-
1
-
-
84876266689
-
Allostery in Disease and in Drug Discovery
-
Nussinov, R.; Tsai, C.-J. Allostery in Disease and in Drug Discovery Cell 2013, 153, 293-305
-
(2013)
Cell
, vol.153
, pp. 293-305
-
-
Nussinov, R.1
Tsai, C.-J.2
-
2
-
-
84898993517
-
The Ensemble Nature of Allostery
-
Motlagh, H. N.; Wrabl, J. O.; Li, J.; Hilser, V. J. The Ensemble Nature of Allostery Nature (London) 2014, 508, 331-339
-
(2014)
Nature (London)
, vol.508
, pp. 331-339
-
-
Motlagh, H.N.1
Wrabl, J.O.2
Li, J.3
Hilser, V.J.4
-
3
-
-
78651189765
-
On the Nature of Allosteric Transitions: A Plausible Model
-
Monod, J.; Wyman, J.; Changeux, J.-P. On the Nature of Allosteric Transitions: A Plausible Model J. Mol. Biol. 1965, 12, 88-118
-
(1965)
J. Mol. Biol.
, vol.12
, pp. 88-118
-
-
Monod, J.1
Wyman, J.2
Changeux, J.-P.3
-
4
-
-
48249141040
-
Allostery and Cooperativity Revisited
-
Cui, Q.; Karplus, M. Allostery and Cooperativity Revisited Protein Sci. 2008, 17, 1295-1307
-
(2008)
Protein Sci.
, vol.17
, pp. 1295-1307
-
-
Cui, Q.1
Karplus, M.2
-
5
-
-
0021658956
-
Allostery without Conformational Change: A Plausible Model
-
Cooper, A.; Dryden, D. Allostery without Conformational Change: A Plausible Model Eur. Biophys. J. Biophys. Lett. 1984, 11, 103-109
-
(1984)
Eur. Biophys. J. Biophys. Lett.
, vol.11
, pp. 103-109
-
-
Cooper, A.1
Dryden, D.2
-
6
-
-
0346220393
-
The Role of Dynamics in Allosteric Regulation
-
Kern, D.; Zuiderweg, E. The Role of Dynamics in Allosteric Regulation Curr. Opin. Struct. Biol. 2003, 13, 748-757
-
(2003)
Curr. Opin. Struct. Biol.
, vol.13
, pp. 748-757
-
-
Kern, D.1
Zuiderweg, E.2
-
7
-
-
33748363077
-
Kalodimos, Dynamically Driven Protein Allostery
-
Popovych, N.; Sun, S.; Ebright, R. Kalodimos, Dynamically Driven Protein Allostery Nat. Struct. Mol. Biol. 2006, 13, 831-838
-
(2006)
Nat. Struct. Mol. Biol.
, vol.13
, pp. 831-838
-
-
Popovych, N.1
Sun, S.2
Ebright, R.3
-
8
-
-
34447503697
-
Conformational Entropy in Molecular Recognition by Proteins
-
Frederick, K. K.; Marlow, M. S.; Valentine, K. G.; Wand, A. J. Conformational Entropy in Molecular Recognition by Proteins Nature 2007, 448, 325-329
-
(2007)
Nature
, vol.448
, pp. 325-329
-
-
Frederick, K.K.1
Marlow, M.S.2
Valentine, K.G.3
Wand, A.J.4
-
9
-
-
64849111005
-
Sending Signal Dynamically
-
Smock, R. G.; Gierasch, L. M. Sending Signal Dynamically Science 2009, 324, 198-203
-
(2009)
Science
, vol.324
, pp. 198-203
-
-
Smock, R.G.1
Gierasch, L.M.2
-
10
-
-
47349099470
-
Mapping of Two Networks of Residues that Exhibit Structural and Dynamical Changes upon Binding in a PDZ Domain Protein
-
Dhulesia, A.; Gsponer, J.; Vendruscolo, M. Mapping of Two Networks of Residues that Exhibit Structural and Dynamical Changes upon Binding in a PDZ Domain Protein J. Am. Chem. Soc. 2008, 130, 8931-8939
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 8931-8939
-
-
Dhulesia, A.1
Gsponer, J.2
Vendruscolo, M.3
-
11
-
-
0347753736
-
Ligand-Dependent Dynamics and Intramolecular Signaling in a PDZ Domain
-
Fuentes, E.; Der, C.; Lee, A. Ligand-Dependent Dynamics and Intramolecular Signaling in a PDZ Domain J. Mol. Biol. 2004, 335, 1105-1115
-
(2004)
J. Mol. Biol.
, vol.335
, pp. 1105-1115
-
-
Fuentes, E.1
Der, C.2
Lee, A.3
-
12
-
-
33750795402
-
Evaluation of Energetic and Dynamic Coupling Networks in a PDZ Domain Protein
-
Fuentes, E. J.; Gilmore, S. A.; Mauldin, R. V.; Lee, A. L. Evaluation of Energetic and Dynamic Coupling Networks in a PDZ Domain Protein J. Mol. Biol. 2006, 364, 337-351
-
(2006)
J. Mol. Biol.
, vol.364
, pp. 337-351
-
-
Fuentes, E.J.1
Gilmore, S.A.2
Mauldin, R.V.3
Lee, A.L.4
-
13
-
-
70849084011
-
Hidden Dynamic Allostery in a PDZ Domain
-
Petit, C. M.; Zhang, J.; Sapienza, P. J.; Fuentes, E. J.; Lee, A. L. Hidden Dynamic Allostery in a PDZ Domain Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 18249-18254
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 18249-18254
-
-
Petit, C.M.1
Zhang, J.2
Sapienza, P.J.3
Fuentes, E.J.4
Lee, A.L.5
-
14
-
-
84870707533
-
Accurate Prediction of the Dynamical Changes within the Second PDZ Domain of PTP1e
-
Cilia, E.; Vuister, G. W.; Lenaerts, T. Accurate Prediction of the Dynamical Changes within the Second PDZ Domain of PTP1e. PLoS Comput. Biol. 2012, 8.
-
(2012)
PLoS Comput. Biol.
, vol.8
-
-
Cilia, E.1
Vuister, G.W.2
Lenaerts, T.3
-
15
-
-
0030604722
-
Crystal Structures of a Complexed and Peptide-Free Membrane Protein-Binding Domain: Molecular Basis of Peptide Recognition by PDZ
-
Doyle, D.; Lee, A.; Lewis, J.; Kim, E.; Sheng, M.; MacKinnon, R. Crystal Structures of a Complexed and Peptide-Free Membrane Protein-Binding Domain: Molecular Basis of Peptide Recognition by PDZ Cell 1996, 85, 1067-1076
-
(1996)
Cell
, vol.85
, pp. 1067-1076
-
-
Doyle, D.1
Lee, A.2
Lewis, J.3
Kim, E.4
Sheng, M.5
MacKinnon, R.6
-
16
-
-
78049307619
-
Crystallographic and Nuclear Magnetic Resonance Evaluation of the Impact of Peptide Binding to the Second PDZ Domain of Protein Tyrosine Phosphatase 1E
-
Zhang, J.; Sapienza, P. J.; Ke, H.; Chang, A.; Hengel, S. R.; Wang, H.; Phillips, G. N., Jr.; Lee, A. L. Crystallographic and Nuclear Magnetic Resonance Evaluation of the Impact of Peptide Binding to the Second PDZ Domain of Protein Tyrosine Phosphatase 1E Biochemistry 2010, 49, 9280-9291
-
(2010)
Biochemistry
, vol.49
, pp. 9280-9291
-
-
Zhang, J.1
Sapienza, P.J.2
Ke, H.3
Chang, A.4
Hengel, S.R.5
Wang, H.6
Phillips, G.N.7
Lee, A.L.8
-
17
-
-
84867725616
-
Ligand Binding by PDZ Domains
-
Chi, C. N.; Bach, A.; Stromgaard, K.; Gianni, S.; Jemth, P. Ligand Binding by PDZ Domains Biofactors 2012, 38, 338-348
-
(2012)
Biofactors
, vol.38
, pp. 338-348
-
-
Chi, C.N.1
Bach, A.2
Stromgaard, K.3
Gianni, S.4
Jemth, P.5
-
18
-
-
0034740693
-
Mechanism and Role of PDZ Domains in Signaling Complex Assembly
-
Harris, B.; Lim, W. Mechanism and Role of PDZ Domains in Signaling Complex Assembly J. Cell Sci. 2001, 114, 3219-3231
-
(2001)
J. Cell Sci.
, vol.114
, pp. 3219-3231
-
-
Harris, B.1
Lim, W.2
-
20
-
-
77952705907
-
PDZ Domains and their Binding Partners: Structure, Specificity, and Modification
-
Lee, H.-J.; Zheng, J. J. PDZ Domains and their Binding Partners: Structure, Specificity, and Modification. Cell Commun. Signal. 2010, 8.
-
(2010)
Cell Commun. Signal.
, vol.8
-
-
Lee, H.-J.1
Zheng, J.J.2
-
22
-
-
67650032475
-
Energy Flow and Long-Range Correlations in Guanine-Binding Riboswitch: A Nonequilibrium Molecular Dynamics Study
-
Nguyen, P. H.; Derreumaux, P.; Stock, G. Energy Flow and Long-Range Correlations in Guanine-Binding Riboswitch: A Nonequilibrium Molecular Dynamics Study J. Phys. Chem. B 2009, 113, 9340-9347
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 9340-9347
-
-
Nguyen, P.H.1
Derreumaux, P.2
Stock, G.3
-
23
-
-
77955505542
-
Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation
-
Hub, J. S.; Kubitzki, M.; de Groot, B. L. Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation PLoS Comput. Biol. 2010, 6, e1000774
-
(2010)
PLoS Comput. Biol.
, vol.6
, pp. 1000774
-
-
Hub, J.S.1
Kubitzki, M.2
De Groot, B.L.3
-
24
-
-
80051867711
-
Communication Maps Computed for Homodimeric Hemoglobin: Computational Study of Water-Mediated Energy Transport in Proteins
-
Gnanasekaran, R.; Agbo, J. K.; Leitner, D. M. Communication Maps Computed for Homodimeric Hemoglobin: Computational Study of Water-Mediated Energy Transport in Proteins J. Chem. Phys. 2011, 135, 065103
-
(2011)
J. Chem. Phys.
, vol.135
, pp. 065103
-
-
Gnanasekaran, R.1
Agbo, J.K.2
Leitner, D.M.3
-
25
-
-
79953100071
-
Simulations of Allosteric Transitions
-
Elber, R. Simulations of Allosteric Transitions Curr. Opin. Struct. Biol. 2011, 21, 167-172
-
(2011)
Curr. Opin. Struct. Biol.
, vol.21
, pp. 167-172
-
-
Elber, R.1
-
26
-
-
84884688109
-
Collective Dynamics Underlying Allosteric Transitions in Hemoglobin
-
Vesper, M. D.; de Groot, B. L. Collective Dynamics Underlying Allosteric Transitions in Hemoglobin PLoS Comp. Biol. 2013, 9, e1003232
-
(2013)
PLoS Comp. Biol.
, vol.9
, pp. 1003232
-
-
Vesper, M.D.1
De Groot, B.L.2
-
27
-
-
84887037245
-
Allostery without Conformational Change: Modelling Protein Dynamics at Multiple Scales
-
McLeish, T. C. B.; Rodgers, T. L.; Wilson, M. R. Allostery without Conformational Change: Modelling Protein Dynamics at Multiple Scales Phys. Biol. 2013, 10, 056004
-
(2013)
Phys. Biol.
, vol.10
, pp. 056004
-
-
McLeish, T.C.B.1
Rodgers, T.L.2
Wilson, M.R.3
-
28
-
-
84884546753
-
Modulation of Global Low-Frequency Motions Underlies Allosteric Regulation: Demonstration in CRP/FNR Family Transcription Factors
-
Rodgers, T. L.; Townsend, P. D.; Burnell, D.; Jones, M. L.; Richards, S. A.; McLeish, T. C. B.; Pohl, E.; Wilson, M. R.; Cann, M. J. Modulation of Global Low-Frequency Motions Underlies Allosteric Regulation: Demonstration in CRP/FNR Family Transcription Factors PLoS Biol. 2013, 11, e1001651
-
(2013)
PLoS Biol.
, vol.11
, pp. 1001651
-
-
Rodgers, T.L.1
Townsend, P.D.2
Burnell, D.3
Jones, M.L.4
Richards, S.A.5
McLeish, T.C.B.6
Pohl, E.7
Wilson, M.R.8
Cann, M.J.9
-
29
-
-
84896778565
-
Allosteric Control of Kinesin’s Motor Domain by Tubulin: A Molecular Dynamics Study
-
Krukau, A.; Knecht, V.; Lipowsky, R. Allosteric Control of Kinesin’s Motor Domain by Tubulin: A Molecular Dynamics Study Phys. Chem. Chem. Phys. 2014, 16, 6189-6198
-
(2014)
Phys. Chem. Chem. Phys.
, vol.16
, pp. 6189-6198
-
-
Krukau, A.1
Knecht, V.2
Lipowsky, R.3
-
30
-
-
0033536602
-
Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families
-
Lockless, S. W.; Ranganathan, R. Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families Science 1999, 286, 295-299
-
(1999)
Science
, vol.286
, pp. 295-299
-
-
Lockless, S.W.1
Ranganathan, R.2
-
31
-
-
42449111332
-
Reassessing a Sparse Energetic Network within a Single Protein Domain
-
Chi, C. N.; Elfstrom, L.; Shi, Y.; Snall, T.; Engstrom, A.; Jemth, P. Reassessing a Sparse Energetic Network within a Single Protein Domain Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 4679-4684
-
(2008)
Proc. Natl. Acad. Sci. U.S.A.
, vol.105
, pp. 4679-4684
-
-
Chi, C.N.1
Elfstrom, L.2
Shi, Y.3
Snall, T.4
Engstrom, A.5
Jemth, P.6
-
32
-
-
22444450449
-
Intramolecular Signaling Pathways Revealed by Molecular Anisotropic Thermal Diffusion
-
Ota, N.; Agard, D. A. Intramolecular Signaling Pathways Revealed by Molecular Anisotropic Thermal Diffusion J. Mol. Biol. 2005, 351, 345-354
-
(2005)
J. Mol. Biol.
, vol.351
, pp. 345-354
-
-
Ota, N.1
Agard, D.A.2
-
33
-
-
33749029273
-
Pump-Probe Molecular Dynamics as a Tool for Studying Protein Motion and Long Range Coupling
-
Sharp, K.; Skinner, J. J. Pump-Probe Molecular Dynamics as a Tool for Studying Protein Motion and Long Range Coupling Proteins 2006, 65, 347-361
-
(2006)
Proteins
, vol.65
, pp. 347-361
-
-
Sharp, K.1
Skinner, J.J.2
-
34
-
-
58949102247
-
Signaling Pathways of PDZ2 Domain: A Molecular Dynamics Interaction Correlation Analysis
-
Kong, Y.; Karplus, M. Signaling Pathways of PDZ2 Domain: A Molecular Dynamics Interaction Correlation Analysis Proteins 2009, 74, 145-154
-
(2009)
Proteins
, vol.74
, pp. 145-154
-
-
Kong, Y.1
Karplus, M.2
-
35
-
-
78649883885
-
Interaction Energy Based Protein Structure Networks
-
S.Vijayabaskar, M.; Vishveshwara, S. Interaction Energy Based Protein Structure Networks Biophys. J. 2010, 99, 3704-3715
-
(2010)
Biophys. J.
, vol.99
, pp. 3704-3715
-
-
Vijayabaskar, M.S.1
Vishveshwara, S.2
-
36
-
-
23244447873
-
Functional Dynamics of PDZ Binding Domains: A Normal-Mode Analysis
-
De Los Rios, P.; Cecconi, F.; Pretre, A.; Dietler, G.; Michielin, O.; Piazza, F.; Juanico, B. Functional Dynamics of PDZ Binding Domains: A Normal-Mode Analysis Biophys. J. 2005, 89, 14-21
-
(2005)
Biophys. J.
, vol.89
, pp. 14-21
-
-
De Los Rios, P.1
Cecconi, F.2
Pretre, A.3
Dietler, G.4
Michielin, O.5
Piazza, F.6
Juanico, B.7
-
37
-
-
70450065485
-
Identification of Specificity and Promiscuity of PDZ Domain Interactions through their Dynamic Behavior
-
Gerek, Z. N.; Keskin, O.; Ozkan, S. B. Identification of Specificity and Promiscuity of PDZ Domain Interactions through their Dynamic Behavior Proteins 2009, 77, 796-811
-
(2009)
Proteins
, vol.77
, pp. 796-811
-
-
Gerek, Z.N.1
Keskin, O.2
Ozkan, S.B.3
-
38
-
-
80055066238
-
Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning
-
Gerek, Z. N.; Ozkan, S. B. Change in Allosteric Network Affects Binding Affinities of PDZ Domains: Analysis through Perturbation Response Scanning PLoS Comput. Biol. 2011, 7, e1002154
-
(2011)
PLoS Comput. Biol.
, vol.7
, pp. 1002154
-
-
Gerek, Z.N.1
Ozkan, S.B.2
-
39
-
-
84863939894
-
Equilibrium Fluctuations of a Single Folded Protein Reveal a Multitude of Potential Cryptic Allosteric Sites
-
Bowman, G. R.; Geissler, P. L. Equilibrium Fluctuations of a Single Folded Protein Reveal a Multitude of Potential Cryptic Allosteric Sites Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 11681-11686
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 11681-11686
-
-
Bowman, G.R.1
Geissler, P.L.2
-
40
-
-
73449144096
-
Dynamic Allostery in the Methionine Repressor Revealed by Force Distribution Analysis
-
Stacklies, W.; Xia, F.; Gräter, F. Dynamic Allostery in the Methionine Repressor Revealed by Force Distribution Analysis PLoS Comput. Biol. 2009, 5 (e1000574) 11
-
(2009)
PLoS Comput. Biol.
, vol.5
, pp. 11
-
-
Stacklies, W.1
Xia, F.2
Gräter, F.3
-
41
-
-
34848882812
-
Signal Propagation in Proteins and Relation to Equilibrium Fluctuations
-
Chennubhotla, C.; Bahar, I. Signal Propagation in Proteins and Relation to Equilibrium Fluctuations PloS Comput. Biol. 2007, 9 (e172) 1716-1726
-
(2007)
PloS Comput. Biol.
, vol.9
, pp. 1716-1726
-
-
Chennubhotla, C.1
Bahar, I.2
-
42
-
-
84856514490
-
Detection of Allosteric Signal Transmission by Information-Theoretic Analysis of Protein Dynamics
-
Pandini, A.; Fornili, A.; Fraternali, F.; Kleinjung, J. Detection of Allosteric Signal Transmission by Information-Theoretic Analysis of Protein Dynamics FASEB J. 2012, 26, 868-881
-
(2012)
FASEB J.
, vol.26
, pp. 868-881
-
-
Pandini, A.1
Fornili, A.2
Fraternali, F.3
Kleinjung, J.4
-
43
-
-
84901660019
-
NbIT: A New Information Theory-Based Analysis of Allosteric Mechanisms Reveals Residues that Underlie Function in the Leucine Transporter LeuT
-
LeVine, M. V.; Weinstein, H. NbIT: A New Information Theory-Based Analysis of Allosteric Mechanisms Reveals Residues that Underlie Function in the Leucine Transporter LeuT PLoS Comput. Biol. 2014, 10, e1003603
-
(2014)
PLoS Comput. Biol.
, vol.10
, pp. 1003603
-
-
Levine, M.V.1
Weinstein, H.2
-
44
-
-
84880355882
-
Kinetic Response of a Photoperturbed Allosteric Protein
-
Buchli, B.; Waldauer, S. A.; Walser, R.; Donten, M. L.; Pfister, R.; Bloechliger, N.; Steiner, S.; Caflisch, A.; Zerbe, O.; Hamm, P. Kinetic Response of a Photoperturbed Allosteric Protein Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 11725-11730
-
(2013)
Proc. Natl. Acad. Sci. U.S.A.
, vol.110
, pp. 11725-11730
-
-
Buchli, B.1
Waldauer, S.A.2
Walser, R.3
Donten, M.L.4
Pfister, R.5
Bloechliger, N.6
Steiner, S.7
Caflisch, A.8
Zerbe, O.9
Hamm, P.10
-
45
-
-
0034635998
-
Photo-Control of Helix Content in a Short Peptide
-
Kumita, J. R.; Smart, O. S.; Woolley, G. A. Photo-Control of Helix Content in a Short Peptide Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 3803-3808
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 3803-3808
-
-
Kumita, J.R.1
Smart, O.S.2
Woolley, G.A.3
-
46
-
-
33745294757
-
Azobenzene as Conformational Switch in Model Peptides
-
Renner, C.; Moroder, L. Azobenzene as Conformational Switch in Model Peptides Chem. Biol. Chem. 2006, 7, 869-878
-
(2006)
Chem. Biol. Chem.
, vol.7
, pp. 869-878
-
-
Renner, C.1
Moroder, L.2
-
47
-
-
0038313065
-
Picosecond Conformational Transition and Equilibration of a Cyclic Peptide
-
Bredenbeck, J.; Helbing, J.; Sieg, A.; Schrader, T.; Zinth, W.; Renner, C.; Behrendt, R.; Moroder, L.; Wachtveitl, J.; Hamm, P. Picosecond Conformational Transition and Equilibration of a Cyclic Peptide Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 6452-6457
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 6452-6457
-
-
Bredenbeck, J.1
Helbing, J.2
Sieg, A.3
Schrader, T.4
Zinth, W.5
Renner, C.6
Behrendt, R.7
Moroder, L.8
Wachtveitl, J.9
Hamm, P.10
-
48
-
-
33645218213
-
Allosteric Control of an Ionotropic Glutamate Receptor with an Optical Switch
-
Volgraf, M.; Gorostiza, P.; Numano, R.; Kramer, R. H.; Isacoff, E. Y.; Trauner, D. Allosteric Control of an Ionotropic Glutamate Receptor with an Optical Switch Nat. Chem. Biol. 2006, 2, 47-52
-
(2006)
Nat. Chem. Biol.
, vol.2
, pp. 47-52
-
-
Volgraf, M.1
Gorostiza, P.2
Numano, R.3
Kramer, R.H.4
Isacoff, E.Y.5
Trauner, D.6
-
49
-
-
66149153105
-
Nanosculpting Reversed Wavelength Sensitivity into a Photoswitchable iGluR
-
Numano, R.; Szobota, S.; Lau, A. Y.; Gorostiza, P.; Volgraf, M.; Roux, B.; Trauner, D.; Isacoff, E. Y. Nanosculpting Reversed Wavelength Sensitivity into a Photoswitchable iGluR Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 6814-6819
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 6814-6819
-
-
Numano, R.1
Szobota, S.2
Lau, A.Y.3
Gorostiza, P.4
Volgraf, M.5
Roux, B.6
Trauner, D.7
Isacoff, E.Y.8
-
50
-
-
80455127006
-
Real Time Observation of Ultrafast Peptide Conformational Dynamics: MD Simulation vs. IR Experiment
-
Nguyen, P. H.; Staudt, H.; Wachtveitl, J.; Stock, G. Real Time Observation of Ultrafast Peptide Conformational Dynamics: MD Simulation vs. IR Experiment J. Phys. Chem. B 2011, 115, 13084-13092
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 13084-13092
-
-
Nguyen, P.H.1
Staudt, H.2
Wachtveitl, J.3
Stock, G.4
-
51
-
-
84875592758
-
GROMACS 4.5: A High-Throughput and Highly Parallel Open Source Molecular Simulation Toolkit
-
Pronk GROMACS 4.5: a High-Throughput and Highly Parallel Open Source Molecular Simulation Toolkit Bioinformatics 2013, 29, 845-854
-
(2013)
Bioinformatics
, vol.29
, pp. 845-854
-
-
Pronk1
-
52
-
-
33748518255
-
Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters
-
Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Comparison of Multiple Amber Force Fields and Development of Improved Protein Backbone Parameters Proteins 2006, 65, 712-725
-
(2006)
Proteins
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
53
-
-
67649494492
-
Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides
-
Best, R. B.; Hummer, G. Optimized Molecular Dynamics Force Fields Applied to the Helix-Coil Transition of Polypeptides J. Phys. Chem. B 2009, 113, 9004-9015
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 9004-9015
-
-
Best, R.B.1
Hummer, G.2
-
54
-
-
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 2010, 78, 1950-1958
-
(2010)
Proteins
, 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
-
55
-
-
0004016501
-
Comparison of Simple Potential Functions for Simulating Liquid Water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983, 79, 926
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.5
-
56
-
-
49449085241
-
Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations
-
Joung, I. S.; Cheatham, T. E., III Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations J. Phys. Chem. B 2008, 112, 9020-9041
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 9020-9041
-
-
Joung, I.S.1
Cheatham, E.T.2
-
57
-
-
70450206724
-
-
revision A.1; Gaussian Inc: Wallingford, CT.
-
Frisch, M. J. Gaussian 09, revision A.1; Gaussian Inc: Wallingford, CT, 2009.
-
(2009)
Gaussian 09
-
-
Frisch, M.J.1
-
58
-
-
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. D.; 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.D.3
Kollman, P.A.4
-
59
-
-
33645200462
-
Antechamber, An Accessory Software Package for Molecular Mechanical Calculations
-
Wang, J.; Wang, W.; Kollman, P. A.; Case, D. A. Antechamber, An Accessory Software Package for Molecular Mechanical Calculations J. Comput. Chem. 2005, 25, 1157-1174
-
(2005)
J. Comput. Chem.
, vol.25
, pp. 1157-1174
-
-
Wang, J.1
Wang, W.2
Kollman, P.A.3
Case, D.A.4
-
60
-
-
46249092554
-
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
-
Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theor. Comp. 2008, 4, 435-447
-
(2008)
J. Chem. Theor. Comp.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
61
-
-
33846823909
-
Particle mesh Ewald: An N log(N) Method for Ewald Sums in Large Systems
-
Darden, T.; York, D.; Petersen, L. Particle mesh Ewald: An N log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089-10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Petersen, L.3
-
62
-
-
33846086933
-
Canonical Sampling through Velocity Rescaling
-
Bussi, G.; Donadio, D.; Parrinello, M. Canonical Sampling through Velocity Rescaling J. Chem. Phys. 2007, 126, 0141011-0141017
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 0141011-0141017
-
-
Bussi, G.1
Donadio, D.2
Parrinello, M.3
-
63
-
-
33750587438
-
Molecular Dynamics with Coupling to an External Bath
-
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Dinola, A.; Haak, J. R. Molecular Dynamics with Coupling to an External Bath J. Chem. Phys. 1984, 81, 3684-3690
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
64
-
-
68349093958
-
TALOS Plus: A Hybrid Method for Predicting Protein Torsion Angles from NMR Chemical Shifts
-
Shen, Y.; Delaglio, F.; Cornilescu, G.; Bax, A. TALOS Plus: A Hybrid Method for Predicting Protein Torsion Angles from NMR Chemical Shifts J. Biomol. NMR 2009, 44, 213-223
-
(2009)
J. Biomol. NMR
, vol.44
, pp. 213-223
-
-
Shen, Y.1
Delaglio, F.2
Cornilescu, G.3
Bax, A.4
-
65
-
-
34547297406
-
Dihedral Angle Principal Component Analysis of Molecular Dynamics Simulations
-
Altis, A.; Nguyen, P. H.; Hegger, R.; Stock, G. Dihedral Angle Principal Component Analysis of Molecular Dynamics Simulations J. Chem. Phys. 2007, 126, 244111
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 244111
-
-
Altis, A.1
Nguyen, P.H.2
Hegger, R.3
Stock, G.4
-
66
-
-
0020997912
-
Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen Bonded and Geometrical Features
-
Kabsch, W.; Sander, C. Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen Bonded and Geometrical Features Biopolymers 1983, 22, 2577-2637
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
67
-
-
0041819710
-
Relative Stability of Protein Structures Determined by X-ray Crystallography or NMR Spectroscopy: A Molecular Dynamics Simulation Study
-
Fan, H.; Mark, A. E. Relative Stability of Protein Structures Determined by X-ray Crystallography or NMR Spectroscopy: A Molecular Dynamics Simulation Study Proteins 2003, 53, 111-120
-
(2003)
Proteins
, vol.53
, pp. 111-120
-
-
Fan, H.1
Mark, A.E.2
-
68
-
-
0027441950
-
Essential Dynamics of Proteins
-
Amadei, A.; Linssen, A. B. M.; Berendsen, H. J. C. Essential Dynamics of Proteins Proteins 1993, 17, 412-425
-
(1993)
Proteins
, vol.17
, pp. 412-425
-
-
Amadei, A.1
Linssen, A.B.M.2
Berendsen, H.J.C.3
-
69
-
-
84908053063
-
Effect of Viscogens on the Kinetic Response of a Photoperturbed Allosteric Protein
-
Waldauer, S. A.; Stucki-Buchli, B.; Frey, L.; Hamm, P. Effect of Viscogens on the Kinetic Response of a Photoperturbed Allosteric Protein J. Chem. Phys. 2014, 141, 22D514
-
(2014)
J. Chem. Phys.
, vol.141
, pp. 22D514
-
-
Waldauer, S.A.1
Stucki-Buchli, B.2
Frey, L.3
Hamm, P.4
-
70
-
-
0029881007
-
Molmol: A Program for Display and Analysis of Macromolecular Structures
-
Koradi, R.; Billeter, M.; Wüthrich, K. Molmol: A Program for Display and Analysis of Macromolecular Structures J. Mol. Graphics 1996, 14, 51-55
-
(1996)
J. Mol. Graphics
, vol.14
, pp. 51-55
-
-
Koradi, R.1
Billeter, M.2
Wüthrich, K.3
|