-
1
-
-
70349778502
-
Common structural transitions in explicit-solvent simulations of villin headpiece folding
-
P.L. Freddolino, and K. Schulten Common structural transitions in explicit-solvent simulations of villin headpiece folding Biophys. J. 97 2009 2338 2347
-
(2009)
Biophys. J.
, vol.97
, pp. 2338-2347
-
-
Freddolino, P.L.1
Schulten, K.2
-
2
-
-
35648943228
-
Heterogeneity even at the speed limit of folding: Large-scale molecular dynamics study of a fast-folding variant of the villin headpiece
-
D.L. Ensign, P.M. Kasson, and V.S. Pande Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece J. Mol. Biol. 374 2007 806 816
-
(2007)
J. Mol. Biol.
, vol.374
, pp. 806-816
-
-
Ensign, D.L.1
Kasson, P.M.2
Pande, V.S.3
-
3
-
-
4444351490
-
Empirical force fields for biological macromolecules: Overview and issues
-
A.D. Mackerell Jr. Empirical force fields for biological macromolecules: overview and issues J. Comput. Chem. 25 2004 1584 1604
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1584-1604
-
-
Mackerell Jr., A.D.1
-
4
-
-
77957572546
-
Challenges in protein folding simulations: Timescale, representation, and analysis
-
P.L. Freddolino, and C.B. Harrison K. Schulten Challenges in protein folding simulations: timescale, representation, and analysis Nat. Phys. 6 2010 751 758
-
(2010)
Nat. Phys.
, vol.6
, pp. 751-758
-
-
Freddolino, P.L.1
Harrison, C.B.2
Schulten, K.3
-
5
-
-
46749105987
-
A test on peptide stability of AMBER force fields with implicit solvation
-
M.S. Shell, R. Ritterson, and K.A. Dill A test on peptide stability of AMBER force fields with implicit solvation J. Phys. Chem. B 112 2008 6878 6886
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 6878-6886
-
-
Shell, M.S.1
Ritterson, R.2
Dill, K.A.3
-
6
-
-
68949107624
-
Secondary structure propensities in peptide folding simulations: A systematic comparison of molecular mechanics interaction schemes
-
D. Matthes, and B.L. de Groot Secondary structure propensities in peptide folding simulations: a systematic comparison of molecular mechanics interaction schemes Biophys. J. 97 2009 599 608
-
(2009)
Biophys. J.
, vol.97
, pp. 599-608
-
-
Matthes, D.1
De Groot, B.L.2
-
7
-
-
46749127364
-
Are current molecular dynamics force fields too helical?
-
R.B. Best, N.-V. Buchete, and G. Hummer Are current molecular dynamics force fields too helical? Biophys. J. 95 2008 L07 L09
-
(2008)
Biophys. J.
, vol.95
-
-
Best, R.B.1
Buchete, N.-V.2
Hummer, G.3
-
8
-
-
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
-
9
-
-
77954320896
-
Balance between alpha and beta structures in ab initio protein folding
-
R.B. Best, and J. Mittal Balance between alpha and beta structures in ab initio protein folding J. Phys. Chem. B 114 2010 8790 8798
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 8790-8798
-
-
Best, R.B.1
Mittal, J.2
-
10
-
-
78649551877
-
Protein simulations with an optimized water model: Cooperative helix formation and temperature-induced unfolded state collapse
-
R.B. Best, and J. Mittal Protein simulations with an optimized water model: cooperative helix formation and temperature-induced unfolded state collapse J. Phys. Chem. B 114 2010 14916 14923
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 14916-14923
-
-
Best, R.B.1
Mittal, J.2
-
11
-
-
77955606360
-
Tackling force-field bias in protein folding simulations: Folding of Villin HP35 and Pin WW domains in explicit water
-
J. Mittal, and R.B. Best Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water Biophys. J. 99 2010 L26 L28
-
(2010)
Biophys. J.
, vol.99
-
-
Mittal, J.1
Best, R.B.2
-
12
-
-
27344455346
-
Reproducible polypeptide folding and structure prediction using molecular dynamics simulations
-
M.M. Seibert, and A. Patriksson D. van der Spoel Reproducible polypeptide folding and structure prediction using molecular dynamics simulations J. Mol. Biol. 354 2005 173 183
-
(2005)
J. Mol. Biol.
, vol.354
, pp. 173-183
-
-
Seibert, M.M.1
Patriksson, A.2
Van Der Spoel, D.3
-
13
-
-
84865723813
-
Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone , ψ and side-chain χ1 and χ2 dihedral angles
-
Best, R. B.; X. Zhu,...; A. D. MacKerell, Jr. 2012. Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone, ψ and side-chain χ1 and χ2 dihedral angles. J. Chem. Theory Comput. http://dx.doi.org/10.1021/ct300400x.
-
(2012)
J. Chem. Theory Comput.
-
-
Best, R.B.1
Zhu, X.2
MacKerell Jr., A.D.3
-
14
-
-
77955135754
-
Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data
-
O.F. Lange, D. van der Spoel, and B.L. de Groot Scrutinizing molecular mechanics force fields on the submicrosecond timescale with NMR data Biophys. J. 99 2010 647 655
-
(2010)
Biophys. J.
, vol.99
, pp. 647-655
-
-
Lange, O.F.1
Van Der Spoel, D.2
De Groot, B.L.3
-
15
-
-
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
-
16
-
-
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
-
18
-
-
49449089306
-
Intermolecular potentials
-
A.J. Stone Intermolecular potentials Science 321 2008 787 789
-
(2008)
Science
, vol.321
, pp. 787-789
-
-
Stone, A.J.1
-
19
-
-
33645519934
-
Electron density redistribution accounts for half the cooperativity of alpha helix formation
-
A.V. Morozov, K. Tsemekhman, and D. Baker Electron density redistribution accounts for half the cooperativity of alpha 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
-
20
-
-
2342593131
-
Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations
-
A.V. Morozov, and T. Kortemme D. Baker Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations Proc. Natl. Acad. Sci. USA 101 2004 6946 6951
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 6946-6951
-
-
Morozov, A.V.1
Kortemme, T.2
Baker, D.3
-
22
-
-
79954518426
-
Optimizing protein-solvent force fields to reproduce intrinsic conformational preferences of model peptides
-
P.S. Nerenberg, and T. Head-Gordon Optimizing protein-solvent force fields to reproduce intrinsic conformational preferences of model peptides J. Chem. Theory Comput. 7 2011 1220 1230
-
(2011)
J. Chem. Theory Comput.
, vol.7
, pp. 1220-1230
-
-
Nerenberg, P.S.1
Head-Gordon, T.2
-
23
-
-
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 78 2010 1889 1899
-
(2010)
Proteins
, vol.78
, pp. 1889-1899
-
-
Day, R.1
Paschek, D.2
Garcia, A.E.3
-
24
-
-
84859910432
-
Force-field dependence of chignolin folding and misfolding: Comparison with experiment and redesign
-
P. Kührová, and A. De Simone R.B. Best Force-field dependence of chignolin folding and misfolding: comparison with experiment and redesign Biophys. J. 102 2012 1897 1906
-
(2012)
Biophys. J.
, vol.102
, pp. 1897-1906
-
-
Kührová, P.1
De Simone, A.2
Best, R.B.3
-
25
-
-
33745184030
-
Protein folding kinetics and thermodynamics from atomistic simulations
-
D. van der Spoel, and M.M. Seibert Protein folding kinetics and thermodynamics from atomistic simulations Phys. Rev. Lett. 96 2006 238102
-
(2006)
Phys. Rev. Lett.
, vol.96
, pp. 238102
-
-
Van Der Spoel, D.1
Seibert, M.M.2
-
26
-
-
0035909921
-
The free energy landscape for beta hairpin folding in explicit water
-
R. Zhou, B.J. Berne, and R. Germain The free energy landscape for beta hairpin folding in explicit water Proc. Natl. Acad. Sci. USA 98 2001 14931 14936
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 14931-14936
-
-
Zhou, R.1
Berne, B.J.2
Germain, R.3
-
27
-
-
0344824394
-
Trp-cage: Folding free energy landscape in explicit water
-
R. Zhou Trp-cage: folding free energy landscape in explicit water Proc. Natl. Acad. Sci. USA 100 2003 13280 13285
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 13280-13285
-
-
Zhou, R.1
-
28
-
-
37649031797
-
Reversible temperature and pressure denaturation of a protein fragment: A replica exchange molecular dynamics simulation study
-
D. Paschek, and A.E. García Reversible temperature and pressure denaturation of a protein fragment: a replica exchange molecular dynamics simulation study Phys. Rev. Lett. 93 2004 238105
-
(2004)
Phys. Rev. Lett.
, vol.93
, pp. 238105
-
-
Paschek, D.1
García, A.E.2
-
29
-
-
56649083699
-
Computing the stability diagram of the Trp-cage miniprotein
-
D. Paschek, S. Hempel, and A.E. García Computing the stability diagram of the Trp-cage miniprotein Proc. Natl. Acad. Sci. USA 105 2008 17754 17759
-
(2008)
Proc. Natl. Acad. Sci. USA
, vol.105
, pp. 17754-17759
-
-
Paschek, D.1
Hempel, S.2
García, A.E.3
-
31
-
-
1642576012
-
Improved treatment of the protein backbone in empirical force fields
-
A.D. MacKerell Jr.; M. Feig, and C.L. Brooks 3rd Improved treatment of the protein backbone in empirical force fields J. Am. Chem. Soc. 126 2004 698 699
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 698-699
-
-
Mackerell Jr., A.D.1
Feig, M.2
Brooks III, C.L.3
-
32
-
-
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
-
34
-
-
8644237364
-
Understanding the key factors that control the rate of β-hairpin folding
-
D. Du, and Y. Zhu F. Gai Understanding the key factors that control the rate of β-hairpin folding Proc. Natl. Acad. Sci. USA 101 2004 15915 15920
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 15915-15920
-
-
Du, D.1
Zhu, Y.2
Gai, F.3
-
35
-
-
79958220797
-
Direct assessment of the α-helix nucleation time
-
A.L. Serrano, M.J. Tucker, and F. Gai Direct assessment of the α-helix nucleation time J. Phys. Chem. B 115 2011 7472 7478
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 7472-7478
-
-
Serrano, A.L.1
Tucker, M.J.2
Gai, F.3
-
36
-
-
46249092554
-
GROMACS4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
B. Hess, and C. Kutzner E. Lindahl GROMACS4: algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 4 2008 435 447
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Lindahl, E.3
-
37
-
-
73549111807
-
Convergence and heterogeneity in peptide folding with replica exchange molecular dynamics
-
E. Lin, and M.S. Shell Convergence and heterogeneity in peptide folding with replica exchange molecular dynamics J. Chem. Theory Comput. 5 2009 2062 2073
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 2062-2073
-
-
Lin, E.1
Shell, M.S.2
-
38
-
-
0242385345
-
Role of backbone hydration and salt-bridge formation in stability of alpha-helix in solution
-
T. Ghosh, S. Garde, and A.E. García Role of backbone hydration and salt-bridge formation in stability of alpha-helix in solution Biophys. J. 85 2003 3187 3193
-
(2003)
Biophys. J.
, vol.85
, pp. 3187-3193
-
-
Ghosh, T.1
Garde, S.2
García, A.E.3
-
39
-
-
0028500779
-
A short linear peptide that folds into a native stable beta-hairpin in aqueous solution
-
F.J. Blanco, G. Rivas, and L. Serrano A short linear peptide that folds into a native stable beta-hairpin in aqueous solution Nat. Struct. Biol. 1 1994 584 590
-
(1994)
Nat. Struct. Biol.
, vol.1
, pp. 584-590
-
-
Blanco, F.J.1
Rivas, G.2
Serrano, L.3
-
40
-
-
0038502170
-
Folding dynamics and mechanism of beta-hairpin formation
-
V. Muñoz, and P.A. Thompson W.A. Eaton Folding dynamics and mechanism of beta-hairpin formation Nature 390 1997 196 199
-
(1997)
Nature
, vol.390
, pp. 196-199
-
-
Muñoz, V.1
Thompson, P.A.2
Eaton, W.A.3
-
41
-
-
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 79 2011 1318 1328
-
(2011)
Proteins
, vol.79
, pp. 1318-1328
-
-
Best, R.B.1
Mittal, J.2
-
43
-
-
0028873081
-
Elucidating the folding problem of helical peptides using empirical parameters. II. Helix macrodipole effects and rational modification of the helical content of natural peptides
-
V. Muñoz, and L. Serrano Elucidating the folding problem of helical peptides using empirical parameters. II. Helix macrodipole effects and rational modification of the helical content of natural peptides J. Mol. Biol. 245 1995 275 296
-
(1995)
J. Mol. Biol.
, vol.245
, pp. 275-296
-
-
Muñoz, V.1
Serrano, L.2
-
44
-
-
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 2000 3586 3616
-
(2000)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
Mackerell Jr., A.D.1
Bashford, D.2
Karplus, M.3
-
45
-
-
0000333671
-
On the theory of the helix-coil transition in polypeptides
-
S. Lifson, and A. Roig On the theory of the helix-coil transition in polypeptides J. Chem. Phys. 34 1961 1963 1974
-
(1961)
J. Chem. Phys.
, vol.34
, pp. 1963-1974
-
-
Lifson, S.1
Roig, A.2
-
46
-
-
77956478902
-
SPARTA+: A modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network
-
Y. Shen, and A. Bax SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network J. Biomol. NMR 48 2010 13 22
-
(2010)
J. Biomol. NMR
, vol.48
, pp. 13-22
-
-
Shen, Y.1
Bax, A.2
-
48
-
-
84859950079
-
Optimizing solute-water van der Waals interactions to reproduce solvation free energies
-
P.S. Nerenberg, and B. Jo T. Head-Gordon Optimizing solute-water van der Waals interactions to reproduce solvation free energies J. Phys. Chem. B 116 2012 4524 4534
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 4524-4534
-
-
Nerenberg, P.S.1
Jo, B.2
Head-Gordon, T.3
-
49
-
-
0034645735
-
Thermodynamics of a beta-hairpin structure: Evidence for cooperative formation of folding nucleus
-
S. Honda, N. Kobayashi, and E. Munekata Thermodynamics of a beta-hairpin structure: evidence for cooperative formation of folding nucleus J. Mol. Biol. 295 2000 269 278
-
(2000)
J. Mol. Biol.
, vol.295
, pp. 269-278
-
-
Honda, S.1
Kobayashi, N.2
Munekata, E.3
-
50
-
-
70349085815
-
Context-independent, temperature-dependent helical propensities for amino acid residues
-
R.J. Moreau, and C.R. Schubert D.S. Kemp Context-independent, temperature-dependent helical propensities for amino acid residues J. Am. Chem. Soc. 131 2009 13107 13116
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 13107-13116
-
-
Moreau, R.J.1
Schubert, C.R.2
Kemp, D.S.3
-
51
-
-
0030874298
-
Comparison of NH exchange and circular dichroism as techniques for measuring the parameters of the helix-coil transition in peptides
-
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
-
(1997)
Biochemistry
, vol.36
, pp. 8435-8442
-
-
Rohl, C.A.1
Baldwin, R.L.2
|