-
1
-
-
0025845767
-
Ligand binding to heme proteins: Connection between dynamics and function
-
Steinbach, P. J., A. Ansari, J. Berendzen, D. Braunstein, K. Chu, B. R. Cowen, D. Ehrenstein, H. Frauenfelder, J. B. Johnson, and D. C. Lamb. 1991. Ligand binding to heme proteins: connection between dynamics and function. Biochemistry. 30:3988-4001.
-
(1991)
Biochemistry
, vol.30
, pp. 3988-4001
-
-
Steinbach, P.J.1
Ansari, A.2
Berendzen, J.3
Braunstein, D.4
Chu, K.5
Cowen, B.R.6
Ehrenstein, D.7
Frauenfelder, H.8
Johnson, J.B.9
Lamb, D.C.10
-
2
-
-
9944258521
-
New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate
-
Dixon, R. D., Y. Chen, F. Ding, S. D. Khare, K. C. Prutzman, M. D. Schaller, S. L. Campbell, and N. V. Dokholyan. 2004. New insights into FAK signaling and localization based on detection of a FAT domain folding intermediate. Structure. 12:2161-2171.
-
(2004)
Structure
, vol.12
, pp. 2161-2171
-
-
Dixon, R.D.1
Chen, Y.2
Ding, F.3
Khare, S.D.4
Prutzman, K.C.5
Schaller, M.D.6
Campbell, S.L.7
Dokholyan, N.V.8
-
3
-
-
4344649812
-
CBFβ allosterically regulates the Runx1 Runt domain via a dynamic conformational equilibrium
-
Yan, J., Y. Liu, S. M. Lukasik, N. A. Speck, and J. H. Bushweller. 2004. CBFβ allosterically regulates the Runx1 Runt domain via a dynamic conformational equilibrium. Nat. Struct. Mol. Biol. 11:901-906.
-
(2004)
Nat. Struct. Mol. Biol
, vol.11
, pp. 901-906
-
-
Yan, J.1
Liu, Y.2
Lukasik, S.M.3
Speck, N.A.4
Bushweller, J.H.5
-
4
-
-
33749386789
-
Insights into allosteric control of vinculin function from its large scale conformational dynamics
-
Chen, Y., and N. V. Dokholyan. 2006. Insights into allosteric control of vinculin function from its large scale conformational dynamics. J. Biol. Chem. 281:29148-29154.
-
(2006)
J. Biol. Chem
, vol.281
, pp. 29148-29154
-
-
Chen, Y.1
Dokholyan, N.V.2
-
5
-
-
0033525126
-
Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: Implications for the entropy of association with DNA
-
Bracken, C., P. A. Carr, J. Cavanagh, and A. G. Palmer III. 1999. Temperature dependence of intramolecular dynamics of the basic leucine zipper of GCN4: implications for the entropy of association with DNA. J. Mol. Biol. 285:2133-2146.
-
(1999)
J. Mol. Biol
, vol.285
, pp. 2133-2146
-
-
Bracken, C.1
Carr, P.A.2
Cavanagh, J.3
Palmer III, A.G.4
-
6
-
-
0041852853
-
The role of dynamics in enzyme activity
-
Daniel, R. M., R. V. Dunn, J. L. Finney, and J. C. Smith. 2003. The role of dynamics in enzyme activity. Annu. Rev. Biophys. Biomol. Struct. 32:69-92.
-
(2003)
Annu. Rev. Biophys. Biomol. Struct
, vol.32
, pp. 69-92
-
-
Daniel, R.M.1
Dunn, R.V.2
Finney, J.L.3
Smith, J.C.4
-
7
-
-
0346220393
-
The role of dynamics in allosteric regulation
-
Kern, D., and E. R. Zuiderweg. 2003. The role of dynamics in allosteric regulation. Curr. Opin. Struct. Biol. 13:748-757.
-
(2003)
Curr. Opin. Struct. Biol
, vol.13
, pp. 748-757
-
-
Kern, D.1
Zuiderweg, E.R.2
-
8
-
-
0034760077
-
Dynamic activation of protein function: A view emerging from NMR spectroscopy
-
Wand, A. J. 2001. Dynamic activation of protein function: a view emerging from NMR spectroscopy. Nat. Struct. Biol. 8:926-931.
-
(2001)
Nat. Struct. Biol
, vol.8
, pp. 926-931
-
-
Wand, A.J.1
-
9
-
-
0031853060
-
Protein dynamics from NMR
-
Kay, L. E. 1998. Protein dynamics from NMR. Nat. Struct. Biol. 5(Suppl):513-517.
-
(1998)
Nat. Struct. Biol
, vol.5
, Issue.SUPPL.
, pp. 513-517
-
-
Kay, L.E.1
-
10
-
-
0027166162
-
Dynamic properties of proteins from NMR spectroscopy
-
Palmer III, A. G. 1993. Dynamic properties of proteins from NMR spectroscopy. Curr. Opin. Biotechnol. 4:385-391.
-
(1993)
Curr. Opin. Biotechnol
, vol.4
, pp. 385-391
-
-
Palmer III, A.G.1
-
11
-
-
0034984208
-
NMR probes of molecular dynamics: Overview and comparison with other techniques
-
Palmer III, A. G. 2001. NMR probes of molecular dynamics: overview and comparison with other techniques. Annu. Rev. Biophys. Biomol. Struct. 30:129-155.
-
(2001)
Annu. Rev. Biophys. Biomol. Struct
, vol.30
, pp. 129-155
-
-
Palmer III, A.G.1
-
12
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus, M., and J. A. McCammon. 2002. Molecular dynamics simulations of biomolecules. Nat. Struct. Biol. 9:646-652.
-
(2002)
Nat. Struct. Biol
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
13
-
-
0036283096
-
Molecular dynamics and NMR spin relaxation in proteins
-
Case, D. A. 2002. Molecular dynamics and NMR spin relaxation in proteins. Acc. Chem. Res. 35:325-331.
-
(2002)
Acc. Chem. Res
, vol.35
, pp. 325-331
-
-
Case, D.A.1
-
14
-
-
3042846748
-
Determination of protein structures consistent with NMR order parameters
-
Best, R. B., and M. Vendruscolo. 2004. Determination of protein structures consistent with NMR order parameters. J. Am. Chem. Soc. 126:8090-8091.
-
(2004)
J. Am. Chem. Soc
, vol.126
, pp. 8090-8091
-
-
Best, R.B.1
Vendruscolo, M.2
-
15
-
-
33646719091
-
Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity
-
Lipari, G., and A. Szabo. 1982. Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity. J. Am. Chem. Soc. 104:4546-4559.
-
(1982)
J. Am. Chem. Soc
, vol.104
, pp. 4546-4559
-
-
Lipari, G.1
Szabo, A.2
-
16
-
-
0345707599
-
Increased rigidity of eglin c at acidic pH: Evidence from NMR spin relaxation and MD simulations
-
Hu, H., M. W. Clarkson, J. Hermans, and A. L. Lee. 2003. Increased rigidity of eglin c at acidic pH: evidence from NMR spin relaxation and MD simulations. Biochemistry. 42:13856-13868.
-
(2003)
Biochemistry
, vol.42
, pp. 13856-13868
-
-
Hu, H.1
Clarkson, M.W.2
Hermans, J.3
Lee, A.L.4
-
17
-
-
0034823221
-
Simulated and NMR-derived backbone dynamics of a protein with significant flexibility: A comparison of spectral densities for the βARK1 PH domain
-
Pfeiffer, S., D. Fushman, and D. Cowburn. 2001. Simulated and NMR-derived backbone dynamics of a protein with significant flexibility: a comparison of spectral densities for the βARK1 PH domain. J. Am. Chem. Soc. 123:3021-3036.
-
(2001)
J. Am. Chem. Soc
, vol.123
, pp. 3021-3036
-
-
Pfeiffer, S.1
Fushman, D.2
Cowburn, D.3
-
18
-
-
0037457815
-
Dynamics and entropy of a calmodulin-peptide complex studied by NMR and molecular dynamics
-
Prabhu, N. V., A. L. Lee, A. J. Wand, and K. A. Sharp. 2003. Dynamics and entropy of a calmodulin-peptide complex studied by NMR and molecular dynamics. Biochemistry. 42:562-570.
-
(2003)
Biochemistry
, vol.42
, pp. 562-570
-
-
Prabhu, N.V.1
Lee, A.L.2
Wand, A.J.3
Sharp, K.A.4
-
19
-
-
0037176836
-
13C NMR relaxation and computational molecular dynamics
-
13C NMR relaxation and computational molecular dynamics. Biochemistry. 41:2655-2666.
-
(2002)
Biochemistry
, vol.41
, pp. 2655-2666
-
-
Pang, Y.1
Buck, M.2
Zuiderweg, E.R.3
-
21
-
-
0037441479
-
Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution
-
Hu, H., M. Elstner, and J. Hermans. 2003. Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution. Proteins. 50:451-463.
-
(2003)
Proteins
, vol.50
, pp. 451-463
-
-
Hu, H.1
Elstner, M.2
Hermans, J.3
-
22
-
-
12744263121
-
Simultaneous determination of protein structure and dynamics
-
Lindorff-Larsen, K., R. B. Best, M. A. Depristo, C. M. Dobson, and M. Vendruscolo. 2005. Simultaneous determination of protein structure and dynamics. Nature. 433:128-132.
-
(2005)
Nature
, vol.433
, pp. 128-132
-
-
Lindorff-Larsen, K.1
Best, R.B.2
Depristo, M.A.3
Dobson, C.M.4
Vendruscolo, M.5
-
23
-
-
27244432202
-
Interpreting dynamically averaged scalar couplings in proteins
-
Lindorff-Larsen, K., R. B. Best, and M. Vendruscolo. 2005. Interpreting dynamically averaged scalar couplings in proteins. J. Biomol. NMR. 32:273-280.
-
(2005)
J. Biomol. NMR
, vol.32
, pp. 273-280
-
-
Lindorff-Larsen, K.1
Best, R.B.2
Vendruscolo, M.3
-
24
-
-
0037215324
-
Weak alignment offers new NMR opportunities to study protein structure and dynamics
-
Bax, A. 2003. Weak alignment offers new NMR opportunities to study protein structure and dynamics. Protein Sci. 12:1-16.
-
(2003)
Protein Sci
, vol.12
, pp. 1-16
-
-
Bax, A.1
-
25
-
-
33645834303
-
New tools provide new insights in NMR studies of protein dynamics
-
Mittermaier, A., and L. E. Kay. 2006. New tools provide new insights in NMR studies of protein dynamics. Science. 312:224-228.
-
(2006)
Science
, vol.312
, pp. 224-228
-
-
Mittermaier, A.1
Kay, L.E.2
-
26
-
-
0032443390
-
Discrete molecular dynamics studies of the folding of a protein-like model
-
Dokholyan, N. V., S. V. Buldyrev, H. E. Stanley, and E. I. Shakhnovich. 1998. Discrete molecular dynamics studies of the folding of a protein-like model. Fold. Des. 3:577-587.
-
(1998)
Fold. Des
, vol.3
, pp. 577-587
-
-
Dokholyan, N.V.1
Buldyrev, S.V.2
Stanley, H.E.3
Shakhnovich, E.I.4
-
27
-
-
0842283895
-
Hydrophobic core fluidity of homologous protein domains: Relation of side-chain dynamics to core composition and packing
-
Best, R. B., T. J. Rutherford, S. M. Freund, and J. Clarke. 2004. Hydrophobic core fluidity of homologous protein domains: relation of side-chain dynamics to core composition and packing. Biochemistry. 43:1145-1155.
-
(2004)
Biochemistry
, vol.43
, pp. 1145-1155
-
-
Best, R.B.1
Rutherford, T.J.2
Freund, S.M.3
Clarke, J.4
-
29
-
-
0029633186
-
AMBER, a package of computer programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules
-
Pearlman, D. A., D. A. Case, J. W. Caldwell, W. S. Ross, T. E. Cheatham, S. Debolt, D. Ferguson, G. Seibel, and P. Kollman. 1995. AMBER, a package of computer programs for applying molecular mechanics, normal-mode analysis, molecular-dynamics and free-energy calculations to simulate the structural and energetic properties of molecules. Comput. Phys. Commun. 91:1-41.
-
(1995)
Comput. Phys. Commun
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham, T.E.5
Debolt, S.6
Ferguson, D.7
Seibel, G.8
Kollman, P.9
-
30
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23:327-341.
-
(1977)
J. Comput. Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
31
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J. C., J. P. M. Postma, W. F. Vangunsteren, A. Dinola, and J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
-
(1984)
J. Chem. Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Vangunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
36
-
-
0033620360
-
13C NMR relaxation techniques for the study of protein methyl group dynamics in solution
-
13C NMR relaxation techniques for the study of protein methyl group dynamics in solution. J. Am. Chem. Soc. 121:2891-2902.
-
(1999)
J. Am. Chem. Soc
, vol.121
, pp. 2891-2902
-
-
Lee, A.L.1
Flynn, P.F.2
Wand, A.J.3
-
38
-
-
33748518255
-
Comparison of multiple AMBER force fields and development of improved protein backbone parameters
-
Hornak, V., R. Abel, A. Okur, B. Strockbine, A. Roitberg, and C. Simmerling. 2006. Comparison of multiple AMBER force fields and development of improved protein backbone parameters. Proteins. 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
-
39
-
-
3042639229
-
The origin of protein sidechain order parameter distributions
-
Best, R. B., J. Clarke, and M. Karplus. 2004. The origin of protein sidechain order parameter distributions. J. Am. Chem. Soc. 126:7734-7735.
-
(2004)
J. Am. Chem. Soc
, vol.126
, pp. 7734-7735
-
-
Best, R.B.1
Clarke, J.2
Karplus, M.3
-
40
-
-
23344451429
-
Relating side-chain mobility in proteins to rotameric transitions: Insights from molecular dynamics simulations and NMR
-
Hu, H., J. Hermans, and A. L. Lee. 2005. Relating side-chain mobility in proteins to rotameric transitions: insights from molecular dynamics simulations and NMR. J. Biomol. NMR. 32:151-162.
-
(2005)
J. Biomol. NMR
, vol.32
, pp. 151-162
-
-
Hu, H.1
Hermans, J.2
Lee, A.L.3
-
42
-
-
1942456697
-
Recent advances in the development and application of implicit solvent models in biomolecule simulations
-
Feig, M., and C. L. Brooks III. 2004. Recent advances in the development and application of implicit solvent models in biomolecule simulations. Curr. Opin. Struct. Biol. 14:217-224.
-
(2004)
Curr. Opin. Struct. Biol
, vol.14
, pp. 217-224
-
-
Feig, M.1
Brooks III, C.L.2
-
43
-
-
0035906650
-
Calculation of ensembles of structures representing the unfolded state of an SH3 domain
-
Choy, W. Y., and J. D. Forman-Kay. 2001. Calculation of ensembles of structures representing the unfolded state of an SH3 domain. J. Mol. Biol. 308:1011-1032.
-
(2001)
J. Mol. Biol
, vol.308
, pp. 1011-1032
-
-
Choy, W.Y.1
Forman-Kay, J.D.2
-
44
-
-
0000243829
-
PROCHECK - a program to check the stereochemical quality of protein structures
-
Laskowski, R. A., M. W. Macarthur, D. S. Moss, and J. M. Thornton. 1993. PROCHECK - a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26:283-291.
-
(1993)
J. Appl. Cryst
, vol.26
, pp. 283-291
-
-
Laskowski, R.A.1
Macarthur, M.W.2
Moss, D.S.3
Thornton, J.M.4
-
45
-
-
0026655361
-
Stereochemical quality of protein structure coordinates
-
Morris, A. L., M. W. MacArthur, E. G. Hutchinson, and J. M. Thornton. 1992. Stereochemical quality of protein structure coordinates. Proteins. 12:345-364.
-
(1992)
Proteins
, vol.12
, pp. 345-364
-
-
Morris, A.L.1
MacArthur, M.W.2
Hutchinson, E.G.3
Thornton, J.M.4
-
46
-
-
0033954256
-
The Protein DataBank
-
Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. 2000. The Protein DataBank. Nucleic Acids Res. 28:235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
47
-
-
23944480351
-
Simple but predictive protein models
-
Ding, F., and N. V. Dokholyan. 2005. Simple but predictive protein models. Trends Biotechnol. 23:450-455.
-
(2005)
Trends Biotechnol
, vol.23
, pp. 450-455
-
-
Ding, F.1
Dokholyan, N.V.2
-
48
-
-
11244291006
-
Folding Tr-pcage to NMR resolution native structure using a coarse-grained protein model
-
Ding, F., S. V. Buldyrev, and N. V. Dokholyan. 2005. Folding Tr-pcage to NMR resolution native structure using a coarse-grained protein model. Biophys. J. 88:147-155.
-
(2005)
Biophys. J
, vol.88
, pp. 147-155
-
-
Ding, F.1
Buldyrev, S.V.2
Dokholyan, N.V.3
-
49
-
-
0242662235
-
Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis
-
Khare, S. D., F. Ding, and N. V. Dokholyan. 2003. Folding of Cu, Zn superoxide dismutase and familial amyotrophic lateral sclerosis. J. Mol. Biol. 334:515-525.
-
(2003)
J. Mol. Biol
, vol.334
, pp. 515-525
-
-
Khare, S.D.1
Ding, F.2
Dokholyan, N.V.3
|