-
1
-
-
84883681327
-
Detection of dihydrofolate reductase conformational change by FRET using two fluorescent amino acids
-
Chen S, et al. (2013) Detection of dihydrofolate reductase conformational change by FRET using two fluorescent amino acids. J Am Chem Soc 135(35):12924-12927.
-
(2013)
J Am Chem Soc
, vol.135
, Issue.35
, pp. 12924-12927
-
-
Chen, S.1
-
2
-
-
3042660150
-
Structure, dynamics, and catalytic function of dihydrofolate reductase
-
Schnell JR, Dyson HJ, Wright PE (2004) Structure, dynamics, and catalytic function of dihydrofolate reductase. Annu Rev Biophys Biomol Struct 33:119-140.
-
(2004)
Annu Rev Biophys Biomol Struct
, vol.33
, pp. 119-140
-
-
Schnell, J.R.1
Dyson, H.J.2
Wright, P.E.3
-
3
-
-
71449103005
-
Hidden alternative structures of proline isomerase essential for catalysis
-
Fraser JS, et al. (2009) Hidden alternative structures of proline isomerase essential for catalysis. Nature 462(7273):669-673.
-
(2009)
Nature
, vol.462
, Issue.7273
, pp. 669-673
-
-
Fraser, J.S.1
-
4
-
-
36849048228
-
Intrinsic motions along an enzymatic reaction trajectory
-
Henzler-Wildman KA, et al. (2007) Intrinsic motions along an enzymatic reaction trajectory. Nature 450(7171):838-844.
-
(2007)
Nature
, vol.450
, Issue.7171
, pp. 838-844
-
-
Henzler-Wildman, K.A.1
-
6
-
-
37249032102
-
Dynamic personalities of proteins
-
Henzler-Wildman K, Kern D (2007) Dynamic personalities of proteins. Nature 450(7172):964-972.
-
(2007)
Nature
, vol.450
, Issue.7172
, pp. 964-972
-
-
Henzler-Wildman, K.1
Kern, D.2
-
7
-
-
15444362906
-
Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins
-
Whitten ST, García-Moreno E B, Hilser VJ (2005) Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins. Proc Natl Acad Sci USA 102(12):4282-4287.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, Issue.12
, pp. 4282-4287
-
-
Whitten, S.T.1
García-Moreno, E.B.2
Hilser, V.J.3
-
8
-
-
84883072253
-
Precision vs flexibility in GPCR signaling
-
Elgeti M, et al. (2013) Precision vs flexibility in GPCR signaling. J Am Chem Soc 135(33): 12305-12312.
-
(2013)
J Am Chem Soc
, vol.135
, Issue.33
, pp. 12305-12312
-
-
Elgeti, M.1
-
9
-
-
80053357815
-
Conformational changes in the G protein Gs induced by the β2 adrenergic receptor
-
Chung KY, et al. (2011) Conformational changes in the G protein Gs induced by the β2 adrenergic receptor. Nature 477(7366):611-615.
-
(2011)
Nature
, vol.477
, Issue.7366
, pp. 611-615
-
-
Chung, K.Y.1
-
10
-
-
84887620421
-
Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs
-
Dror RO, et al. (2013) Structural basis for modulation of a G-protein-coupled receptor by allosteric drugs. Nature 503(7475):295-299.
-
(2013)
Nature
, vol.503
, Issue.7475
, pp. 295-299
-
-
Dror, R.O.1
-
11
-
-
84923169971
-
Molecular dynamics and Monte Carlo simulations for protein-ligand binding and inhibitor design
-
Cole DJ, Tirado-Rives J, Jorgensen WL (2015) Molecular dynamics and Monte Carlo simulations for protein-ligand binding and inhibitor design. Biochim Biophys Acta 1850(5):966-971.
-
(2015)
Biochim Biophys Acta
, vol.1850
, Issue.5
, pp. 966-971
-
-
Cole, D.J.1
Tirado-Rives, J.2
Jorgensen, W.L.3
-
12
-
-
84873861097
-
Fluoroketone inhibition of Ca(2+)-independent phospholipase A2 through binding pocket association defined by hydrogen/deuterium exchange and molecular dynamics
-
Hsu YH, et al. (2013) Fluoroketone inhibition of Ca(2+)-independent phospholipase A2 through binding pocket association defined by hydrogen/deuterium exchange and molecular dynamics. J Am Chem Soc 135(4):1330-1337.
-
(2013)
J Am Chem Soc
, vol.135
, Issue.4
, pp. 1330-1337
-
-
Hsu, Y.H.1
-
13
-
-
84913603703
-
Insights into the role of Asp79(2.50) in β2 adrenergic receptor activation from molecular dynamics simulations
-
Ranganathan A, Dror RO, Carlsson J (2014) Insights into the role of Asp79(2.50) in β2 adrenergic receptor activation from molecular dynamics simulations. Biochemistry 53(46):7283-7296.
-
(2014)
Biochemistry
, vol.53
, Issue.46
, pp. 7283-7296
-
-
Ranganathan, A.1
Dror, R.O.2
Carlsson, J.3
-
14
-
-
33846524439
-
Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding
-
Young T, Abel R, Kim B, Berne BJ, Friesner RA (2007) Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding. Proc Natl Acad Sci USA 104(3):808-813.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, Issue.3
, pp. 808-813
-
-
Young, T.1
Abel, R.2
Kim, B.3
Berne, B.J.4
Friesner, R.A.5
-
15
-
-
84857782430
-
Validating the vitality strategy for fighting drug resistance
-
Singh N, Frushicheva MP, Warshel A (2012) Validating the vitality strategy for fighting drug resistance. Proteins 80(4):1110-1122.
-
(2012)
Proteins
, vol.80
, Issue.4
, pp. 1110-1122
-
-
Singh, N.1
Frushicheva, M.P.2
Warshel, A.3
-
16
-
-
77951210462
-
Absolute binding free energy calculations: On the accuracy of computational scoring of protein-ligand interactions
-
Singh N, Warshel A (2010) Absolute binding free energy calculations: On the accuracy of computational scoring of protein-ligand interactions. Proteins 78(7):1705-1723.
-
(2010)
Proteins
, vol.78
, Issue.7
, pp. 1705-1723
-
-
Singh, N.1
Warshel, A.2
-
17
-
-
2642569349
-
Probing flexibility and "induced-fit" phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations
-
Sotriffer CA, Krämer O, Klebe G (2004) Probing flexibility and "induced-fit" phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations. Proteins 56(1):52-66.
-
(2004)
Proteins
, vol.56
, Issue.1
, pp. 52-66
-
-
Sotriffer, C.A.1
Krämer, O.2
Klebe, G.3
-
18
-
-
0142011623
-
Flexible adaptations in the structure of the tRNA-modifying enzyme tRNA-guanine transglycosylase and their implications for substrate selectivity, reaction mechanism and structure-based drug design
-
Brenk R, Stubbs MT, Heine A, Reuter K, Klebe G (2003) Flexible adaptations in the structure of the tRNA-modifying enzyme tRNA-guanine transglycosylase and their implications for substrate selectivity, reaction mechanism and structure-based drug design. ChemBioChem 4(10):1066-1077.
-
(2003)
ChemBioChem
, vol.4
, Issue.10
, pp. 1066-1077
-
-
Brenk, R.1
Stubbs, M.T.2
Heine, A.3
Reuter, K.4
Klebe, G.5
-
19
-
-
0028367343
-
Analogous inhibitors of elastase do not always bind analogously
-
Mattos C, Rasmussen B, Ding X, Petsko GA, Ringe D (1994) Analogous inhibitors of elastase do not always bind analogously. Nat Struct Biol 1(1):55-58.
-
(1994)
Nat Struct Biol
, vol.1
, Issue.1
, pp. 55-58
-
-
Mattos, C.1
Rasmussen, B.2
Ding, X.3
Petsko, G.A.4
Ringe, D.5
-
20
-
-
0029016268
-
Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme
-
Morton A, Baase WA, Matthews BW (1995) Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme. Biochemistry 34(27):8564-8575.
-
(1995)
Biochemistry
, vol.34
, Issue.27
, pp. 8564-8575
-
-
Morton, A.1
Baase, W.A.2
Matthews, B.W.3
-
21
-
-
0029067489
-
Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: Linkage of dynamics and structural plasticity
-
Morton A, Matthews BW (1995) Specificity of ligand binding in a buried nonpolar cavity of T4 lysozyme: Linkage of dynamics and structural plasticity. Biochemistry 34(27):8576-8588.
-
(1995)
Biochemistry
, vol.34
, Issue.27
, pp. 8576-8588
-
-
Morton, A.1
Matthews, B.W.2
-
22
-
-
70449522914
-
Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site
-
Boyce SE, et al. (2009) Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J Mol Biol 394(4):747-763.
-
(2009)
J Mol Biol
, vol.394
, Issue.4
, pp. 747-763
-
-
Boyce, S.E.1
-
23
-
-
0036382728
-
A model binding site for testing scoring functions in molecular docking
-
Wei BQ, Baase WA, Weaver LH, Matthews BW, Shoichet BK (2002) A model binding site for testing scoring functions in molecular docking. J Mol Biol 322(2):339-355.
-
(2002)
J Mol Biol
, vol.322
, Issue.2
, pp. 339-355
-
-
Wei, B.Q.1
Baase, W.A.2
Weaver, L.H.3
Matthews, B.W.4
Shoichet, B.K.5
-
24
-
-
36049017659
-
The confine-and-release method: Obtaining correct binding free energies in the presence of protein conformational change
-
Mobley DL, Chodera JD, Dill KA (2007) The confine-and-release method: Obtaining correct binding free energies in the presence of protein conformational change. J Chem Theory Comput 3(4):1231-1235.
-
(2007)
J Chem Theory Comput
, vol.3
, Issue.4
, pp. 1231-1235
-
-
Mobley, D.L.1
Chodera, J.D.2
Dill, K.A.3
-
25
-
-
84891852541
-
Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics
-
Wang K, Chodera JD, Yang Y, Shirts MR (2013) Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics. J Comput Aided Mol Des 27(12):989-1007.
-
(2013)
J Comput Aided Mol Des
, vol.27
, Issue.12
, pp. 989-1007
-
-
Wang, K.1
Chodera, J.D.2
Yang, Y.3
Shirts, M.R.4
-
26
-
-
84907192008
-
Role of cavities and hydration in the pressure unfolding of T4 lysozyme
-
Nucci NV, Fuglestad B, Athanasoula EA, Wand AJ (2014) Role of cavities and hydration in the pressure unfolding of T4 lysozyme. Proc Natl Acad Sci USA 111(38):13846-13851.
-
(2014)
Proc Natl Acad Sci USA
, vol.111
, Issue.38
, pp. 13846-13851
-
-
Nucci, N.V.1
Fuglestad, B.2
Athanasoula, E.A.3
Wand, A.J.4
-
27
-
-
84896306703
-
Bringing clarity to the prediction of protein-ligand binding free energies via "blurring."
-
Ucisik MN, Zheng Z, Faver JC, Merz KM (2014) Bringing clarity to the prediction of protein-ligand binding free energies via "blurring." J Chem Theory Comput 10(3):1314-1325.
-
(2014)
J Chem Theory Comput
, vol.10
, Issue.3
, pp. 1314-1325
-
-
Ucisik, M.N.1
Zheng, Z.2
Faver, J.C.3
Merz, K.M.4
-
28
-
-
84902186999
-
Sampling of organic solutes in aqueous and heterogeneous environments using oscillating excess chemical potentials in grand canonical-like Monte Carlo-molecular dynamics simulations
-
Lakkaraju SK, Raman EP, Yu W, MacKerell AD, Jr (2014) Sampling of organic solutes in aqueous and heterogeneous environments using oscillating excess chemical potentials in grand canonical-like Monte Carlo-molecular dynamics simulations. J Chem Theory Comput 10(6):2281-2290.
-
(2014)
J Chem Theory Comput
, vol.10
, Issue.6
, pp. 2281-2290
-
-
Lakkaraju, S.K.1
Raman, E.P.2
Yu, W.3
MacKerell, A.D.4
-
29
-
-
80052401629
-
Solution structure of a minor and transiently formed state of a T4 lysozyme mutant
-
Bouvignies G, et al. (2011) Solution structure of a minor and transiently formed state of a T4 lysozyme mutant. Nature 477(7362):111-114.
-
(2011)
Nature
, vol.477
, Issue.7362
, pp. 111-114
-
-
Bouvignies, G.1
-
30
-
-
76449098262
-
PHENIX: A comprehensive Python-based system for macromolecular structure solution
-
Adams PD, et al. (2010) PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66(Pt 2):213-221.
-
(2010)
Acta Crystallogr D Biol Crystallogr
, vol.66
, Issue.2
, pp. 213-221
-
-
Adams, P.D.1
-
31
-
-
84903133311
-
Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery
-
Fischer M, Coleman RG, Fraser JS, Shoichet BK (2014) Incorporation of protein flexibility and conformational energy penalties in docking screens to improve ligand discovery. Nat Chem 6(7):575-583.
-
(2014)
Nat Chem
, vol.6
, Issue.7
, pp. 575-583
-
-
Fischer, M.1
Coleman, R.G.2
Fraser, J.S.3
Shoichet, B.K.4
-
32
-
-
84942048668
-
Octanol-water partition coefficients of simple organic compounds
-
Sangster J (1989) Octanol-water partition coefficients of simple organic compounds. J Phys Chem Ref Data 18(3):1111-1227.
-
(1989)
J Phys Chem Ref Data
, vol.18
, Issue.3
, pp. 1111-1227
-
-
Sangster, J.1
-
33
-
-
0001232509
-
On the properties of bit string-based measures of chemical similarity
-
Flower DR (1998) On the properties of bit string-based measures of chemical similarity. J Chem Inf Comput Sci 38(3):379-386.
-
(1998)
J Chem Inf Comput Sci
, vol.38
, Issue.3
, pp. 379-386
-
-
Flower, D.R.1
-
34
-
-
67650075330
-
Development of a compound class-directed similarity coefficient that accounts for molecular complexity effects in fingerprint searching
-
Wang Y, Bajorath J (2009) Development of a compound class-directed similarity coefficient that accounts for molecular complexity effects in fingerprint searching. J Chem Inf Model 49(6):1369-1376.
-
(2009)
J Chem Inf Model
, vol.49
, Issue.6
, pp. 1369-1376
-
-
Wang, Y.1
Bajorath, J.2
-
35
-
-
84859706377
-
Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin
-
Biela A, et al. (2012) Impact of ligand and protein desolvation on ligand binding to the S1 pocket of thrombin. J Mol Biol 418(5):350-366.
-
(2012)
J Mol Biol
, vol.418
, Issue.5
, pp. 350-366
-
-
Biela, A.1
-
36
-
-
84867919842
-
Fragment-guided design of subnanomolar β-lactamase inhibitors active in vivo
-
Eidam O, et al. (2012) Fragment-guided design of subnanomolar β-lactamase inhibitors active in vivo. Proc Natl Acad Sci USA 109(43):17448-17453.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.43
, pp. 17448-17453
-
-
Eidam, O.1
-
37
-
-
80052308982
-
Fluoroalkyl and alkyl chains have similar hydrophobicities in binding to the "hydrophobic wall" of carbonic anhydrase
-
Mecinovxc J, et al. (2011) Fluoroalkyl and alkyl chains have similar hydrophobicities in binding to the "hydrophobic wall" of carbonic anhydrase. JAmChemSoc133(35):14017-14026.
-
(2011)
JAmChemSoc
, vol.133
, Issue.35
, pp. 14017-14026
-
-
Mecinovxc, J.1
-
38
-
-
0346022974
-
Understanding protein-ligand interactions: The price of protein flexibility
-
Rauh D, Klebe G, Stubbs MT (2004) Understanding protein-ligand interactions: The price of protein flexibility. J Mol Biol 335(5):1325-1341.
-
(2004)
J Mol Biol
, vol.335
, Issue.5
, pp. 1325-1341
-
-
Rauh, D.1
Klebe, G.2
Stubbs, M.T.3
-
39
-
-
84898006931
-
Methyl, ethyl, propyl, butyl: Futile but not for water, as the correlation of structure and thermodynamic signature shows in a congeneric series of thermolysin inhibitors
-
Krimmer SG, Betz M, Heine A, Klebe G (2014) Methyl, ethyl, propyl, butyl: Futile but not for water, as the correlation of structure and thermodynamic signature shows in a congeneric series of thermolysin inhibitors. ChemMedChem 9(4):833-846.
-
(2014)
ChemMedChem
, vol.9
, Issue.4
, pp. 833-846
-
-
Krimmer, S.G.1
Betz, M.2
Heine, A.3
Klebe, G.4
-
40
-
-
84879237996
-
Rational optimization of drug-target residence time: Insights from inhibitor binding to the Staphylococcus aureus FabI enzyme-product complex
-
Chang A, et al. (2013) Rational optimization of drug-target residence time: Insights from inhibitor binding to the Staphylococcus aureus FabI enzyme-product complex. Biochemistry 52(24):4217-4228.
-
(2013)
Biochemistry
, vol.52
, Issue.24
, pp. 4217-4228
-
-
Chang, A.1
-
41
-
-
84868097065
-
Synthesis and structural characterisation of selective non-carbohydrate-based inhibitors of bacterial sialidases
-
Brear P, Telford J, Taylor GL, Westwood NJ (2012) Synthesis and structural characterisation of selective non-carbohydrate-based inhibitors of bacterial sialidases. ChemBioChem 13(16):2374-2383.
-
(2012)
ChemBioChem
, vol.13
, Issue.16
, pp. 2374-2383
-
-
Brear, P.1
Telford, J.2
Taylor, G.L.3
Westwood, N.J.4
-
42
-
-
84879115207
-
Ligand-binding dynamics rewire cellular signaling via estrogen receptor-α
-
Srinivasan S, et al. (2013) Ligand-binding dynamics rewire cellular signaling via estrogen receptor-α. Nat Chem Biol 9(5):326-332.
-
(2013)
Nat Chem Biol
, vol.9
, Issue.5
, pp. 326-332
-
-
Srinivasan, S.1
-
43
-
-
48249141040
-
Allostery and cooperativity revisited
-
Cui Q, Karplus M (2008) Allostery and cooperativity revisited. Protein Sci 17(8):1295-1307.
-
(2008)
Protein Sci
, vol.17
, Issue.8
, pp. 1295-1307
-
-
Cui, Q.1
Karplus, M.2
-
44
-
-
6344219895
-
Is allostery an intrinsic property of all dynamic proteins?
-
Gunasekaran K, Ma B, Nussinov R (2004) Is allostery an intrinsic property of all dynamic proteins? Proteins 57(3):433-443.
-
(2004)
Proteins
, vol.57
, Issue.3
, pp. 433-443
-
-
Gunasekaran, K.1
Ma, B.2
Nussinov, R.3
-
45
-
-
84861367246
-
Biomolecular simulation: A computational microscope for molecular biology
-
Dror RO, Dirks RM, Grossman JP, Xu H, Shaw DE (2012) Biomolecular simulation: A computational microscope for molecular biology. Annu Rev Biophys 41:429-452.
-
(2012)
Annu Rev Biophys
, vol.41
, pp. 429-452
-
-
Dror, R.O.1
Dirks, R.M.2
Grossman, J.P.3
Xu, H.4
Shaw, D.E.5
-
46
-
-
80755172456
-
Markov state model reveals folding and functional dynamics in ultra-long MD trajectories
-
Lane TJ, Bowman GR, Beauchamp K, Voelz VA, Pande VS (2011) Markov state model reveals folding and functional dynamics in ultra-long MD trajectories. J Am Chem Soc 133(45):18413-18419.
-
(2011)
J Am Chem Soc
, vol.133
, Issue.45
, pp. 18413-18419
-
-
Lane, T.J.1
Bowman, G.R.2
Beauchamp, K.3
Voelz, V.A.4
Pande, V.S.5
-
47
-
-
84873526912
-
To milliseconds and beyond: Challenges in the simulation of protein folding
-
Lane TJ, Shukla D, Beauchamp KA, Pande VS (2013) To milliseconds and beyond: Challenges in the simulation of protein folding. Curr Opin Struct Biol 23(1):58-65.
-
(2013)
Curr Opin Struct Biol
, vol.23
, Issue.1
, pp. 58-65
-
-
Lane, T.J.1
Shukla, D.2
Beauchamp, K.A.3
Pande, V.S.4
-
48
-
-
84870579518
-
Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding
-
Fenley AT, Muddana HS, Gilson MK (2012) Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding. Proc Natl Acad Sci USA 109(49):20006-20011.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, Issue.49
, pp. 20006-20011
-
-
Fenley, A.T.1
Muddana, H.S.2
Gilson, M.K.3
-
49
-
-
84955572918
-
Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model
-
Das A, et al. (2014) Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model. PLOS Comput Biol 10(4):e1003521.
-
(2014)
PLOS Comput Biol
, vol.10
, Issue.4
-
-
Das, A.1
-
50
-
-
2942536134
-
Sampling protein conformations and pathways
-
Lei M, Zavodszky MI, Kuhn LA, Thorpe MF (2004) Sampling protein conformations and pathways. J Comput Chem 25(9):1133-1148.
-
(2004)
J Comput Chem
, vol.25
, Issue.9
, pp. 1133-1148
-
-
Lei, M.1
Zavodszky, M.I.2
Kuhn, L.A.3
Thorpe, M.F.4
-
51
-
-
84885432778
-
Efficient and robust analysis of biomacromolecular flexibility using ensembles of network topologies based on fuzzy noncovalent constraints
-
Pfleger C, Gohlke H (2013) Efficient and robust analysis of biomacromolecular flexibility using ensembles of network topologies based on fuzzy noncovalent constraints. Structure 21(10):1725-1734.
-
(2013)
Structure
, vol.21
, Issue.10
, pp. 1725-1734
-
-
Pfleger, C.1
Gohlke, H.2
-
53
-
-
34447508216
-
Phaser crystallographic software
-
McCoy AJ, et al. (2007) Phaser crystallographic software. J Appl Crystallogr 40(Pt 4): 658-674.
-
(2007)
J Appl Crystallogr
, vol.40
, Issue.4
, pp. 658-674
-
-
McCoy, A.J.1
-
54
-
-
4444221565
-
UCSF Chimera-A visualization system for exploratory research and analysis
-
Pettersen EF, et al. (2004) UCSF Chimera-A visualization system for exploratory research and analysis. J Comput Chem 25(13):1605-1612.
-
(2004)
J Comput Chem
, vol.25
, Issue.13
, pp. 1605-1612
-
-
Pettersen, E.F.1
|