-
2
-
-
0036815758
-
NMR methods for characterizing microsecond to millisecond dynamics in recognition and catalysis
-
M. Akke NMR methods for characterizing microsecond to millisecond dynamics in recognition and catalysis Curr. Opin. Struct. Biol. 12 2002 642 647
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 642-647
-
-
Akke, M.1
-
3
-
-
22244445788
-
Imaging α-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability, and the electrostatic potential map
-
A. Aksimentiev, and K. Schulten Imaging α-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map Biophys. J. 88 2005 3745 3761
-
(2005)
Biophys. J.
, vol.88
, pp. 3745-3761
-
-
Aksimentiev, A.1
Schulten, K.2
-
4
-
-
0036384269
-
Simple physical models connect theory and experiment in protein folding kinetics
-
E. Alm, A.V. Morozov, T. Kortemme, and D. Baker Simple physical models connect theory and experiment in protein folding kinetics J. Mol. Biol. 322 2002 463 476
-
(2002)
J. Mol. Biol.
, vol.322
, pp. 463-476
-
-
Alm, E.1
Morozov, A.V.2
Kortemme, T.3
Baker, D.4
-
5
-
-
0030623823
-
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
-
I. Bahar, A.R. Atilgan, and B. Erman Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential Fold. Des. 2 1997 173 181
-
(1997)
Fold. Des.
, vol.2
, pp. 173-181
-
-
Bahar, I.1
Atilgan, A.R.2
Erman, B.3
-
6
-
-
22944465793
-
One-dimensional reaction coordinates for diffusive activated rate processes in many dimensions
-
A. Berezhkovskii, and A. Szabo One-dimensional reaction coordinates for diffusive activated rate processes in many dimensions J. Chem. Phys. 122 2005 14503
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 14503
-
-
Berezhkovskii, A.1
Szabo, A.2
-
7
-
-
18744387720
-
Reaction coordinates and rates from transition paths
-
R.B. Best, and G. Hummer Reaction coordinates and rates from transition paths Proc. Natl. Acad. Sci. USA 102 2005 6732 6737
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 6732-6737
-
-
Best, R.B.1
Hummer, G.2
-
8
-
-
3042846748
-
Determination of ensembles of protein structures consistent with NMR order parameters
-
R.B. Best, and M. Vendruscolo Determination of ensembles of protein structures consistent with NMR order parameters J. Am. Chem. Soc. 126 2004 8090 8091
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 8090-8091
-
-
Best, R.B.1
Vendruscolo, M.2
-
9
-
-
0242362716
-
Conformational changes of G protein-coupled receptors during their activation by agonist binding
-
C. Bissantz Conformational changes of G protein-coupled receptors during their activation by agonist binding J. Recept. Signal Transduct. Res. 23 2003 123 153
-
(2003)
J. Recept. Signal Transduct. Res.
, vol.23
, pp. 123-153
-
-
Bissantz, C.1
-
11
-
-
0025336625
-
Structure of Arc repressor in solution: Evidence for a family of β-sheet DNA-binding proteins
-
J.N. Breg, J.H.J. van Opheusden, M.J.M. Burgering, R. Boelens, and R. Kaptein Structure of Arc repressor in solution: evidence for a family of β-sheet DNA-binding proteins Nature 346 1990 586 589
-
(1990)
Nature
, vol.346
, pp. 586-589
-
-
Breg, J.N.1
Van Opheusden, J.H.J.2
Burgering, M.J.M.3
Boelens, R.4
Kaptein, R.5
-
12
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus CHARMM: a program for macromolecular energy, minimization, and dynamics calculations J. Comput. Chem. 4 1983 187 217
-
(1983)
J. Comput. Chem.
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
13
-
-
48749137581
-
Stochastic boundary-conditions for molecular dynamics simulations of ST2 water
-
C.L. Brooks III, A. Brünger, and M. Karplus Stochastic boundary-conditions for molecular dynamics simulations of ST2 water Chem. Phys. Lett. 105 1984 495 500
-
(1984)
Chem. Phys. Lett.
, vol.105
, pp. 495-500
-
-
Brooks III, C.L.1
Brünger, A.2
Karplus, M.3
-
14
-
-
0024733407
-
Intermediates and barrier crossing in a random energy model (with applications to protein folding)
-
J.D. Bryngelson, and P.G. Wolynes Intermediates and barrier crossing in a random energy model (with applications to protein folding) J. Phys. Chem. 93 1989 6902 6915
-
(1989)
J. Phys. Chem.
, vol.93
, pp. 6902-6915
-
-
Bryngelson, J.D.1
Wolynes, P.G.2
-
15
-
-
3142782241
-
Quantifying the roughness on the free energy landscape: Entropic bottlenecks and protein folding rates
-
L.L. Chavez, J.N. Onuchic, and C. Clementi Quantifying the roughness on the free energy landscape: entropic bottlenecks and protein folding rates J. Am. Chem. Soc. 126 2004 8426 8432
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 8426-8432
-
-
Chavez, L.L.1
Onuchic, J.N.2
Clementi, C.3
-
16
-
-
0034685604
-
Topological and energetic factors: What determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins
-
C. Clementi, H. Nymeyer, and J.N. Onuchic Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins J. Mol. Biol. 298 2000 937 953
-
(2000)
J. Mol. Biol.
, vol.298
, pp. 937-953
-
-
Clementi, C.1
Nymeyer, H.2
Onuchic, J.N.3
-
18
-
-
0033668488
-
An evolutionary bridge to a new protein fold
-
M.H.J. Cordes, R.E. Burton, N.P. Walsh, C.J. McKnight, and R.T. Sauer An evolutionary bridge to a new protein fold Nat. Struct. Biol. 7 2000 1129 1132
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 1129-1132
-
-
Cordes, M.H.J.1
Burton, R.E.2
Walsh, N.P.3
McKnight, C.J.4
Sauer, R.T.5
-
20
-
-
0026511656
-
The folding of an enzyme. 1. Theory of protein engineering analysis of stability and pathway of protein folding
-
A.R. Fersht, A. Matouschek, and L. Serrano The folding of an enzyme. 1. Theory of protein engineering analysis of stability and pathway of protein folding J. Mol. Biol. 224 1992 771 782
-
(1992)
J. Mol. Biol.
, vol.224
, pp. 771-782
-
-
Fersht, A.R.1
Matouschek, A.2
Serrano, L.3
-
21
-
-
6344219895
-
Is allostery an intrinsic property of all dynamic proteins?
-
K. Gunasekaran, B.Y. Ma, and R. Nussinov Is allostery an intrinsic property of all dynamic proteins? Proteins 57 2004 433 443
-
(2004)
Proteins
, vol.57
, pp. 433-443
-
-
Gunasekaran, K.1
Ma, B.Y.2
Nussinov, R.3
-
22
-
-
8644232696
-
Combinatorial modeling of protein folding kinetics: Free energy profiles and rates
-
E.R. Henry, and W.A. Eaton Combinatorial modeling of protein folding kinetics: free energy profiles and rates Chem. Phys. 307 2004 163 185
-
(2004)
Chem. Phys.
, vol.307
, pp. 163-185
-
-
Henry, E.R.1
Eaton, W.A.2
-
23
-
-
0030907624
-
Can a two-state MWC allosteric model explain hemoglobin kinetics?
-
E.R. Henry, C.M. Jones, J. Hofrichter, and W.A. Eaton Can a two-state MWC allosteric model explain hemoglobin kinetics? Biochemistry 36 1997 6511 6528
-
(1997)
Biochemistry
, vol.36
, pp. 6511-6528
-
-
Henry, E.R.1
Jones, C.M.2
Hofrichter, J.3
Eaton, W.A.4
-
24
-
-
2942590388
-
Simulation, experiment, and evolution: Understanding nucleation in protein S6 folding
-
I.A. Hubner, M. Oliveberg, and E.I. Shakhnovich Simulation, experiment, and evolution: understanding nucleation in protein S6 folding Proc. Natl. Acad. Sci. USA 101 2004 8354 8359
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 8354-8359
-
-
Hubner, I.A.1
Oliveberg, M.2
Shakhnovich, E.I.3
-
25
-
-
0842311640
-
From transition paths to transition states and rate coefficients
-
G. Hummer From transition paths to transition states and rate coefficients J. Chem. Phys. 120 2004 516 523
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 516-523
-
-
Hummer, G.1
-
26
-
-
0030774472
-
Multistate Gaussian model for electrostatic solvation free energies
-
G. Hummer, L.R. Pratt, and A.E. García Multistate Gaussian model for electrostatic solvation free energies J. Am. Chem. Soc. 119 1997 8523 8527
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 8523-8527
-
-
Hummer, G.1
Pratt, L.R.2
García, A.E.3
-
27
-
-
0036785556
-
The origins of asymmetry in the folding transition states of protein L and protein G
-
J. Karanicolas, and C.L. Brooks III The origins of asymmetry in the folding transition states of protein L and protein G Protein Sci. 11 2002 2351 2361
-
(2002)
Protein Sci.
, vol.11
, pp. 2351-2361
-
-
Karanicolas, J.1
Brooks III, C.L.2
-
28
-
-
0037386699
-
The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: Lessons for protein design?
-
J. Karanicolas, and C.L. Brooks III The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design? Proc. Natl. Acad. Sci. USA 100 2003 3954 3959
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 3954-3959
-
-
Karanicolas, J.1
Brooks III, C.L.2
-
29
-
-
0242383943
-
Improved Gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions
-
J. Karanicolas, and C.L. Brooks III Improved Gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions J. Mol. Biol. 334 2003 309 325
-
(2003)
J. Mol. Biol.
, vol.334
, pp. 309-325
-
-
Karanicolas, J.1
Brooks III, C.L.2
-
30
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
M. Karplus, and J.A. McCammon Molecular dynamics simulations of biomolecules Nat. Struct. Biol. 9 2002 646 652
-
(2002)
Nat. Struct. Biol.
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
31
-
-
14844361989
-
NMR studies of protein structure and dynamics
-
L.E. Kay NMR studies of protein structure and dynamics J. Magn. Reson. 173 2005 193 207
-
(2005)
J. Magn. Reson.
, vol.173
, pp. 193-207
-
-
Kay, L.E.1
-
33
-
-
0036775029
-
Elastic models of conformational transitions in macromolecules
-
M.K. Kim, G.S. Chirikjian, and R.L. Jernigan Elastic models of conformational transitions in macromolecules J. Mol. Graph. Model. 21 2002 151 160
-
(2002)
J. Mol. Graph. Model.
, vol.21
, pp. 151-160
-
-
Kim, M.K.1
Chirikjian, G.S.2
Jernigan, R.L.3
-
34
-
-
23244465157
-
Rigid-cluster models of conformational transitions in macromolecular machines and assemblies
-
M.K. Kim, R.L. Jernigan, and G.S. Chirikjian Rigid-cluster models of conformational transitions in macromolecular machines and assemblies Biophys. J. 89 2005 43 55
-
(2005)
Biophys. J.
, vol.89
, pp. 43-55
-
-
Kim, M.K.1
Jernigan, R.L.2
Chirikjian, G.S.3
-
35
-
-
0035850732
-
Roles of native topology and chain-length scaling in protein folding: A simulation study with a Gō-like model
-
N. Koga, and S. Takada Roles of native topology and chain-length scaling in protein folding: a simulation study with a Gō-like model J. Mol. Biol. 313 2001 171 180
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 171-180
-
-
Koga, N.1
Takada, S.2
-
37
-
-
13444301037
-
A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes
-
Y. Levy, S.S. Cho, J.N. Onuchic, and P.G. Wolynes A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes J. Mol. Biol. 346 2005 1121 1145
-
(2005)
J. Mol. Biol.
, vol.346
, pp. 1121-1145
-
-
Levy, Y.1
Cho, S.S.2
Onuchic, J.N.3
Wolynes, P.G.4
-
38
-
-
14044275168
-
Symmetry and frustration in protein energy landscapes: A near degeneracy resolves the Rop dimer-folding mystery
-
Y. Levy, S.S. Cho, J.N. Onuchic, and P.G. Wolynes Symmetry and frustration in protein energy landscapes: a near degeneracy resolves the Rop dimer-folding mystery Proc. Natl. Acad. Sci. USA 102 2005 2373 2378
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 2373-2378
-
-
Levy, Y.1
Cho, S.S.2
Onuchic, J.N.3
Wolynes, P.G.4
-
39
-
-
0037441653
-
Structure validation by Cα geometry: φ, ψ and Cβ deviation
-
S.C. Lovell, I.W. Davis, W.B. Arendall III, P.I. de Bakker, J.M. Word, M.G. Prisant, J.S. Richardson, and D.C. Richardson Structure validation by Cα geometry: φ, ψ and Cβ deviation Proteins 50 2003 437 450
-
(2003)
Proteins
, vol.50
, pp. 437-450
-
-
Lovell, S.C.1
Davis, I.W.2
Arendall III, W.B.3
De Bakker, P.I.4
Word, J.M.5
Prisant, M.G.6
Richardson, J.S.7
Richardson, D.C.8
-
40
-
-
0037457899
-
Quaternary structure of hemoglobin in solution
-
J.A. Lukin, G. Kontaxis, V. Simplaceanu, Y. Yuan, A. Bax, and C. Ho Quaternary structure of hemoglobin in solution Proc. Natl. Acad. Sci. USA 100 2003 517 520
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 517-520
-
-
Lukin, J.A.1
Kontaxis, G.2
Simplaceanu, V.3
Yuan, Y.4
Bax, A.5
Ho, C.6
-
41
-
-
1642365068
-
New advances in normal mode analysis of supermolecular complexes and applications to structural refinement
-
J.P. Ma New advances in normal mode analysis of supermolecular complexes and applications to structural refinement Curr. Protein Pept. Sci. 5 2004 119 123
-
(2004)
Curr. Protein Pept. Sci.
, vol.5
, pp. 119-123
-
-
Ma, J.P.1
-
42
-
-
0028325298
-
P22 Arc repressor - Folding kinetics of a single-domain dimeric protein
-
M.E. Milla, and R.T. Sauer P22 Arc repressor - folding kinetics of a single-domain dimeric protein Biochemistry 33 1994 1125 1133
-
(1994)
Biochemistry
, vol.33
, pp. 1125-1133
-
-
Milla, M.E.1
Sauer, R.T.2
-
43
-
-
0028882589
-
P22 Arc repressor: Transition state properties inferred from mutational effects on the rates of protein unfolding and refolding
-
M.E. Milla, B.M. Brown, C.D. Waldburger, and R.T. Sauer P22 Arc repressor: transition state properties inferred from mutational effects on the rates of protein unfolding and refolding Biochemistry 34 1995 13914 13919
-
(1995)
Biochemistry
, vol.34
, pp. 13914-13919
-
-
Milla, M.E.1
Brown, B.M.2
Waldburger, C.D.3
Sauer, R.T.4
-
44
-
-
0242268469
-
Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins
-
O. Miyashita, J.N. Onuchic, and P.G. Wolynes Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins Proc. Natl. Acad. Sci. USA 100 2003 12570 12575
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 12570-12575
-
-
Miyashita, O.1
Onuchic, J.N.2
Wolynes, P.G.3
-
45
-
-
13444305369
-
Simple energy landscape model for the kinetics of functional transitions in proteins
-
O. Miyashita, P.G. Wolynes, and J.N. Onuchic Simple energy landscape model for the kinetics of functional transitions in proteins J. Phys. Chem. B 109 2005 1959 1969
-
(2005)
J. Phys. Chem. B
, vol.109
, pp. 1959-1969
-
-
Miyashita, O.1
Wolynes, P.G.2
Onuchic, J.N.3
-
46
-
-
0029919190
-
Residue-residue potentials with a favourable contact pair term and an unfavourable high packing density term, for simulation and threading
-
S. Miyazawa, and R.L. Jernigan Residue-residue potentials with a favourable contact pair term and an unfavourable high packing density term, for simulation and threading J. Mol. Biol. 256 1996 623 644
-
(1996)
J. Mol. Biol.
, vol.256
, pp. 623-644
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
47
-
-
11844285690
-
Temperature dependence of three-body hydrophobic interactions: Potential of mean force, enthalpy, entropy, heat capacity and nonadditivity
-
M.S. Moghaddam, S. Shimizu, and H.S. Chan Temperature dependence of three-body hydrophobic interactions: potential of mean force, enthalpy, entropy, heat capacity and nonadditivity J. Am. Chem. Soc. 127 2005 303 316
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 303-316
-
-
Moghaddam, M.S.1
Shimizu, S.2
Chan, H.S.3
-
48
-
-
0033613165
-
A simple model for calculating the kinetics of protein folding from three-dimensional structures
-
V. Muñoz, and W.A. Eaton A simple model for calculating the kinetics of protein folding from three-dimensional structures Proc. Natl. Acad. Sci. USA 96 1999 11311 11316
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 11311-11316
-
-
Muñoz, V.1
Eaton, W.A.2
-
49
-
-
1042291214
-
Myosin flexibility: Structural domains and collective vibrations
-
I. Navizet, R. Lavery, and R.L. Jernigan Myosin flexibility: structural domains and collective vibrations Proteins 54 2004 384 393
-
(2004)
Proteins
, vol.54
, pp. 384-393
-
-
Navizet, I.1
Lavery, R.2
Jernigan, R.L.3
-
50
-
-
0033545908
-
The solution structure and dynamics of an Arc repressor mutant reveal premelting conformational changes related to DNA binding
-
I.M.A. Nooren, A.W.M. Rietveld, G. Melacini, R.T. Sauer, R. Kaptein, and R. Boelens The solution structure and dynamics of an Arc repressor mutant reveal premelting conformational changes related to DNA binding Biochemistry 38 1999 6035 6042
-
(1999)
Biochemistry
, vol.38
, pp. 6035-6042
-
-
Nooren, I.M.A.1
Rietveld, A.W.M.2
Melacini, G.3
Sauer, R.T.4
Kaptein, R.5
Boelens, R.6
-
51
-
-
6944250414
-
Sparsely populated folding intermediates of the Fyn SH3 domain: Matching native-centric essential dynamics and experiment
-
J.E. Ollerenshaw, H. Kaya, H.S. Chan, and L. Kay Sparsely populated folding intermediates of the Fyn SH3 domain: matching native-centric essential dynamics and experiment Proc. Natl. Acad. Sci. USA 101 2004 14748 14753
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 14748-14753
-
-
Ollerenshaw, J.E.1
Kaya, H.2
Chan, H.S.3
Kay, L.4
-
52
-
-
0000735048
-
Inertial effects in butane stochastic dynamics
-
R.W. Pastor, and M. Karplus Inertial effects in butane stochastic dynamics J. Chem. Phys. 91 1989 211 218
-
(1989)
J. Chem. Phys.
, vol.91
, pp. 211-218
-
-
Pastor, R.W.1
Karplus, M.2
-
53
-
-
84952104504
-
An analysis of the accuracy of Langevin and molecular dynamics algorithms
-
R.W. Pastor, B.R. Brooks, and A. Szabo An analysis of the accuracy of Langevin and molecular dynamics algorithms Mol. Phys. 65 1988 1409 1419
-
(1988)
Mol. Phys.
, vol.65
, pp. 1409-1419
-
-
Pastor, R.W.1
Brooks, B.R.2
Szabo, A.3
-
55
-
-
14844300852
-
Maturation dynamics of bacteriophage HK97 capsid
-
A.J. Rader, D.H. Vlad, and I. Bahar Maturation dynamics of bacteriophage HK97 capsid Structure 13 2005 413 421
-
(2005)
Structure
, vol.13
, pp. 413-421
-
-
Rader, A.J.1
Vlad, D.H.2
Bahar, I.3
-
56
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
J.P. Ryckaert, G. Cicotti, and H.J.C. Berendsen Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes J. Comput. Phys. 23 1977 327 341
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Cicotti, G.2
Berendsen, H.J.C.3
-
57
-
-
0037143694
-
The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation
-
J. Shimada, and E.I. Shakhnovich The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation Proc. Natl. Acad. Sci. USA 99 2002 11175 11180
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 11175-11180
-
-
Shimada, J.1
Shakhnovich, E.I.2
-
58
-
-
0033515615
-
Exploring structures in protein folding funnels with free energy functionals: The transition state ensemble
-
B.A. Shoemaker, J. Wang, and P.G. Wolynes Exploring structures in protein folding funnels with free energy functionals: the transition state ensemble J. Mol. Biol. 287 1999 675 694
-
(1999)
J. Mol. Biol.
, vol.287
, pp. 675-694
-
-
Shoemaker, B.A.1
Wang, J.2
Wolynes, P.G.3
-
60
-
-
0037038372
-
Absolute comparison of simulated and experimental protein-folding dynamics
-
C.D. Snow, H. Nguyen, V.S. Pande, and M. Gruebele Absolute comparison of simulated and experimental protein-folding dynamics Nature 420 2002 102 106
-
(2002)
Nature
, vol.420
, pp. 102-106
-
-
Snow, C.D.1
Nguyen, H.2
Pande, V.S.3
Gruebele, M.4
-
61
-
-
0034520923
-
The rotary mechanism of ATP synthase
-
D. Stock, C. Gibbons, I. Arechaga, A.G.W. Leslie, and J.E. Walker The rotary mechanism of ATP synthase Curr. Opin. Struct. Biol. 10 2000 672 679
-
(2000)
Curr. Opin. Struct. Biol.
, vol.10
, pp. 672-679
-
-
Stock, D.1
Gibbons, C.2
Arechaga, I.3
Leslie, A.G.W.4
Walker, J.E.5
-
62
-
-
9644266693
-
Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis
-
F. Tama, and C.L. Brooks III Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis J. Mol. Biol. 345 2005 299 314
-
(2005)
J. Mol. Biol.
, vol.345
, pp. 299-314
-
-
Tama, F.1
Brooks III, C.L.2
-
63
-
-
0042424707
-
Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy
-
F. Tama, M. Valle, J. Frank, and C.L. Brooks III Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy Proc. Natl. Acad. Sci. USA 100 2003 9319 9323
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 9319-9323
-
-
Tama, F.1
Valle, M.2
Frank, J.3
Brooks III, C.L.4
-
64
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
-
M.M. Tirion Large amplitude elastic motions in proteins from a single-parameter, atomic analysis Phys. Rev. Lett. 77 1996 1905 1908
-
(1996)
Phys. Rev. Lett.
, vol.77
, pp. 1905-1908
-
-
Tirion, M.M.1
-
65
-
-
17044393884
-
Coarse-grained models for proteins
-
V. Tozzini Coarse-grained models for proteins Curr. Opin. Struct. Biol. 15 2005 144 150
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 144-150
-
-
Tozzini, V.1
-
66
-
-
0016696599
-
Studies on protein folding, unfolding and fluctuations by computer simulation. I. the effects of specific amino acid sequence represented by specific inter-unit interactions
-
Y. Ueda, H. Taketomi, and N. Gō Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effects of specific amino acid sequence represented by specific inter-unit interactions Int. J. Pept. Protein Res. 7 1975 445 459
-
(1975)
Int. J. Pept. Protein Res.
, vol.7
, pp. 445-459
-
-
Ueda, Y.1
Taketomi, H.2
Go, N.3
-
67
-
-
0000171351
-
Pairwise contact potentials are unsuitable for protein folding
-
M. Vendruscolo, and E. Domany Pairwise contact potentials are unsuitable for protein folding J. Chem. Phys. 109 1998 11101 11108
-
(1998)
J. Chem. Phys.
, vol.109
, pp. 11101-11108
-
-
Vendruscolo, M.1
Domany, E.2
-
69
-
-
4644301408
-
Domain swapping is a consequence of minimal frustration
-
S. Yang, S.S. Cho, Y. Levy, M.S. Cheung, H. Levine, P.G. Wolynes, and J.N. Onuchic Domain swapping is a consequence of minimal frustration Proc. Natl. Acad. Sci. USA 101 2004 13786 13791
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 13786-13791
-
-
Yang, S.1
Cho, S.S.2
Levy, Y.3
Cheung, M.S.4
Levine, H.5
Wolynes, P.G.6
Onuchic, J.N.7
-
70
-
-
13844276692
-
Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model
-
W. Zheng, and B. Brooks Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model J. Mol. Biol. 346 2005 745 759
-
(2005)
J. Mol. Biol.
, vol.346
, pp. 745-759
-
-
Zheng, W.1
Brooks, B.2
-
71
-
-
0345687171
-
A comparative study of motor-protein motions by using a simple elastic-network model
-
W. Zheng, and S. Doniach A comparative study of motor-protein motions by using a simple elastic-network model Proc. Natl. Acad. Sci. USA 100 2003 13253 13258
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 13253-13258
-
-
Zheng, W.1
Doniach, S.2
-
72
-
-
17044427535
-
Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved
-
W. Zheng, B.R. Brooks, S. Doniach, and D. Thirumalai Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved Structure 13 2005 565 577
-
(2005)
Structure
, vol.13
, pp. 565-577
-
-
Zheng, W.1
Brooks, B.R.2
Doniach, S.3
Thirumalai, D.4
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