-
1
-
-
43649103922
-
(Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding
-
Baron R., McCammon J.A. (Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding. ChemPhysChem 2008, 9:983-988.
-
(2008)
ChemPhysChem
, vol.9
, pp. 983-988
-
-
Baron, R.1
McCammon, J.A.2
-
2
-
-
70349664218
-
A computational analysis of ATP binding of SV40 large tumor antigen helicase motor
-
Shi Y., Liu H., Gai D., Ma J., Chen X.S. A computational analysis of ATP binding of SV40 large tumor antigen helicase motor. PLoS Comput Biol 2009, 5:e1000514.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Shi, Y.1
Liu, H.2
Gai, D.3
Ma, J.4
Chen, X.S.5
-
4
-
-
33646588326
-
Conformational equilibrium of cytochrome p450 bm-3 complexed with n-palmitoylglycine: a replica exchange molecular dynamics study
-
Ravindranathan K.P., Gallicchio E., Friesner R.A., McDermott A.E., Levy R.M. Conformational equilibrium of cytochrome p450 bm-3 complexed with n-palmitoylglycine: a replica exchange molecular dynamics study. J Am Chem Soc 2006, 128:5786-5791.
-
(2006)
J Am Chem Soc
, vol.128
, pp. 5786-5791
-
-
Ravindranathan, K.P.1
Gallicchio, E.2
Friesner, R.A.3
McDermott, A.E.4
Levy, R.M.5
-
5
-
-
79958862887
-
Free-energy calculations in structure-based drug design
-
Brown Drug Design-Structure- and Ligand-Based Approaches, Cambridge University Press
-
Shirts MR, Mobley DL, Scott P: Free-energy calculations in structure-based drug design. Brown Drug Design-Structure- and Ligand-Based Approaches, Cambridge University Press; 2010:61-86.
-
(2010)
, pp. 61-86
-
-
Shirts, M.R.1
Mobley, D.L.2
Scott, P.3
-
6
-
-
70349100806
-
Theory of free energy and entropy in noncovalent binding
-
Zhou H.-X., Gilson M.K. Theory of free energy and entropy in noncovalent binding. Chem Rev 2009, 109:4092-4107.
-
(2009)
Chem Rev
, vol.109
, pp. 4092-4107
-
-
Zhou, H.-X.1
Gilson, M.K.2
-
7
-
-
67649225348
-
Efficient drug lead discovery and optimization
-
Jorgensen W.L. Efficient drug lead discovery and optimization. Acc Chem Res 2009, 42:724-733.
-
(2009)
Acc Chem Res
, vol.42
, pp. 724-733
-
-
Jorgensen, W.L.1
-
8
-
-
64049102289
-
Binding of small-molecule ligands to proteins: " what you see" is not always " what you get"
-
Mobley D.L., Dill K.A. Binding of small-molecule ligands to proteins: " what you see" is not always " what you get" Structure 2009, 17:489-498.
-
(2009)
Structure
, vol.17
, pp. 489-498
-
-
Mobley, D.L.1
Dill, K.A.2
-
9
-
-
77955663115
-
Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations
-
Michel J., Essex J.W. Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations. J Comput Aided Mol Des 2010, 24:639-658.
-
(2010)
J Comput Aided Mol Des
, vol.24
, pp. 639-658
-
-
Michel, J.1
Essex, J.W.2
-
11
-
-
60349109713
-
Computational evaluation of protein-small molecule binding
-
Guvench O., MacKerell A.D. Computational evaluation of protein-small molecule binding. Curr Opin Struct Biol 2009, 19:56-61.
-
(2009)
Curr Opin Struct Biol
, vol.19
, pp. 56-61
-
-
Guvench, O.1
MacKerell, A.D.2
-
12
-
-
34547661861
-
Comparative performance of several flexible docking programs and scoring functions: enrichment studies for a diverse set of pharmaceutically relevant targets
-
Zhou Z., Felts A.K., Friesner R.A., Levy R.M. Comparative performance of several flexible docking programs and scoring functions: enrichment studies for a diverse set of pharmaceutically relevant targets. J Chem Inf Model 2007, 47:1599-1608.
-
(2007)
J Chem Inf Model
, vol.47
, pp. 1599-1608
-
-
Zhou, Z.1
Felts, A.K.2
Friesner, R.A.3
Levy, R.M.4
-
13
-
-
77956607370
-
Binding energy distribution analysis method (BEDAM) for estimation of protein-ligand binding affinities
-
Gallicchio E., Lapelosa M., Levy R.M. Binding energy distribution analysis method (BEDAM) for estimation of protein-ligand binding affinities. J Chem Theor Comput 2010, 6:2961-2977.
-
(2010)
J Chem Theor Comput
, vol.6
, pp. 2961-2977
-
-
Gallicchio, E.1
Lapelosa, M.2
Levy, R.M.3
-
14
-
-
76649121530
-
Dynamical aspects of molecular recognition
-
Karplus M. Dynamical aspects of molecular recognition. J Mol Recognit 2010, 23:102-104.
-
(2010)
J Mol Recognit
, vol.23
, pp. 102-104
-
-
Karplus, M.1
-
15
-
-
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
-
16
-
-
18744372751
-
Calculation of absolute protein-ligand binding free energy from computer simulations
-
Woo H.-J., 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.-J.1
Roux, B.2
-
17
-
-
52949088587
-
Statistically optimal analysis of samples from multiple equilibrium states
-
Shirts M.R., Chodera J.D. Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys 2008, 129:124105.
-
(2008)
J Chem Phys
, vol.129
, pp. 124105
-
-
Shirts, M.R.1
Chodera, J.D.2
-
18
-
-
0346255348
-
Enhanced configurational sampling in binding free-energy calculations
-
Woods C.J., Essex J.W., King M.A. Enhanced configurational sampling in binding free-energy calculations. J Phys Chem B 2003, 107:13711-13718.
-
(2003)
J Phys Chem B
, vol.107
, pp. 13711-13718
-
-
Woods, C.J.1
Essex, J.W.2
King, M.A.3
-
19
-
-
67650495212
-
Lambda-dynamics free energy simulation methods
-
Knight J.L., Brooks C.L. Lambda-dynamics free energy simulation methods. J Comput Chem 2009, 30:1692-1700.
-
(2009)
J Comput Chem
, vol.30
, pp. 1692-1700
-
-
Knight, J.L.1
Brooks, C.L.2
-
20
-
-
73949121918
-
Computation of absolute hydration and binding free energy with free energy perturbation distributed replica-exchange molecular dynamics
-
Jiang W., Hodoscek M., Roux B. Computation of absolute hydration and binding free energy with free energy perturbation distributed replica-exchange molecular dynamics. J Chem Theor Comput 2009, 5:2583-2588.
-
(2009)
J Chem Theor Comput
, vol.5
, pp. 2583-2588
-
-
Jiang, W.1
Hodoscek, M.2
Roux, B.3
-
21
-
-
79953099240
-
Lambda hopping: an efficient replica exchange-based sampling method for relative free energy perturbation calculations
-
In preparation
-
Wu Y, Lin T, Shelley JC, Sherman W: Lambda hopping: an efficient replica exchange-based sampling method for relative free energy perturbation calculations. In preparation.
-
-
-
Wu, Y.1
Lin, T.2
Shelley, J.C.3
Sherman, W.4
-
22
-
-
70349286319
-
Efficient free energy calculations for compounds with multiple stable conformations separated by high energy barriers
-
Hritz J., Oostenbrink C. Efficient free energy calculations for compounds with multiple stable conformations separated by high energy barriers. J Phys Chem B 2009, 113:12711-12720.
-
(2009)
J Phys Chem B
, vol.113
, pp. 12711-12720
-
-
Hritz, J.1
Oostenbrink, C.2
-
23
-
-
77952390528
-
Basic ingredients of free energy calculations: a review
-
Christ C.D., Mark A.E., van Gunsteren W.F. Basic ingredients of free energy calculations: a review. 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
-
24
-
-
33748267063
-
Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics
-
Jayachandran G., Shirts M.R., Park S., Pande V.S. Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics. J Chem Phys 2006, 125:084901.
-
(2006)
J Chem Phys
, vol.125
, pp. 084901
-
-
Jayachandran, G.1
Shirts, M.R.2
Park, S.3
Pande, V.S.4
-
25
-
-
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
-
26
-
-
70449522914
-
Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site
-
Boyce S.E., Mobley D.L., Rocklin G.J., Graves A.P., Dill K.A., Shoichet B.K. Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J Mol Biol 2009, 394:747-763.
-
(2009)
J Mol Biol
, vol.394
, pp. 747-763
-
-
Boyce, S.E.1
Mobley, D.L.2
Rocklin, G.J.3
Graves, A.P.4
Dill, K.A.5
Shoichet, B.K.6
-
27
-
-
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
-
28
-
-
3042736867
-
On the theory of noncovalent binding
-
Mihailescu M., Gilson M.K. On the theory of noncovalent binding. Biophys J 2004, 87:23-36.
-
(2004)
Biophys J
, vol.87
, pp. 23-36
-
-
Mihailescu, M.1
Gilson, M.K.2
-
30
-
-
77957231785
-
Induced fit, conformational selection and independent dynamic segments: an extended view of binding events
-
Csermely P, Palotai R, Nussinov R: Induced fit, conformational selection and independent dynamic segments: an extended view of binding events. Trends Biochem Sci 2010, 35:539-546.
-
(2010)
Trends Biochem Sci
, vol.35
, pp. 539-546
-
-
Csermely, P.1
Palotai, R.2
Nussinov, R.3
-
31
-
-
77649339799
-
Antigenic characteristics of rhinovirus chimeras designed in silico for enhanced presentation of HIV-1 gp41 epitopes
-
Lapelosa M., Arnold G.F., Gallicchio E., Arnold E., Levy R.M. Antigenic characteristics of rhinovirus chimeras designed in silico for enhanced presentation of HIV-1 gp41 epitopes. J Mol Biol 2010, 397:752-766.
-
(2010)
J Mol Biol
, vol.397
, pp. 752-766
-
-
Lapelosa, M.1
Arnold, G.F.2
Gallicchio, E.3
Arnold, E.4
Levy, R.M.5
-
32
-
-
70450194691
-
Thermodynamic and structural effects of conformational constraints in protein-ligand interactions. Entropic paradoxy associated with ligand preorganization
-
DeLorbe J.E., Clements J.H., Teresk M.G., Benfield A.P., Plake H.R., Millspaugh L.E., Martin S.F. Thermodynamic and structural effects of conformational constraints in protein-ligand interactions. Entropic paradoxy associated with ligand preorganization. J Am Chem Soc 2009, 131:16758-16770.
-
(2009)
J Am Chem Soc
, vol.131
, pp. 16758-16770
-
-
DeLorbe, J.E.1
Clements, J.H.2
Teresk, M.G.3
Benfield, A.P.4
Plake, H.R.5
Millspaugh, L.E.6
Martin, S.F.7
-
33
-
-
35348821202
-
Virtual screening strategies in drug discovery
-
McInnes C. Virtual screening strategies in drug discovery. Curr Opin Chem Biol 2007, 11:494-502.
-
(2007)
Curr Opin Chem Biol
, vol.11
, pp. 494-502
-
-
McInnes, C.1
-
34
-
-
77749317221
-
Accounting for ligand conformational restriction in calculations of protein-ligand binding affinities
-
Gao C., Park M.-S., Stern H.A. Accounting for ligand conformational restriction in calculations of protein-ligand binding affinities. Biophys J 2010, 98:901-910.
-
(2010)
Biophys J
, vol.98
, pp. 901-910
-
-
Gao, C.1
Park, M.-S.2
Stern, H.A.3
-
35
-
-
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., et al. 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
-
36
-
-
33845335781
-
Towards predictive ligand design with free-energy based computational methods?
-
Foloppe N., Hubbard R. Towards predictive ligand design with free-energy based computational methods?. Curr Med Chem 2006, 13:3583-3608.
-
(2006)
Curr Med Chem
, vol.13
, pp. 3583-3608
-
-
Foloppe, N.1
Hubbard, R.2
-
37
-
-
70349755625
-
Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction
-
Yang C.-Y., Sun H., Chen J., Nikolovska-Coleska Z., Wang S. Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction. J Am Chem Soc 2009, 131:13709-13721.
-
(2009)
J Am Chem Soc
, vol.131
, pp. 13709-13721
-
-
Yang, C.-Y.1
Sun, H.2
Chen, J.3
Nikolovska-Coleska, Z.4
Wang, S.5
-
38
-
-
2342586724
-
Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding
-
Perola E., Charifson P.S. Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding. J Med Chem. 2004, 47:2499-2510.
-
(2004)
J Med Chem.
, vol.47
, pp. 2499-2510
-
-
Perola, E.1
Charifson, P.S.2
-
39
-
-
77950878170
-
Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting
-
Okumura H., Gallicchio E., Levy R.M. Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting. J Comput Chem 2010, 31:1357-1367.
-
(2010)
J Comput Chem
, vol.31
, pp. 1357-1367
-
-
Okumura, H.1
Gallicchio, E.2
Levy, R.M.3
-
40
-
-
36049017659
-
The 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. The confine-and-release method: obtaining correct binding free energies in the presence of protein conformational change. J Chem Theor Comput 2007, 3:1231-1235.
-
(2007)
J Chem Theor Comput
, vol.3
, pp. 1231-1235
-
-
Mobley, D.L.1
Chodera, J.D.2
Dill, K.A.3
-
41
-
-
77956574437
-
Free energy perturbation hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) for absolute ligand binding free energy calculations
-
Jiang W., Roux B. Free energy perturbation hamiltonian replica-exchange molecular dynamics (FEP/H-REMD) for absolute ligand binding free energy calculations. J Chem Theor Comput 2010, 6:2559-2565.
-
(2010)
J Chem Theor Comput
, vol.6
, pp. 2559-2565
-
-
Jiang, W.1
Roux, B.2
-
42
-
-
34247187356
-
Analysis of ligand-bound water molecules in high-resolution crystal structures of protein-ligand complexes
-
Lu Y., Wang R., Yang C.-Y., Wang S. Analysis of ligand-bound water molecules in high-resolution crystal structures of protein-ligand complexes. J Chem Inf Model 2007, 47:668-675.
-
(2007)
J Chem Inf Model
, vol.47
, pp. 668-675
-
-
Lu, Y.1
Wang, R.2
Yang, C.-Y.3
Wang, S.4
-
43
-
-
33846424559
-
Water at biomolecular binding interfaces
-
Li Z., Lazaridis T. Water at biomolecular binding interfaces. Phys Chem Chem Phys 2007, 9:573-581.
-
(2007)
Phys Chem Chem Phys
, vol.9
, pp. 573-581
-
-
Li, Z.1
Lazaridis, T.2
-
44
-
-
33845493850
-
Protein-ligand binding affinity predictions by implicit solvent simulations: a tool for lead optimization?
-
Essex
-
Michel, Julien M.L., Verdonk J.W., Essex Protein-ligand binding affinity predictions by implicit solvent simulations: a tool for lead optimization?. J Med Chem 2006, 49:7427-7439.
-
(2006)
J Med Chem
, vol.49
, pp. 7427-7439
-
-
Michel1
Julien, M.L.2
Verdonk, J.W.3
-
45
-
-
70149093410
-
Free energies and entropies of water molecules at the inhibitor-protein interface of dna gyrase
-
Yu H., Rick S.W. Free energies and entropies of water molecules at the inhibitor-protein interface of dna gyrase. J Am Chem Soc 2009, 131:6608-6613.
-
(2009)
J Am Chem Soc
, vol.131
, pp. 6608-6613
-
-
Yu, H.1
Rick, S.W.2
-
47
-
-
33847655150
-
Classification of water molecules in protein binding sites
-
Barillari C., Taylor J., Viner R., Essex J.W. Classification of water molecules in protein binding sites. J Am Chem Soc 2007, 129:2577-2587.
-
(2007)
J Am Chem Soc
, vol.129
, pp. 2577-2587
-
-
Barillari, C.1
Taylor, J.2
Viner, R.3
Essex, J.W.4
-
48
-
-
70350315092
-
Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization
-
Michel J., Tirado-Rives J., Jorgensen W.L. Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization. J Am Chem Soc 2009, 131:15403-15411.
-
(2009)
J Am Chem Soc
, vol.131
, pp. 15403-15411
-
-
Michel, J.1
Tirado-Rives, J.2
Jorgensen, W.L.3
-
49
-
-
70349683018
-
Prediction of the water content in protein binding sites
-
Michel J., Tirado-Rives J., Jorgensen W.L. Prediction of the water content in protein binding sites. J Phys Chem B 2009, 113:13337-13346.
-
(2009)
J Phys Chem B
, vol.113
, pp. 13337-13346
-
-
Michel, J.1
Tirado-Rives, J.2
Jorgensen, W.L.3
-
50
-
-
2942659093
-
Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method
-
Hamelberg D., McCammon A.J. Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method. J Am Chem Soc 2004, 126:7683-7689.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 7683-7689
-
-
Hamelberg, D.1
McCammon, A.J.2
-
51
-
-
77953502244
-
Dewetting transitions in protein cavities
-
Young T., Hua L., Huang X., Abel R., Friesner R., Berne B.J. Dewetting transitions in protein cavities. Proteins 2010, 78:1856-1869.
-
(2010)
Proteins
, vol.78
, pp. 1856-1869
-
-
Young, T.1
Hua, L.2
Huang, X.3
Abel, R.4
Friesner, R.5
Berne, B.J.6
-
52
-
-
33644527925
-
Thermodynamics of buried water clusters at a protein-ligand binding interface
-
Li Z., Lazaridis T. Thermodynamics of buried water clusters at a protein-ligand binding interface. J Phys Chem B 2006, 110:1464-1475.
-
(2006)
J Phys Chem B
, vol.110
, pp. 1464-1475
-
-
Li, Z.1
Lazaridis, T.2
-
53
-
-
40949163431
-
Role of the active-site solvent in the thermodynamics of factor Xa ligand binding
-
Robert A., Young T., Farid R., Berne B.J., Friesner R.A. Role of the active-site solvent in the thermodynamics of factor Xa ligand binding. J Am Chem Soc 2008, 130:2817-2831.
-
(2008)
J Am Chem Soc
, vol.130
, pp. 2817-2831
-
-
Robert, A.1
Young, T.2
Farid, R.3
Berne, B.J.4
Friesner, R.A.5
-
54
-
-
33846524439
-
Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding
-
Young T., Abel R., Kim B., Berne B.J., Friesner R.A. Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding. Proc Natl Acad Sci U S A 2007, 104:808-813.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 808-813
-
-
Young, T.1
Abel, R.2
Kim, B.3
Berne, B.J.4
Friesner, R.A.5
-
55
-
-
41049115037
-
Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations
-
Deng Y., Roux B. Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations. J Chem Phys 2008, 128:115103.
-
(2008)
J Chem Phys
, vol.128
, pp. 115103
-
-
Deng, Y.1
Roux, B.2
-
56
-
-
77954950739
-
Absolute binding free energy calculations of sparsomycin analogs to the bacterial ribosome
-
Ge X., Roux B. Absolute binding free energy calculations of sparsomycin analogs to the bacterial ribosome. J Phys Chem B 2010, 114:9525-9539.
-
(2010)
J Phys Chem B
, vol.114
, pp. 9525-9539
-
-
Ge, X.1
Roux, B.2
-
57
-
-
79953075221
-
Alchemical free energy methods for drug discovery: progress and challenges
-
doi:10.1016/j.sbi.2011.01.011
-
Chodera JD, Mobley DL, Shirts MR, Dixon RW, Branson K, Pande VS: Alchemical free energy methods for drug discovery: progress and challenges. Curr Opin Struct Biol, (2011), doi:10.1016/j.sbi.2011.01.011.
-
(2011)
Curr Opin Struct Biol
-
-
Chodera, J.D.1
Mobley, D.L.2
Shirts, M.R.3
Dixon, R.W.4
Branson, K.5
Pande, V.S.6
|