-
1
-
-
0347357617
-
Protein folding and misfolding
-
DOI 10.1038/nature02261
-
C.M. Dobson Protein folding and misfolding Nature 426 2003 884 890 (Pubitemid 38056880)
-
(2003)
Nature
, vol.426
, Issue.6968
, pp. 884-890
-
-
Dobson, C.M.1
-
2
-
-
34447297323
-
Energetics of Protein Folding
-
DOI 10.1016/j.jmb.2007.05.078, PII S0022283607007371
-
R.L. Baldwin Energetics of protein folding J. Mol. Biol. 371 2007 283 301 (Pubitemid 47049810)
-
(2007)
Journal of Molecular Biology
, vol.371
, Issue.2
, pp. 283-301
-
-
Baldwin, R.L.1
-
3
-
-
0037038372
-
Absolute comparison of simulated and experimental protein-folding dynamics
-
DOI 10.1038/nature01160
-
C.D. Snow, and H. Nguyen M. Gruebele Absolute comparison of simulated and experimental protein-folding dynamics Nature 420 2002 102 106 (Pubitemid 35291448)
-
(2002)
Nature
, vol.420
, Issue.6911
, pp. 102-106
-
-
Snow, C.D.1
Nguyen, H.2
Pande, V.S.3
Gruebele, M.4
-
5
-
-
79959720287
-
How robust are protein folding simulations with respect to force field parameterization?
-
S. Piana, K. Lindorff-Larsen, and D.E. Shaw How robust are protein folding simulations with respect to force field parameterization? Biophys. J. 100 2011 L47 L49
-
(2011)
Biophys. J.
, vol.100
-
-
Piana, S.1
Lindorff-Larsen, K.2
Shaw, D.E.3
-
9
-
-
67649494492
-
Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides
-
R.B. Best, and G. Hummer Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides J. Phys. Chem. B 113 2009 9004 9015
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 9004-9015
-
-
Best, R.B.1
Hummer, G.2
-
10
-
-
84857463877
-
Systematic validation of protein force fields against experimental data
-
K. Lindorff-Larsen, and P. Maragakis D.E. Shaw Systematic validation of protein force fields against experimental data PLoS ONE 7 2012 e32131
-
(2012)
PLoS ONE
, vol.7
, pp. 32131
-
-
Lindorff-Larsen, K.1
Maragakis, P.2
Shaw, D.E.3
-
11
-
-
84865758046
-
Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation
-
R.B. Best, and J. Mittal A.D. MacKerell Jr. Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation Biophys. J. 103 2012 1045 1051
-
(2012)
Biophys. J.
, vol.103
, pp. 1045-1051
-
-
Best, R.B.1
Mittal, J.2
Mackerell, Jr.A.D.3
-
12
-
-
0029864379
-
Collapse and cooperativity in protein folding
-
DOI 10.1016/S0959-440X(96)80092-3
-
A.D. Miranker, and C.M. Dobson Collapse and cooperativity in protein folding Curr. Opin. Struct. Biol. 6 1996 31 42 (Pubitemid 26073942)
-
(1996)
Current Opinion in Structural Biology
, vol.6
, Issue.1
, pp. 31-42
-
-
Miranker, A.D.1
Dobson, C.M.2
-
14
-
-
0031056829
-
Instability, unfolding and aggregation of human lysozyme variants underlying amyloid fibrillogenesis
-
DOI 10.1038/385787a0
-
D.R. Booth, and M. Sunde M.B. Pepys Instability, unfolding and aggregation of human lysozyme variants underlying amyloid fibrillogenesis Nature 385 1997 787 793 (Pubitemid 27106061)
-
(1997)
Nature
, vol.385
, Issue.6619
, pp. 787-793
-
-
Booth, D.R.1
Sunde, M.2
Bellotti, V.3
Robinson, C.V.4
Hutchinson, W.L.5
Fraser, P.E.6
Hawkins, P.N.7
Dobson, C.M.8
Radford, S.E.9
Blake, C.C.F.10
Pepys, M.B.11
-
15
-
-
0042467574
-
A camelid antibody fragment inhibits the formation of amyloid fibrils by human lysozyme
-
DOI 10.1038/nature01870
-
M. Dumoulin, and A.M. Last C.M. Dobson A camelid antibody fragment inhibits the formation of amyloid fibrils by human lysozyme Nature 424 2003 783 788 (Pubitemid 37021708)
-
(2003)
Nature
, vol.424
, Issue.6950
, pp. 783-788
-
-
Dumoulin, M.1
Last, A.M.2
Desmyter, A.3
Decanniere, K.4
Canet, D.5
Larsson, G.6
Spencer, A.7
Archer, D.B.8
Sasse, J.9
Muyldermans, S.10
Wyns, L.11
Redfield, C.12
Matagne, A.13
Robinson, C.V.14
Dobson, C.M.15
-
16
-
-
77957937199
-
Atomic-level characterization of the structural dynamics of proteins
-
D.E. Shaw, and P. Maragakis W. Wriggers Atomic-level characterization of the structural dynamics of proteins Science 330 2010 341 346
-
(2010)
Science
, vol.330
, pp. 341-346
-
-
Shaw, D.E.1
Maragakis, P.2
Wriggers, W.3
-
17
-
-
20544435097
-
Exploring the helix-coil transition via all-atom equilibrium ensemble simulations
-
DOI 10.1529/biophysj.104.051938
-
E.J. Sorin, and V.S. Pande Exploring the helix-coil transition via all-atom equilibrium ensemble simulations Biophys. J. 88 2005 2472 2493 (Pubitemid 40976118)
-
(2005)
Biophysical Journal
, vol.88
, Issue.4
, pp. 2472-2493
-
-
Sorin, E.J.1
Pande, V.S.2
-
18
-
-
0037065310
-
The Trp cage: Folding kinetics and unfolded state topology via molecular dynamics simulations
-
DOI 10.1021/ja028604l
-
C.D. Snow, B. Zagrovic, and V.S. Pande The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations J. Am. Chem. Soc. 124 2002 14548 14549 (Pubitemid 35425023)
-
(2002)
Journal of the American Chemical Society
, vol.124
, Issue.49
, pp. 14548-14549
-
-
Snow, C.D.1
Zagrovic, B.2
Pande, V.S.3
-
19
-
-
77953508894
-
Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein
-
R. Day, D. Paschek, and A.E. Garcia Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein Proteins Struct. Funct. Bioinf. 78 2010 1889 1899
-
(2010)
Proteins Struct. Funct. Bioinf.
, vol.78
, pp. 1889-1899
-
-
Day, R.1
Paschek, D.2
Garcia, A.E.3
-
20
-
-
79952476196
-
Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences
-
R.B. Best, and J. Mittal Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: similarities and differences Proteins Struct. Funct. Bioinf. 79 2011 1318 1328
-
(2011)
Proteins Struct. Funct. Bioinf.
, vol.79
, pp. 1318-1328
-
-
Best, R.B.1
Mittal, J.2
-
21
-
-
79960592580
-
Microscopic events in β-hairpin folding from alternative unfolded ensembles
-
R.B. Best, and J. Mittal Microscopic events in β-hairpin folding from alternative unfolded ensembles Proc. Natl. Acad. Sci. USA 108 2011 11087 11092
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 11087-11092
-
-
Best, R.B.1
Mittal, J.2
-
22
-
-
54249091171
-
The unfolded ensemble and folding mechanism of the C-terminal GB1 β-hairpin
-
M. Bonomi, and D. Branduardi M. Parrinello The unfolded ensemble and folding mechanism of the C-terminal GB1 β-hairpin J. Am. Chem. Soc. 130 2008 13938 13944
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 13938-13944
-
-
Bonomi, M.1
Branduardi, D.2
Parrinello, M.3
-
24
-
-
0028222235
-
Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions
-
A. Chakrabartty, T. Kortemme, and R.L. Baldwin Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions Protein Sci. 3 1994 843 852 (Pubitemid 24139910)
-
(1994)
Protein Science
, vol.3
, Issue.5
, pp. 843-852
-
-
Chakrabartty, A.1
Kortemme, T.2
Baldwin, R.L.3
-
25
-
-
0030447864
-
Helix propagation and N-cap propensities of the amino acids measured in alanine-based peptides in 40 volume percent trifluoroethanol
-
C.A. Rohl, A. Chakrabartty, and R.L. Baldwin Helix propagation and N-cap propensities of the amino acids measured in alanine-based peptides in 40 volume percent trifluoroethanol Protein Sci. 5 1996 2623 2637 (Pubitemid 26424875)
-
(1996)
Protein Science
, vol.5
, Issue.12
, pp. 2623-2637
-
-
Rohl, C.A.1
Chakrabartty, A.2
Baldwin, R.L.3
-
26
-
-
0030874298
-
Comparison of nh exchange and circular dichroism as techniques for measuring the parameters of the helix-coil transition in peptides
-
DOI 10.1021/bi9706677
-
C.A. Rohl, and R.L. Baldwin Comparison of NH exchange and circular dichroism as techniques for measuring the parameters of the helix-coil transition in peptides Biochemistry 36 1997 8435 8442 (Pubitemid 27305125)
-
(1997)
Biochemistry
, vol.36
, Issue.28
, pp. 8435-8442
-
-
Rohl, C.A.1
Baldwin, R.L.2
-
28
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
A.D. MacKerell Jr., and D. Bashford M. Karplus All-atom empirical potential for molecular modeling and dynamics studies of proteins J. Phys. Chem. B 102 1998 3586 3616 (Pubitemid 128576688)
-
(1998)
Journal of Physical Chemistry B
, vol.102
, Issue.18
, pp. 3586-3616
-
-
MacKerell Jr., A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack Jr., R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher III, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
29
-
-
3142714765
-
Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
-
A.D. Mackerell Jr., M. Feig, and C.L. Brooks 3rd Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations J. Comput. Chem. 25 2004 1400 1415
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1400-1415
-
-
Mackerell Jr., A.D.1
Feig, M.2
Brooks III, C.L.3
-
30
-
-
33748518255
-
Comparison of multiple amber force fields and development of improved protein backbone parameters
-
DOI 10.1002/prot.21123
-
V. Hornak, and R. Abel C. Simmerling Comparison of multiple Amber force fields and development of improved protein backbone parameters Proteins Struct. Funct. Bioinf. 65 2006 712 725 (Pubitemid 44583220)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.65
, Issue.3
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
31
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Y. Duan, and C. Wu P. Kollman A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations J. Comput. Chem. 24 2003 1999 2012
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Kollman, P.3
-
32
-
-
84865723813
-
Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles
-
R.B. Best, and X. Zhu A.D. Mackerell Jr. Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles J. Chem. Theory Comput. 8 2012 3257 3273
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 3257-3273
-
-
Best, R.B.1
Zhu, X.2
Mackerell, Jr.A.D.3
-
33
-
-
84890447773
-
Polarizable force field for peptides and proteins based on the classical Drude oscillator
-
P.E.M. Lopes, and J. Huang A.D. Mackerell Jr. Polarizable force field for peptides and proteins based on the classical Drude oscillator J. Chem. Theory Comput. 9 2013 5430 5449
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 5430-5449
-
-
Lopes, P.E.M.1
Huang, J.2
Mackerell, Jr.A.D.3
-
34
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
W.L. Jorgensen, and J. Chandrasekhar M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Klein, M.L.3
-
35
-
-
30344482264
-
A polarizable model of water for molecular dynamics simulations of biomolecules
-
DOI 10.1016/j.cplett.2005.10.135, PII S0009261405017069
-
G. Lamoureux, and E. Harder A.D. MacKerell Jr. A polarizable model of water for molecular dynamics simulations of biomolecules Chem. Phys. Lett. 418 2006 245 249 (Pubitemid 43063383)
-
(2006)
Chemical Physics Letters
, vol.418
, Issue.1-3
, pp. 245-249
-
-
Lamoureux, G.1
Harder, E.2
Vorobyov, I.V.3
Roux, B.4
MacKerell Jr., A.D.5
-
36
-
-
79960928036
-
Replica exchange with solute scaling: A more efficient version of replica exchange with solute tempering (REST2)
-
L. Wang, R.A. Friesner, and B.J. Berne Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2) J. Phys. Chem. B 115 2011 9431 9438
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 9431-9438
-
-
Wang, L.1
Friesner, R.A.2
Berne, B.J.3
-
38
-
-
34547809547
-
A unified formulation of the constant temperature molecular dynamics methods
-
S. Nosé A unified formulation of the constant temperature molecular dynamics methods J. Chem. Phys. 81 1984 511 519
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 511-519
-
-
Nosé, S.1
-
39
-
-
0001538909
-
Canonical dynamics: Equilibrium phase-space distributions
-
W.G. Hoover Canonical dynamics: equilibrium phase-space distributions Phys. Rev. A 31 1985 1695 1697
-
(1985)
Phys. Rev. A
, vol.31
, pp. 1695-1697
-
-
Hoover, W.G.1
-
40
-
-
36749107785
-
Molecular dynamics simulations at constant pressure and/or temperature
-
H.C. Andersen Molecular dynamics simulations at constant pressure and/or temperature J. Chem. Phys. 72 1980 2384 2393
-
(1980)
J. Chem. Phys.
, vol.72
, pp. 2384-2393
-
-
Andersen, H.C.1
-
41
-
-
0041878923
-
Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm
-
G. Lamoureux, and B. Roux Modeling induced polarization with classical Drude oscillators: theory and molecular dynamics simulation algorithm J. Chem. Phys. 119 2003 3025 3039
-
(2003)
J. Chem. Phys.
, vol.119
, pp. 3025-3039
-
-
Lamoureux, G.1
Roux, B.2
-
42
-
-
33846823909
-
Particle mesh Ewald: An Nlog(N) method for Ewald sums in large systems
-
T. Darden, D. York, and L. Pedersen Particle mesh Ewald: an Nlog(N) method for Ewald sums in large systems J. Chem. Phys. 98 1993 10089 10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
43
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
J.-P. Ryckaert, G. Ciccotti, 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
Ciccotti, G.2
Berendsen, H.J.C.3
-
44
-
-
84898897801
-
Unknown unknowns: The challenge of systematic and statistical error in molecular dynamics simulations
-
T.D. Romo, and A. Grossfield Unknown unknowns: the challenge of systematic and statistical error in molecular dynamics simulations Biophys. J. 106 2014 1553 1554
-
(2014)
Biophys. J.
, vol.106
, pp. 1553-1554
-
-
Romo, T.D.1
Grossfield, A.2
-
45
-
-
0024290488
-
Helix signals in proteins
-
L.G. Presta, and G.D. Rose Helix signals in proteins Science 240 1988 1632 1641
-
(1988)
Science
, vol.240
, pp. 1632-1641
-
-
Presta, L.G.1
Rose, G.D.2
-
46
-
-
33645519934
-
Electron density redistribution accounts for half the cooperativity of α helix formation
-
A.V. Morozov, K. Tsemekhman, and D. Baker Electron density redistribution accounts for half the cooperativity of α helix formation J. Phys. Chem. B 110 2006 4503 4505
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 4503-4505
-
-
Morozov, A.V.1
Tsemekhman, K.2
Baker, D.3
-
47
-
-
0000724150
-
Solvent influence on the stability of the peptide hydrogen bond: A supramolecular cooperative effect
-
H. Guo, and M. Karplus Solvent influence on the stability of the peptide hydrogen bond: a supramolecular cooperative effect J. Phys. Chem. 98 1994 7104 7105
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 7104-7105
-
-
Guo, H.1
Karplus, M.2
-
48
-
-
84884194561
-
The polarizable atomic multipole-based AMOEBA force field for proteins
-
Y. Shi, and Z. Xia P. Ren The polarizable atomic multipole-based AMOEBA force field for proteins J. Chem. Theory Comput. 9 2013 4046 4063
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 4046-4063
-
-
Shi, Y.1
Xia, Z.2
Ren, P.3
-
49
-
-
0036882094
-
Development of a polarizable force field for proteins via ab initio quantum chemistry: First generation model and gas phase tests
-
DOI 10.1002/jcc.10125
-
G.A. Kaminski, and H.A. Stern T.A. Halgren Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests J. Comput. Chem. 23 2002 1515 1531 (Pubitemid 35330854)
-
(2002)
Journal of Computational Chemistry
, vol.23
, Issue.16
, pp. 1515-1531
-
-
Kaminski, G.A.1
Stern, H.A.2
Berne, B.J.3
Friesner, R.A.4
Cao, Y.X.5
Murphy, R.B.6
Zhou, R.7
Halgren, T.A.8
-
50
-
-
4043057278
-
CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model
-
S. Patel, A.D. Mackerell Jr., and C.L. Brooks 3rd CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model J. Comput. Chem. 25 2004 1504 1514
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1504-1514
-
-
Patel, S.1
Mackerell, Jr.A.D.2
Brooks III, C.L.3
|