.318
, pp. 815-817
-
-
Menuz, K.1
Stroud, R.M.2
Nicoll, R.A.3
Hays, F.A.4
-
57
-
-
84875433653
-
Computational Study of Synthetic Agonist Ligands of Ionotropic Glutamate Receptors
-
Wolter, T.; Steinbrecher, T.; Elstner, M. Computational Study of Synthetic Agonist Ligands of Ionotropic Glutamate Receptors PLoS One 2013, 8 e58774
-
(2013)
PLoS One
, vol.8
-
-
Wolter, T.1
Steinbrecher, T.2
Elstner, M.3
-
58
-
-
84873037298
-
CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application
-
Jo, S.; Jiang, W.; Lee, H. S.; Roux, B.; Im, W. CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application J. Chem. Inf. Model. 2012, 53, 267-277
-
(2012)
J. Chem. Inf. Model.
, vol.53
, pp. 267-277
-
-
Jo, S.1
Jiang, W.2
Lee, H.S.3
Roux, B.4
Im, W.5
-
59
-
-
36449002336
-
Separation-Shifted Scaling, a New Scaling Method for Lennard-Jones Interactions in Thermodynamic Integration
-
Zacharias, M.; Straatsma, T. P.; McCammon, J. A. Separation-Shifted Scaling, a New Scaling Method for Lennard-Jones Interactions in Thermodynamic Integration J. Chem. Phys. 1994, 100, 9025-9031
-
(1994)
J. Chem. Phys.
, vol.100
, pp. 9025-9031
-
-
Zacharias, M.1
Straatsma, T.P.2
McCammon, J.A.3
-
60
-
-
0032173123
-
Precision and Accuracy of Staged Free-Energy Perturbation Methods for Computing the Chemical Potential by Molecular Simulation
-
Kofke, D. A.; Cummings, P. T. Precision and Accuracy of Staged Free-Energy Perturbation Methods for Computing the Chemical Potential by Molecular Simulation Fluid Phase Equilib. 1998, 150, 41-49
-
(1998)
Fluid Phase Equilib.
, vol.150
, pp. 41-49
-
-
Kofke, D.A.1
Cummings, P.T.2
-
61
-
-
5244304444
-
Efficient Estimation of Free Energy Differences from Monte Carlo Data
-
Bennett, C. H. Efficient Estimation of Free Energy Differences from Monte Carlo Data J. Comput. Phys. 1976, 22, 245-268
-
(1976)
J. Comput. Phys.
, vol.22
, pp. 245-268
-
-
Bennett, C.H.1
-
62
-
-
77955577540
-
Good Practices in Free-Energy Calculations
-
Pohorille, A.; Jarzynski, C.; Chipot, C. Good Practices in Free-Energy Calculations J. Phys. Chem. B 2010, 114, 10235-10253
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 10235-10253
-
-
Pohorille, A.1
Jarzynski, C.2
Chipot, C.3
-
63
-
-
36049017659
-
Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change
-
Mobley, D. L.; Chodera, J. D.; Dill, K. A. Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change J. Chem. Theory Comput. 2007, 3, 1231-1235
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 1231-1235
-
-
Mobley, D.L.1
Chodera, J.D.2
Dill, K.A.3
-
64
-
-
84986519238
-
The Weighted Histogram Analaysis Method for Free-Energy Calculations on Biomolecules. I. The Method
-
Kumar, S. J.; Rosenberg, M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. The Weighted Histogram Analaysis Method for Free-Energy Calculations on Biomolecules. I. The Method J. Comput. Chem. 1992, 13, 1011-1021
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 1011-1021
-
-
Kumar, S.J.1
Rosenberg, M.2
Bouzida, D.3
Swendsen, R.H.4
Kollman, P.A.5
-
65
-
-
0029878720
-
VMD - Visual Molecular Dynamics
-
Humphrey, W.; Dalke, A.; Schulten, K. VMD-Visual Molecular Dynamics J. Mol. Graphics 1996, 14, 33-38
-
(1996)
J. Mol. Graphics
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
66
-
-
27344436659
-
Scalable Molecular Dynamics with NAMD
-
Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. Scalable Molecular Dynamics with NAMD J. Comput. Chem. 2005, 26, 1781-1802
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
67
-
-
76249087938
-
CHARMM General Force Field: A Force Field for Drug-Like Molecules Compatible with the CHARMM All-Atom Additive Biological Force Field
-
Vanommeslaeghe, K.; Hatcher, E.; Acharya, C.; Kundu, S.; Zhong, S.; Shim, J.; Darian, E.; Guvench, O.; Lopes, P.; Vorobyov, I. CHARMM General Force Field: A Force Field for Drug-Like Molecules Compatible with the CHARMM All-Atom Additive Biological Force Field J. Comput. Chem. 2010, 31, 671-690
-
(2010)
J. Comput. Chem.
, vol.31
, pp. 671-690
-
-
Vanommeslaeghe, K.1
Hatcher, E.2
Acharya, C.3
Kundu, S.4
Zhong, S.5
Shim, J.6
Darian, E.7
Guvench, O.8
Lopes, P.9
Vorobyov, I.10
-
68
-
-
36449007836
-
Constant Pressure Molecular Dynamics: The Langevin Piston Method
-
Feller, S.; Zhang, Y.; Pastor, R.; Brooks, B. Constant Pressure Molecular Dynamics: The Langevin Piston Method J. Chem. Phys. 1995, 103, 4613-4621
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 4613-4621
-
-
Feller, S.1
Zhang, Y.2
Pastor, R.3
Brooks, B.4
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