-
3
-
-
33646759974
-
Sub-microsecond protein folding
-
Kubelka J, Chiu TK, Davies DR, Eaton WA, Hofrichter J (2006) Sub-microsecond protein folding. J Mol Biol 359:546-553.
-
(2006)
J Mol Biol
, vol.359
, pp. 546-553
-
-
Kubelka, J.1
Chiu, T.K.2
Davies, D.R.3
Eaton, W.A.4
Hofrichter, J.5
-
4
-
-
35648943228
-
Heterogeneity even at the speed limit of folding: Large-scale molecular dynamics study of a fast-folding variant of the villin headpiece
-
Ensign DL, Kasson PM, Pande VS (2007) 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 374:806-816.
-
(2007)
J Mol Biol
, vol.374
, pp. 806-816
-
-
Ensign, D.L.1
Kasson, P.M.2
Pande, V.S.3
-
5
-
-
70349778502
-
Common structural transitions in explicit-solvent simulations of villin headpiece folding
-
Freddolino PL, Schulten K (2009) Common structural transitions in explicit-solvent simulations of villin headpiece folding. Biophys J 97:2338-2347.
-
(2009)
Biophys J
, vol.97
, pp. 2338-2347
-
-
Freddolino, P.L.1
Schulten, K.2
-
6
-
-
77955606360
-
Tackling force-field bias in protein folding simulations: Folding of Villin HP35and Pin WW domains in explicit water
-
Mittal J, Best RB (2010) Tackling force-field bias in protein folding simulations: Folding of Villin HP35and Pin WW domains in explicit water. Biophys J 99:L26-L28.
-
(2010)
Biophys J
, vol.99
-
-
Mittal, J.1
Best, R.B.2
-
7
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
-
Duan Y, Kollman PA (1998) Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282:740-744.
-
(1998)
Science
, vol.282
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
9
-
-
84857033265
-
Atomistic molecular simulations of protein folding
-
Best RB (2012) Atomistic molecular simulations of protein folding. Curr Opin Struct Biol 22:52-61.
-
(2012)
Curr Opin Struct Biol
, vol.22
, pp. 52-61
-
-
Best, R.B.1
-
10
-
-
79961218875
-
Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments
-
Beauchamp KA, Ensign DL, Das R, Pande VS (2011) Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments. Proc Natl Acad Sci USA 108:12734-12739.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 12734-12739
-
-
Beauchamp, K.A.1
Ensign, D.L.2
Das, R.3
Pande, V.S.4
-
11
-
-
80053979296
-
MSMBuilder2: Modeling conformational dynamics at the picosecond to millisecond scale
-
Beauchamp KA, et al. (2011) MSMBuilder2: Modeling conformational dynamics at the picosecond to millisecond scale. J Chem Theory Comput 7:3412-3419.
-
(2011)
J Chem Theory Comput
, vol.7
, pp. 3412-3419
-
-
Beauchamp, K.A.1
-
12
-
-
70349631761
-
Progress and challenges in the automated construction of Markov state models for full protein systems
-
Bowman GR, Beauchamp KA, Boxer G, Pande VS (2009) Progress and challenges in the automated construction of Markov state models for full protein systems. J Chem Phys 131:124101.
-
(2009)
J Chem Phys
, vol.131
, pp. 124101
-
-
Bowman, G.R.1
Beauchamp, K.A.2
Boxer, G.3
Pande, V.S.4
-
13
-
-
77954635393
-
Protein folded states are kinetic hubs
-
Bowman GR, Pande VS (2010) Protein folded states are kinetic hubs. Proc Natl Acad Sci USA 107:10890-10895.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 10890-10895
-
-
Bowman, G.R.1
Pande, V.S.2
-
14
-
-
79959720287
-
How robust are protein folding simulations with respect to force field parameterization
-
Piana S, Lindorff-Larsen K, Shaw DE (2011) How robust are protein folding simulations with respect to force field parameterization? Biophys J 100:L47-L49
-
(2011)
Biophys J
, vol.100
-
-
Piana, S.1
Lindorff-Larsen, K.2
Shaw, D.E.3
-
17
-
-
77957937199
-
Atomic-level characterization of the structural dynamics of proteins
-
Shaw DE, et al. (2010) Atomic-level characterization of the structural dynamics of proteins. Science 330:341-346.
-
(2010)
Science
, vol.330
, pp. 341-346
-
-
Shaw, D.E.1
-
18
-
-
33748518255
-
Comparison of multiple Amber force fields and development of improved protein backbone parameters
-
Hornak V, et al. (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
-
19
-
-
67649494492
-
Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides
-
Best RB, Hummer G (2009) Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides. J Phys Chem B 113:9004-9015.
-
(2009)
J Phys Chem B
, vol.113
, pp. 9004-9015
-
-
Best, R.B.1
Hummer, G.2
-
20
-
-
84857463877
-
Systematic validation of protein force fields against experimental data
-
Lindorff-Larsen K, et al. (2012) Systematic validation of protein force fields against experimental data. PLoS ONE 7:e32131.
-
(2012)
PLoS ONE
, vol.7
-
-
Lindorff-Larsen, K.1
-
21
-
-
14144255497
-
Phi-value analysis by molecular dynamics simulations of reversible folding
-
Settanni G, Rao F, Caflisch A (2005) Phi-value analysis by molecular dynamics simulations of reversible folding. Pro Natl Acad Sci USA 102:628-633.
-
(2005)
Pro Natl Acad Sci USA
, vol.102
, pp. 628-633
-
-
Settanni, G.1
Rao, F.2
Caflisch, A.3
-
22
-
-
79955013716
-
Making connections between ultrafast protein folding kinetics and molecular dynamics simulations
-
Cellmer T, Buscaglia M, Henry ER, Hofrichter J, Eaton WA (2011) Making connections between ultrafast protein folding kinetics and molecular dynamics simulations. Pro Natl Acad Sci USA 108:6103-6108.
-
(2011)
Pro Natl Acad Sci USA
, vol.108
, pp. 6103-6108
-
-
Cellmer, T.1
Buscaglia, M.2
Henry, E.R.3
Hofrichter, J.4
Eaton, W.A.5
-
23
-
-
77953513118
-
Improved side-chain torsion potentials for the Amber ff99SB protein force field
-
Lindorff-Larsen K, et al. (2010) Improved side-chain torsion potentials for the Amber ff99SB protein force field. Proteins 78:1950-1958.
-
(2010)
Proteins
, vol.78
, pp. 1950-1958
-
-
Lindorff-Larsen, K.1
-
24
-
-
19644381706
-
High-resolution X-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein
-
Chiu TK, et al. (2005) High-resolution X-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein. Proc Natl Acad Sci USA 102:7517-7522.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 7517-7522
-
-
Chiu, T.K.1
-
25
-
-
34247110703
-
The stable states picture of chemical reactions. I. Formulation for rate constants and initial condition effects
-
Northrup SH, Hynes JT (1980) The stable states picture of chemical reactions. I. Formulation for rate constants and initial condition effects. J Chem Phys 73:2700-2714.
-
(1980)
J Chem Phys
, vol.73
, pp. 2700-2714
-
-
Northrup, S.H.1
Hynes, J.T.2
-
26
-
-
44949178407
-
Coarse master equations for peptide folding dynamics
-
Buchete NV, Hummer G (2008) Coarse master equations for peptide folding dynamics. J Phys Chem B 112:6057-6069.
-
(2008)
J Phys Chem B
, vol.112
, pp. 6057-6069
-
-
Buchete, N.V.1
Hummer, G.2
-
27
-
-
0038054301
-
Experimental tests of villin subdomain folding simulations
-
Kubelka J, Eaton WA, Hofrichter J (2003) Experimental tests of villin subdomain folding simulations. J Mol Biol 329:625-630.
-
(2003)
J Mol Biol
, vol.329
, pp. 625-630
-
-
Kubelka, J.1
Eaton, W.A.2
Hofrichter, J.3
-
28
-
-
80052801453
-
Bridging the gap between folding simulations and experiments: The case of the villin headpiece
-
Saladino G, Marenchino M, Gervasio FL (2011) Bridging the gap between folding simulations and experiments: The case of the villin headpiece. J Chem Theory Comput 7:2675-2680.
-
(2011)
J Chem Theory Comput
, vol.7
, pp. 2675-2680
-
-
Saladino, G.1
Marenchino, M.2
Gervasio, F.L.3
-
29
-
-
57449106823
-
Chemical, physical, and theoretical kinetics of an ultrafast folding protein
-
Kubelka J, Henry ER, Cellmer T, Hofrichter J, Eaton WA (2008) Chemical, physical, and theoretical kinetics of an ultrafast folding protein. Proc Natl Acad Sci USA 105:18655-18662.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 18655-18662
-
-
Kubelka, J.1
Henry, E.R.2
Cellmer, T.3
Hofrichter, J.4
Eaton, W.A.5
-
30
-
-
44949236102
-
Estimating free-energy barrier heights for an ultrafast folding protein from calorimetric and kinetic data
-
Godoy-Ruiz R, et al. (2008) Estimating free-energy barrier heights for an ultrafast folding protein from calorimetric and kinetic data. J Phys Chem B 112:5938-5949.
-
(2008)
J Phys Chem B
, vol.112
, pp. 5938-5949
-
-
Godoy-Ruiz, R.1
-
31
-
-
78649551877
-
Protein simulations with an optimized water model: Cooperative helix formation and temperature-induced unfolded state collapse
-
Best RB, Mittal J (2010) Protein simulations with an optimized water model: Cooperative helix formation and temperature-induced unfolded state collapse. J Phys Chem B 114:14916-14923.
-
(2010)
J Phys Chem B
, vol.114
, pp. 14916-14923
-
-
Best, R.B.1
Mittal, J.2
-
32
-
-
67650550291
-
Probing the folding transition state structure of the villin headpiece subdomain via side chain and backbone mutagenesis
-
Bunagan MR, Gao J, Kelly JW, Gai F (2009) Probing the folding transition state structure of the villin headpiece subdomain via side chain and backbone mutagenesis. J Am Chem Soc 131:7470-7476.
-
(2009)
J Am Chem Soc
, vol.131
, pp. 7470-7476
-
-
Bunagan, M.R.1
Gao, J.2
Kelly, J.W.3
Gai, F.4
-
33
-
-
0029619259
-
STRIDE: A web server for secondary structure assignment from known atomic coordinates of proteins
-
Frishman D, Argos P (1995) STRIDE: A web server for secondary structure assignment from known atomic coordinates of proteins. Proteins 23:566-579.
-
(1995)
Proteins
, vol.23
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
34
-
-
78650859577
-
Predicting fluorescence lifetimes and spectra of biopolymers
-
Callis PR (2011) Predicting fluorescence lifetimes and spectra of biopolymers. Methods Enzymol 487:1-38.
-
(2011)
Methods Enzymol
, vol.487
, pp. 1-38
-
-
Callis, P.R.1
-
35
-
-
84857692227
-
Simulations of tryptophan fluorescence dynamics during folding of the villin headpiece
-
Tusell JR, Callis PR (2012) Simulations of tryptophan fluorescence dynamics during folding of the villin headpiece. J Phys Chem B 116:2586-2594.
-
(2012)
J Phys Chem B
, vol.116
, pp. 2586-2594
-
-
Tusell, J.R.1
Callis, P.R.2
-
36
-
-
77950388103
-
An unlocking/relocking barrier in conformational fluctuations of villin headpiece subdomain
-
Andreas R, Henklein P, Kiefhaber T (2010) An unlocking/relocking barrier in conformational fluctuations of villin headpiece subdomain. Proc Natl Acad Sci 107:4955-4960.
-
(2010)
Proc Natl Acad Sci
, vol.107
, pp. 4955-4960
-
-
Andreas, R.1
Henklein, P.2
Kiefhaber, T.3
-
37
-
-
0024358426
-
Mapping the transition state and pathway of protein folding by protein engineering
-
Matouschek A, Kellis JT, Jr, Serrano L, Fersht AR (1989) Mapping the transition state and pathway of protein folding by protein engineering. Nature 340:122-126.
-
(1989)
Nature
, vol.340
, pp. 122-126
-
-
Matouschek, A.1
Kellis Jr., J.T.2
Serrano, L.3
Fersht, A.R.4
-
38
-
-
79958104526
-
The protein folding network indicates that the ultrafast folding mutant of villin headpiece subdomain has a deeper folding funnel
-
Lei H, Chen C, Xiao Y, Duan Y (2011) The protein folding network indicates that the ultrafast folding mutant of villin headpiece subdomain has a deeper folding funnel. J Chem Phys 134:205104.
-
(2011)
J Chem Phys
, vol.134
, pp. 205104
-
-
Lei, H.1
Chen, C.2
Xiao, Y.3
Duan, Y.4
-
39
-
-
67749147584
-
Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories
-
Chung HS, Louis JM, EatonWA(2009) Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories. Proc Natl Acad Sci USA 106:11837-11844.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 11837-11844
-
-
Chung, H.S.1
Louis, J.M.2
Eaton, W.A.3
-
40
-
-
84857510185
-
Single molecule fluorescence experiments determine protein folding transition path times
-
Chung HS, McHale K, Louis JM, Eaton WA (2012) Single molecule fluorescence experiments determine protein folding transition path times. Science 335:981-984.
-
(2012)
Science
, vol.335
, pp. 981-984
-
-
Chung, H.S.1
McHale, K.2
Louis, J.M.3
Eaton, W.A.4
-
41
-
-
0024121530
-
Diffusion in a rough potential
-
10485
-
Zwanzig R (1988) Diffusion in a rough potential. Proc Natl Acad Sci USA 10485:2029-2030.
-
(1988)
Proc Natl Acad Sci USA
, pp. 2029-2030
-
-
Zwanzig, R.1
-
42
-
-
36749060078
-
Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin
-
Zhang BW, Jasnow D, ZuckermanDM (2007) Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin. Proc Natl Acad Sci USA 104:18403-18048.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 18403-18048
-
-
Zhang, B.W.1
Jasnow, D.2
Zuckerman, D.M.3
-
43
-
-
75749119330
-
Transition times in the low-noise limit of stochastic dynamics
-
Malinin SV, Chernyak VY (2010) Transition times in the low-noise limit of stochastic dynamics. J Chem Phys 132:014504.
-
(2010)
J Chem Phys
, vol.132
, pp. 014504
-
-
Malinin, S.V.1
Chernyak, V.Y.2
-
44
-
-
77956250820
-
A harmonic transition state approximation for the duration of reactive events in complex molecular rearrangements
-
Chaudhury S, Makarov DE (2010) A harmonic transition state approximation for the duration of reactive events in complex molecular rearrangements. J Chem Phys 133:034118.
-
(2010)
J Chem Phys
, vol.133
, pp. 034118
-
-
Chaudhury, S.1
Makarov, D.E.2
-
45
-
-
18744387720
-
Reaction coordinates and rates from transition paths
-
Best RB, Hummer G (2005) Reaction coordinates and rates from transition paths. Proc Natl Acad Sci USA 102:6732-6737.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 6732-6737
-
-
Best, R.B.1
Hummer, G.2
-
46
-
-
23244438863
-
Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations
-
Hummer G (2005) Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations. New J Phys 7:34.
-
(2005)
New J Phys
, vol.7
, pp. 34
-
-
Hummer, G.1
|