-
1
-
-
0017776823
-
Dynamics of folded proteins
-
McCammon, J. A.; Gelin, B. R.; Karplus, M. Dynamics of folded proteins. Nature 1977, 267, 585-590.
-
(1977)
Nature
, vol.267
, pp. 585-590
-
-
McCammon, J.A.1
Gelin, B.R.2
Karplus, M.3
-
2
-
-
0036283096
-
Molecular dynamics and NMR spin relaxation in proteins
-
Case, D. A. Molecular dynamics and NMR spin relaxation in proteins. Acc. Chem. Res. 2002, 35, 325-331.
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 325-331
-
-
Case, D.A.1
-
3
-
-
0037154884
-
Enzyme dynamics during catalysis
-
Eisenmesser, E. Z.; Bosco, D. A.; Akke, M.; Kern, D. Enzyme dynamics during catalysis. Science 2002, 295, 1520-1523.
-
(2002)
Science
, vol.295
, pp. 1520-1523
-
-
Eisenmesser, E.Z.1
Bosco, D.A.2
Akke, M.3
Kern, D.4
-
4
-
-
37249032102
-
Dynamic personalities of proteins
-
Henzler-Wildman, K.; Kern, D. Dynamic personalities of proteins. Nature 2007, 450, 964-972.
-
(2007)
Nature
, vol.450
, pp. 964-972
-
-
Henzler-Wildman, K.1
Kern, D.2
-
5
-
-
0037317303
-
A dynamic mechanism of nuclear receptor activation and its perturbation in a human disease
-
Kallenberger, B. C.; Love, J. D.; Chatterjee, V. K. K.; Schwabe, J. W. R. A dynamic mechanism of nuclear receptor activation and its perturbation in a human disease. Nat. Struct. Biol. 2003, 70, 136-140.
-
(2003)
Nat. Struct. Biol.
, vol.70
, pp. 136-140
-
-
Kallenberger, B.C.1
Love, J.D.2
Chatterjee, V.K.K.3
Schwabe, J.W.R.4
-
6
-
-
0019889036
-
a, proton-transfer reactions, and general acid catalysis reactions in enzymes
-
a, proton-transfer reactions, and general acid catalysis reactions in enzymes. Biochemistry 1981, 20, 3167.
-
(1981)
Biochemistry
, vol.20
, pp. 3167
-
-
Warshel, A.1
-
7
-
-
0346726109
-
How enzymes work: Analysis by modern rate theory and computer simulations
-
Garcia-Viloca, M.; Gao, J.; Karplus, M.; Truhlar, D. G. How enzymes work: Analysis by modern rate theory and computer simulations. Science 2004, 303 (5655), 186-195.
-
(2004)
Science
, vol.303
, Issue.5655
, pp. 186-195
-
-
Garcia-Viloca, M.1
Gao, J.2
Karplus, M.3
Truhlar, D.G.4
-
8
-
-
0029151245
-
First-principles calculation of the folding free energy of a three-helix bundle protein
-
Boczko, E. M.; Brooks, C. L., 3rd. First-principles calculation of the folding free energy of a three-helix bundle protein. Science 1995, 269 (5222), 393-396.
-
(1995)
Science
, vol.269
, Issue.5222
, pp. 393-396
-
-
Boczko, E.M.1
Brooks III, C.L.2
-
9
-
-
27744499156
-
Intrinsic dynamics of an enzyme underlies catalysis
-
DOI 10.1038/nature04105, PII N04105
-
Eisenmesser, E. Z.; Millet, O.; Labeikovsky, W.; Korzhnev, D. M.; Wolf-Watz, M.; Bosco, D. A.; Skalicky, J. J.; Kay, L. E.; Kern, D. Intrinsic dynamics of an enzyme underlies catalysis. Nature 2005, 438 (7064), 117-121. (Pubitemid 41599831)
-
(2005)
Nature
, vol.438
, Issue.7064
, pp. 117-121
-
-
Eisenmesser, E.Z.1
Millet, O.2
Labeikovsky, W.3
Korzhnev, D.M.4
Wolf-Watz, M.5
Bosco, D.A.6
Skalicky, J.J.7
Kay, L.E.8
Kern, D.9
-
10
-
-
34547298869
-
Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking
-
DOI 10.1002/jcc.20720
-
Wroblewska, L.; Skolnick, J. Can a Physics-Based, All-Atom Potential Find a Protein's Native Structure Among Misfolded Structures? I. Large Scale AMBER Benchmarking. J. Comput. Chem. 2007, 28, 2059. (Pubitemid 47153603)
-
(2007)
Journal of Computational Chemistry
, vol.28
, Issue.12
, pp. 2059-2066
-
-
Wroblewska, L.1
Skolnick, J.2
-
12
-
-
0041377620
-
Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy
-
Zhang, D. W.; Zhang, J. Z. H. Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy. J. Chem. Phys. 2003, 119, 3599.
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 3599
-
-
Zhang, D.W.1
Zhang, J.Z.H.2
-
13
-
-
4143088551
-
An efficient linear scaling method for ab initio calculation of electron density of proteins
-
Gao, A. M.; Zhang, D. W.; Zhang, J. Z. H.; Zhang, Y. K. An efficient linear scaling method for ab initio calculation of electron density of proteins. Chem. Phys. Lett. 2004, 394, 193-1191
-
(2004)
Chem. Phys. Lett.
, vol.394
, pp. 193-1191
-
-
Gao, A.M.1
Zhang, D.W.2
Zhang, J.Z.H.3
Zhang, Y.K.4
-
14
-
-
33748569544
-
A new quantum method for electrostatic solvation energy of protein
-
Mei, Y.; Ji, C. G.; Zhang, J. Z. H. A new quantum method for electrostatic solvation energy of protein. J. Chem. Phys. 2006, 125, 94906.
-
(2006)
J. Chem. Phys.
, vol.125
, pp. 94906
-
-
Mei, Y.1
Ji, C.G.2
Zhang, J.Z.H.3
-
15
-
-
0018094892
-
Electrostatic effects in proteins
-
Perutz, M. Electrostatic effects in proteins. Science 1978, 207, 1187.
-
(1978)
Science
, vol.207
, pp. 1187
-
-
Perutz, M.1
-
16
-
-
0021476470
-
Calculations of electrostatic effects in biological systems and in solutions
-
Warshel, A.; Russell, S. Calculations of electrostatic effects in biological systems and in solutions. Q. Rev. Biophys. 1984, 17(191), 283-342.
-
(1984)
Q. Rev. Biophys.
, vol.17
, Issue.191
, pp. 283-342
-
-
Warshel, A.1
Russell, S.2
-
17
-
-
0021935830
-
Electrostatic effects in proteins
-
Matthew, J. B. Electrostatic effects in proteins. Annu. Rev. Biophys. Biochem. 1985, 14, 387-417.
-
(1985)
Annu. Rev. Biophys. Biochem.
, vol.14
, pp. 387-417
-
-
Matthew, J.B.1
-
18
-
-
0029016182
-
Classical electrostatics in biology and chemistry
-
Honig, B.; Nicholls, A. Classical electrostatics in biology and chemistry. Science 1995, 268, 1144.
-
(1995)
Science
, vol.268
, pp. 1144
-
-
Honig, B.1
Nicholls, A.2
-
19
-
-
4243463817
-
Electrostatics in biomolecular structure and dynamics
-
Davis, M. E.; McCammon, J. A. Electrostatics in biomolecular structure and dynamics. Chem. Rev. 1990, 90, 509.
-
(1990)
Chem. Rev.
, vol.90
, pp. 509
-
-
Davis, M.E.1
McCammon, J.A.2
-
20
-
-
58049209744
-
Protein Polarization Is Critical to Stabilizing AF-2 and Helix-2 Domains in Ligand Binding to PPARys
-
Ji, C. G.; Zhang, J. Z. H. Protein Polarization Is Critical to Stabilizing AF-2 and Helix-2 Domains in Ligand Binding to PPARys. J. Am Chem. Soc. 2008, 130, 17129.
-
(2008)
J. Am Chem. Soc.
, vol.130
, pp. 17129
-
-
Ji, C.G.1
Zhang, J.Z.H.2
-
21
-
-
0030628825
-
Theory of protein folding: The energy landscape perspective
-
Onuchic, J. N.; Luthey-Schulten, Z.; Wolynes, P. G. Theory of protein folding: The energy landscape perspective. Annu. Rev. Phys. Chem. 1997, 48, 545.
-
(1997)
Annu. Rev. Phys. Chem.
, vol.48
, pp. 545
-
-
Onuchic, J.N.1
Luthey-Schulten, Z.2
Wolynes, P.G.3
-
22
-
-
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.; 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.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10269
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.3
Kollman, P.A.4
-
23
-
-
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
-
24
-
-
33745362452
-
Variability of the 15N chemical shielding tensors in the B3 domain of protein G from 15N relaxation measurements at several fields. Implications for backbone order parameters
-
Hall, J. B.; Fushman, D. Variability of the 15N chemical shielding tensors in the B3 domain of protein G from 15N relaxation measurements at several fields. Implications for backbone order parameters. J. Am. Chem. Soc. 2006, 128, 7855-7870.
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 7855-7870
-
-
Hall, J.B.1
Fushman, D.2
-
25
-
-
41149138253
-
Structural analysis of protein dynamics by MD simulations and NMR spinrelaxation
-
Trbovic, N.; Kim, B.; Friesner, R. A.; Palmer, A. G. Structural analysis of protein dynamics by MD simulations and NMR spinrelaxation. Proteins 2008, 71, 684-694.
-
(2008)
Proteins
, vol.71
, pp. 684-694
-
-
Trbovic, N.1
Kim, B.2
Friesner, R.A.3
Palmer, A.G.4
-
26
-
-
0032719896
-
Calculations of NMR dipolar coupling strengths in model peptides
-
Case, D. A. Calculations of NMR dipolar coupling strengths in model peptides. J. Biomol. NMR 1999, 15, 95-102.
-
(1999)
J. Biomol. NMR
, vol.15
, pp. 95-102
-
-
Case, D.A.1
-
27
-
-
36649021120
-
Design of a Next Generation Force Field: The X-POL Potential
-
(a) Xie, W. S.; Gao, J. L. Design of a Next Generation Force Field: The X-POL Potential. J. Chem. Theory Comput. 2007, 3, 1890.
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 1890
-
-
Xie, W.S.1
Gao, J.L.2
-
28
-
-
57049120521
-
Incorporation of a QM/MM Buffer Zone in the Variational Double Self-Consistent Field Method
-
(b) Xie, W. S.; Song, L. C.; Truhlař, D. G.; Gao, J. L. Incorporation of a QM/MM Buffer Zone in the Variational Double Self-Consistent Field Method. J. Phys. Chem. B 2008, 112, 14124.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 14124
-
-
Xie, W.S.1
Song, L.C.2
Truhlař, D.G.3
Gao, J.L.4
-
29
-
-
33646565044
-
The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO)
-
Fedorov, D. G.; Kitaura, K.; Li, H.; Jensen, J. H.; Gordon, M. S. The polarizable continuum model (PCM) interfaced with the fragment molecular orbital method (FMO). J. Comput. Chem. 2006, 27, 976.
-
(2006)
J. Comput. Chem.
, vol.27
, pp. 976
-
-
Fedorov, D.G.1
Kitaura, K.2
Li, H.3
Jensen, J.H.4
Gordon, M.S.5
-
30
-
-
33846321576
-
A Fast QM/MM (Quantum Mechanical/ Molecular Mechanical) Approach to Calculate Nuclear Magnetic Resonance Chemical Shifts for Macromolecules
-
Wang, B.; Merz, K. M. A Fast QM/MM (Quantum Mechanical/ Molecular Mechanical) Approach to Calculate Nuclear Magnetic Resonance Chemical Shifts for Macromolecules. J. Chem. Theory Comput. 2006, 2, 209.
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 209
-
-
Wang, B.1
Merz, K.M.2
|