-
1
-
-
6944235051
-
Hidden complexity of free energy surfaces for peptide (protein) folding
-
Krivov SV, Karplus M. Hidden complexity of free energy surfaces for peptide (protein) folding. Proc Natl Acad Sci USA 2004, 101:14766–14770. doi:10.1073/pnas.0406234101.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 14766-14770
-
-
Krivov, S.V.1
Karplus, M.2
-
2
-
-
52949137003
-
Diffusive reaction dynamics on invariant free energy profiles
-
Krivov SV, Karplus M. Diffusive reaction dynamics on invariant free energy profiles. Proc Natl Acad Sci USA 2008, 105:13841–13846. doi:10.1073/pnas.0800228105.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 13841-13846
-
-
Krivov, S.V.1
Karplus, M.2
-
3
-
-
78049438869
-
Is protein folding sub-diffusive?
-
Krivov SV. Is protein folding sub-diffusive? PLoS Comput Biol 2010, 6:e1000921. doi:10.1371/journal.pcbi.1000921.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Krivov, S.V.1
-
4
-
-
78650586007
-
Nonexponential decay of internal rotational correlation functions of native proteins and self-similar structural fluctuations
-
Cote Y, Senet P, Delarue P, Maisuradze GG, Scheraga HA. Nonexponential decay of internal rotational correlation functions of native proteins and self-similar structural fluctuations. Proc Natl Acad Sci USA 2010, 107:19844–19849. doi:10.1073/pnas.1013674107.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 19844-19849
-
-
Cote, Y.1
Senet, P.2
Delarue, P.3
Maisuradze, G.G.4
Scheraga, H.A.5
-
5
-
-
84956771443
-
The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time
-
Hu X, Hong L, Dean Smith M, Neusius T, Cheng X, Smith JC. The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time. Nat Phys 2016, 12:171–174. doi:10.1038/nphys3553.
-
(2016)
Nat Phys
, vol.12
, pp. 171-174
-
-
Hu, X.1
Hong, L.2
Dean Smith, M.3
Neusius, T.4
Cheng, X.5
Smith, J.C.6
-
6
-
-
0000514837
-
Transport, collective motion, and Brownian motion
-
Mori H. Transport, collective motion, and Brownian motion. Prog Theor Phys 1965, 33:423–455. doi:10.1143/PTP.33.423.
-
(1965)
Prog Theor Phys
, vol.33
, pp. 423-455
-
-
Mori, H.1
-
8
-
-
67650468401
-
Computing generalized Langevin equations and generalized Fokker–Planck equations
-
Darve E, Solomon J, Kia A. Computing generalized Langevin equations and generalized Fokker–Planck equations. Proc Natl Acad Sci USA 2009, 106:10884–10889. doi:10.1073/pnas.0902633106.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 10884-10889
-
-
Darve, E.1
Solomon, J.2
Kia, A.3
-
9
-
-
84872164266
-
On reaction coordinate optimality
-
Krivov SV. On reaction coordinate optimality. J Chem Theory Comput 2013, 9:135–146. doi:10.1021/ct3008292.
-
(2013)
J Chem Theory Comput
, vol.9
, pp. 135-146
-
-
Krivov, S.V.1
-
10
-
-
84905821972
-
Recent developments in methods for identifying reaction coordinates
-
Li W, Ma A. Recent developments in methods for identifying reaction coordinates. Mol Simul 2014, 40:784–793. doi:10.1080/08927022.2014.907898.
-
(2014)
Mol Simul
, vol.40
, pp. 784-793
-
-
Li, W.1
Ma, A.2
-
11
-
-
84973320145
-
Reaction coordinates and mechanistic hypothesis tests
-
Peters B. Reaction coordinates and mechanistic hypothesis tests. Annu Rev Phys Chem 2016, 67:669–690. doi:10.1146/annurev-physchem-040215-112215.
-
(2016)
Annu Rev Phys Chem
, vol.67
, pp. 669-690
-
-
Peters, B.1
-
12
-
-
36149016302
-
Initial recombination of ions
-
Onsager L. Initial recombination of ions. Phys Rev 1938, 54:554–557. doi:10.1103/PhysRev.54.554.
-
(1938)
Phys Rev
, vol.54
, pp. 554-557
-
-
Onsager, L.1
-
13
-
-
0001563395
-
On the transition coordinate for protein folding
-
Du R, Pande VS, Grosberg AY, Tanaka T, Shakhnovich ES. On the transition coordinate for protein folding. J Chem Phys 1998, 108:334. doi:10.1063/1.475393.
-
(1998)
J Chem Phys
, vol.108
, pp. 334
-
-
Du, R.1
Pande, V.S.2
Grosberg, A.Y.3
Tanaka, T.4
Shakhnovich, E.S.5
-
14
-
-
33747589472
-
Towards a theory of transition paths
-
Weinan E, Vanden-Eijnden E. Towards a theory of transition paths. J Stat Phys 2006, 123:503–523. doi:10.1007/s10955-005-9003-9.
-
(2006)
J Stat Phys
, vol.123
, pp. 503-523
-
-
Weinan, E.1
Vanden-Eijnden, E.2
-
16
-
-
84905656925
-
Exact dynamical coarse-graining without time-scale separation
-
Lu J, Vanden-Eijnden E. Exact dynamical coarse-graining without time-scale separation. J Chem Phys 2014, 141:044109. doi:10.1063/1.4890367.
-
(2014)
J Chem Phys
, vol.141
, pp. 044109
-
-
Lu, J.1
Vanden-Eijnden, E.2
-
17
-
-
84886655376
-
Diffusion along the splitting/commitment probability reaction coordinate
-
Berezhkovskii AM, Szabo A. Diffusion along the splitting/commitment probability reaction coordinate. J Phys Chem B 2013, 117:13115–13119. doi:10.1021/jp403043a.
-
(2013)
J Phys Chem B
, vol.117
, pp. 13115-13119
-
-
Berezhkovskii, A.M.1
Szabo, A.2
-
18
-
-
84891701652
-
Method to describe stochastic dynamics using an optimal coordinate
-
Krivov SV. Method to describe stochastic dynamics using an optimal coordinate. Phys Rev E 2013, 88:062131. doi:10.1103/PhysRevE.88.062131.
-
(2013)
Phys Rev E
, vol.88
, pp. 062131
-
-
Krivov, S.V.1
-
19
-
-
84894149420
-
Robust estimation of diffusion-optimized ensembles for enhanced sampling
-
Tian P, Jónsson SÆ, Ferkinghoff-Borg J, Krivov SV, Lindorff-Larsen K, Irbäck A, Boomsma W. Robust estimation of diffusion-optimized ensembles for enhanced sampling. J Chem Theory Comput 2014, 10:543–553. doi:10.1021/ct400844x.
-
(2014)
J Chem Theory Comput
, vol.10
, pp. 543-553
-
-
Tian, P.1
Jónsson, S.Æ.2
Ferkinghoff-Borg, J.3
Krivov, S.V.4
Lindorff-Larsen, K.5
Irbäck, A.6
Boomsma, W.7
-
20
-
-
77957937199
-
Atomic-level characterization of the structural dynamics of proteins
-
Shaw DE, Maragakis P, Lindorff-Larsen K, Piana S, Dror RO, Eastwood MP, Bank JA, Jumper JM, Salmon JK, Shan Y, et al. Atomic-level characterization of the structural dynamics of proteins. Science 2010, 330:341–346. doi:10.1126/science.1187409.
-
(2010)
Science
, vol.330
, pp. 341-346
-
-
Shaw, D.E.1
Maragakis, P.2
Lindorff-Larsen, K.3
Piana, S.4
Dror, R.O.5
Eastwood, M.P.6
Bank, J.A.7
Jumper, J.M.8
Salmon, J.K.9
Shan, Y.10
-
21
-
-
84947296867
-
Nonparametric variational optimization of reaction coordinates
-
Banushkina PV, Krivov SV. Nonparametric variational optimization of reaction coordinates. J Chem Phys 2015, 143:184108. doi:10.1063/1.4935180.
-
(2015)
J Chem Phys
, vol.143
, pp. 184108
-
-
Banushkina, P.V.1
Krivov, S.V.2
-
22
-
-
33748366393
-
Illustration of transition path theory on a collection of simple examples
-
Metzner P, Schütte C, Vanden-Eijnden E. Illustration of transition path theory on a collection of simple examples. J Chem Phys 2006, 125:084110. doi:10.1063/1.2335447.
-
(2006)
J Chem Phys
, vol.125
, pp. 084110
-
-
Metzner, P.1
Schütte, C.2
Vanden-Eijnden, E.3
-
23
-
-
0001374686
-
Kinetic pathways of ion pair dissociation in water
-
Geissler PL, Dellago C, Chandler D. Kinetic pathways of ion pair dissociation in water. J Phys Chem B 1999, 103:3706–3710. doi:10.1021/jp984837g.
-
(1999)
J Phys Chem B
, vol.103
, pp. 3706-3710
-
-
Geissler, P.L.1
Dellago, C.2
Chandler, D.3
-
24
-
-
0034705109
-
Reaction coordinates of biomolecular isomerization
-
Bolhuis PG, Dellago C, Chandler D. Reaction coordinates of biomolecular isomerization. Proc Natl Acad Sci USA 2000, 97:5877–5882. doi:10.1073/pnas.100127697.
-
(2000)
Proc Natl Acad Sci USA
, vol.97
, pp. 5877-5882
-
-
Bolhuis, P.G.1
Dellago, C.2
Chandler, D.3
-
25
-
-
17544374740
-
Automatic method for identifying reaction coordinates in complex systems
-
Ma A, Dinner AR. Automatic method for identifying reaction coordinates in complex systems. J Phys Chem B 2005, 109:6769–6779. doi:10.1021/jp045546c.
-
(2005)
J Phys Chem B
, vol.109
, pp. 6769-6779
-
-
Ma, A.1
Dinner, A.R.2
-
26
-
-
84946616226
-
Reducing the cost of evaluating the committor by a fitting procedure
-
Li W, Ma A. Reducing the cost of evaluating the committor by a fitting procedure. J Chem Phys 2015, 143:174103. doi:10.1063/1.4934782.
-
(2015)
J Chem Phys
, vol.143
, pp. 174103
-
-
Li, W.1
Ma, A.2
-
27
-
-
33846071499
-
Using the histogram test to quantify reaction coordinate error
-
Peters B. Using the histogram test to quantify reaction coordinate error. J Chem Phys 2006, 125:241101. doi:10.1063/1.2409924.
-
(2006)
J Chem Phys
, vol.125
, pp. 241101
-
-
Peters, B.1
-
28
-
-
49149121255
-
One-dimensional barrier-preserving free-energy projections of a -sheet miniprotein: new insights into the folding process
-
Krivov SV, Muff S, Caflisch A, Karplus M. One-dimensional barrier-preserving free-energy projections of a -sheet miniprotein: new insights into the folding process. J Phys Chem B 2008, 112:8701–8714. doi:10.1021/jp711864r.
-
(2008)
J Phys Chem B
, vol.112
, pp. 8701-8714
-
-
Krivov, S.V.1
Muff, S.2
Caflisch, A.3
Karplus, M.4
-
29
-
-
84898431921
-
Variational approach to molecular kinetics
-
Nüske F, Keller BG, Pérez-Hernández G, Mey ASJS, Noé F. Variational approach to molecular kinetics. J Chem Theory Comput 2014, 10:1739–1752. doi:10.1021/ct4009156.
-
(2014)
J Chem Theory Comput
, vol.10
, pp. 1739-1752
-
-
Nüske, F.1
Keller, B.G.2
Pérez-Hernández, G.3
Mey, A.S.J.S.4
Noé, F.5
-
30
-
-
84922674715
-
Modeling molecular kinetics with tICA and the Kernel trick
-
Schwantes CR, Pande VS. Modeling molecular kinetics with tICA and the Kernel trick. J Chem Theory Comput 2015, 11:600–6008. doi:10.1021/ct5007357.
-
(2015)
J Chem Theory Comput
, vol.11
, pp. 600-6008
-
-
Schwantes, C.R.1
Pande, V.S.2
-
31
-
-
18744387720
-
Reaction coordinates and rates from transition paths
-
Best RB, Hummer G. Reaction coordinates and rates from transition paths. Proc Natl Acad Sci USA 2005, 102:6732–6737. doi:10.1073/pnas.0408098102.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 6732-6737
-
-
Best, R.B.1
Hummer, G.2
-
32
-
-
80054929399
-
The free energy landscape analysis of protein (FIP35) folding dynamics
-
Krivov SV. The free energy landscape analysis of protein (FIP35) folding dynamics. J Phys Chem B 2011, 115:12315–12324. doi:10.1021/jp208585r.
-
(2011)
J Phys Chem B
, vol.115
, pp. 12315-12324
-
-
Krivov, S.V.1
-
33
-
-
80053433603
-
Numerical construction of the pfold (Committor) reaction coordinate for a Markov process
-
Krivov SV. Numerical construction of the pfold (Committor) reaction coordinate for a Markov process. J Phys Chem B 2011, 115:11382–11388. doi:10.1021/jp205231b.
-
(2011)
J Phys Chem B
, vol.115
, pp. 11382-11388
-
-
Krivov, S.V.1
-
34
-
-
0842311640
-
From transition paths to transition states and rate coefficients
-
Hummer G. From transition paths to transition states and rate coefficients. J Chem Phys 2003, 120:516–523. doi:10.1063/1.1630572.
-
(2003)
J Chem Phys
, vol.120
, pp. 516-523
-
-
Hummer, G.1
-
35
-
-
33746899725
-
Obtaining reaction coordinates by likelihood maximization
-
Peters B, Trout BL. Obtaining reaction coordinates by likelihood maximization. J Chem Phys 2006, 125:054108. doi:10.1063/1.2234477.
-
(2006)
J Chem Phys
, vol.125
, pp. 054108
-
-
Peters, B.1
Trout, B.L.2
-
36
-
-
84869091823
-
Inertial likelihood maximization for reaction coordinates with high transmission coefficients
-
Peters B. Inertial likelihood maximization for reaction coordinates with high transmission coefficients. Chem Phys Lett 2012, 554:248–253. doi:10.1016/j.cplett.2012.10.051.
-
(2012)
Chem Phys Lett
, vol.554
, pp. 248-253
-
-
Peters, B.1
-
37
-
-
79961114440
-
Optimal dimensionality reduction of complex dynamics: the chess game as diffusion on a free-energy landscape
-
Krivov SV. Optimal dimensionality reduction of complex dynamics: the chess game as diffusion on a free-energy landscape. Phys Rev E 2011, 84:011135. doi:10.1103/PhysRevE.84.011135.
-
(2011)
Phys Rev E
, vol.84
, pp. 011135
-
-
Krivov, S.V.1
-
38
-
-
84903397358
-
Optimal reaction coordinate as a biomarker for the dynamics of recovery from kidney transplant
-
Krivov SV, Fenton H, Goldsmith PJ, Prasad RK, Fisher J, Paci E. Optimal reaction coordinate as a biomarker for the dynamics of recovery from kidney transplant. PLoS Comput Biol 2014, 10:e1003685. doi:10.1371/journal.pcbi.1003685.
-
(2014)
PLoS Comput Biol
, vol.10
-
-
Krivov, S.V.1
Fenton, H.2
Goldsmith, P.J.3
Prasad, R.K.4
Fisher, J.5
Paci, E.6
-
39
-
-
80052003642
-
Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments
-
Chodera JD, Pande VS. Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments. Phys Rev Lett 2011, 107:098102. doi:10.1103/PhysRevLett.107.098102.
-
(2011)
Phys Rev Lett
, vol.107
, pp. 098102
-
-
Chodera, J.D.1
Pande, V.S.2
-
40
-
-
34548098593
-
Estimation of protein folding probability from equilibrium simulations
-
Rao F, Settanni G, Guarnera E, Caflisch A. Estimation of protein folding probability from equilibrium simulations. J Chem Phys 2005, 122:184901. doi:10.1063/1.1893753.
-
(2005)
J Chem Phys
, vol.122
, pp. 184901
-
-
Rao, F.1
Settanni, G.2
Guarnera, E.3
Caflisch, A.4
-
41
-
-
23244438863
-
Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations
-
Hummer G. Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations. New J Phys 2005, 7:34. doi:10.1088/1367-2630/7/1/034.
-
(2005)
New J Phys
, vol.7
, pp. 34
-
-
Hummer, G.1
-
42
-
-
77249114204
-
Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein
-
Vreede J, Juraszek J, Bolhuis PG. Predicting the reaction coordinates of millisecond light-induced conformational changes in photoactive yellow protein. Proc Natl Acad Sci USA 2010, 107:2397–2402. doi:10.1073/pnas.0908754107.
-
(2010)
Proc Natl Acad Sci USA
, vol.107
, pp. 2397-2402
-
-
Vreede, J.1
Juraszek, J.2
Bolhuis, P.G.3
-
43
-
-
84921508588
-
Equilibrium kinetic network of the villin headpiece in implicit solvent
-
Du W, Bolhuis PG. Equilibrium kinetic network of the villin headpiece in implicit solvent. Biophys J 2015, 108:368–378. doi:10.1016/j.bpj.2014.11.3476.
-
(2015)
Biophys J
, vol.108
, pp. 368-378
-
-
Du, W.1
Bolhuis, P.G.2
-
44
-
-
84930633101
-
Common features of extraordinary rate theories
-
Peters B. Common features of extraordinary rate theories. J Phys Chem B 2015, 119:6349–6356. doi:10.1021/acs.jpcb.5b02547.
-
(2015)
J Phys Chem B
, vol.119
, pp. 6349-6356
-
-
Peters, B.1
-
45
-
-
84873639466
-
Reaction coordinates, one-dimensional Smoluchowski equations, and a test for dynamical self-consistency
-
Peters B, Bolhuis PG, Mullen RG, Shea JE. Reaction coordinates, one-dimensional Smoluchowski equations, and a test for dynamical self-consistency. J Chem Phys 2013, 138:054106. doi:10.1063/1.4775807.
-
(2013)
J Chem Phys
, vol.138
, pp. 054106
-
-
Peters, B.1
Bolhuis, P.G.2
Mullen, R.G.3
Shea, J.E.4
-
46
-
-
9744236584
-
Ensemble of transition states for two-state protein folding from the eigenvectors of rate matrices
-
Berezhkovskii A, Szabo A. Ensemble of transition states for two-state protein folding from the eigenvectors of rate matrices. J Chem Phys 2004, 121:9186–9187. doi:10.1063/1.1802674.
-
(2004)
J Chem Phys
, vol.121
, pp. 9186-9187
-
-
Berezhkovskii, A.1
Szabo, A.2
-
47
-
-
84926429486
-
Fep1d: a script for the analysis of reaction coordinates
-
Banushkina PV, Krivov SV. Fep1d: a script for the analysis of reaction coordinates. J Comput Chem 2015, 36:878–882. doi:10.1002/jcc.23868.
-
(2015)
J Comput Chem
, vol.36
, pp. 878-882
-
-
Banushkina, P.V.1
Krivov, S.V.2
-
48
-
-
10844292652
-
Energy landscape of a small peptide revealed by dihedral angle principal component analysis
-
Mu Y, Nguyen PH, Stock G. Energy landscape of a small peptide revealed by dihedral angle principal component analysis. Proteins 2005, 58:45–52. doi:10.1002/prot.20310.
-
(2005)
Proteins
, vol.58
, pp. 45-52
-
-
Mu, Y.1
Nguyen, P.H.2
Stock, G.3
-
50
-
-
0042378381
-
Laplacian eigenmaps for dimensionality reduction and data representation
-
Belkin M, Niyogi P. Laplacian eigenmaps for dimensionality reduction and data representation. Neural Comput 2003, 15:1373–1396. doi:10.1162/089976603321780317.
-
(2003)
Neural Comput
, vol.15
, pp. 1373-1396
-
-
Belkin, M.1
Niyogi, P.2
-
51
-
-
0034704222
-
Nonlinear dimensionality reduction by locally linear embedding
-
Roweis ST, Saul LK. Nonlinear dimensionality reduction by locally linear embedding. Science 2000, 290:2323–2326. doi:10.1126/science.290.5500.2323.
-
(2000)
Science
, vol.290
, pp. 2323-2326
-
-
Roweis, S.T.1
Saul, L.K.2
-
52
-
-
33745611125
-
Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction
-
Das P, Moll M, Stamati H, Kavraki LE, Clementi C. Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction. Proc Natl Acad Sci USA 2006, 103:9885–9890. doi:10.1073/pnas.0603553103.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 9885-9890
-
-
Das, P.1
Moll, M.2
Stamati, H.3
Kavraki, L.E.4
Clementi, C.5
-
53
-
-
80051959824
-
Simplifying the representation of complex free-energy landscapes using sketch-map
-
Ceriotti M, Tribello GA, Parrinello M. Simplifying the representation of complex free-energy landscapes using sketch-map. Proc Natl Acad Sci USA 2011, 108:13023–13028. doi:10.1073/pnas.1108486108.
-
(2011)
Proc Natl Acad Sci USA
, vol.108
, pp. 13023-13028
-
-
Ceriotti, M.1
Tribello, G.A.2
Parrinello, M.3
-
54
-
-
85128858890
-
Equation-free, coarse-grained multiscale computation: enabling mocroscopic simulators to perform system-level analysis
-
Kevrekidis IG, Gear CW, Hyman JM, Kevrekidid PG, Runborg O, Theodoropoulos C. Equation-free, coarse-grained multiscale computation: enabling mocroscopic simulators to perform system-level analysis. Commun Math Sci 2003, 1:715–762.
-
(2003)
Commun Math Sci
, vol.1
, pp. 715-762
-
-
Kevrekidis, I.G.1
Gear, C.W.2
Hyman, J.M.3
Kevrekidid, P.G.4
Runborg, O.5
Theodoropoulos, C.6
-
55
-
-
84945465279
-
A data-driven approximation of the koopman operator: extending dynamic mode decomposition
-
Williams MO, Kevrekidis IG, Rowley CW. A data-driven approximation of the koopman operator: extending dynamic mode decomposition. J Nonlinear Sci 2015, 25:1307–1346. doi:10.1007/s00332-015-9258-5.
-
(2015)
J Nonlinear Sci
, vol.25
, pp. 1307-1346
-
-
Williams, M.O.1
Kevrekidis, I.G.2
Rowley, C.W.3
-
56
-
-
76349094911
-
Spectral analysis of nonlinear flows
-
Rowley CW, Mezic I, Bagheri S, Schlatter P, Henningson DS. Spectral analysis of nonlinear flows. J Fluid Mech 2009, 641:115–127. doi:10.1017/S0022112009992059.
-
(2009)
J Fluid Mech
, vol.641
, pp. 115-127
-
-
Rowley, C.W.1
Mezic, I.2
Bagheri, S.3
Schlatter, P.4
Henningson, D.S.5
-
58
-
-
79551684199
-
The folding of single domain proteins—have we reached a consensus?
-
Sosnick TR, Barrick D. The folding of single domain proteins—have we reached a consensus? Curr Opin Struct Biol 2011, 21:12–24. doi:10.1016/j.sbi.2010.11.002.
-
(2011)
Curr Opin Struct Biol
, vol.21
, pp. 12-24
-
-
Sosnick, T.R.1
Barrick, D.2
-
59
-
-
84857510185
-
Single-molecule fluorescence experiments determine protein folding transition path times
-
Chung HS, McHale K, Louis JM, Eaton WA. Single-molecule fluorescence experiments determine protein folding transition path times. Science 2012, 335:981–984. doi:10.1126/science.1215768.
-
(2012)
Science
, vol.335
, pp. 981-984
-
-
Chung, H.S.1
McHale, K.2
Louis, J.M.3
Eaton, W.A.4
-
60
-
-
84942424865
-
Structural origin of slow diffusion in protein folding
-
Chung HS, Piana-Agostinetti S, Shaw DE, Eaton WA. Structural origin of slow diffusion in protein folding. Science 2015, 349:1504–1510. doi:10.1126/science.aab1369.
-
(2015)
Science
, vol.349
, pp. 1504-1510
-
-
Chung, H.S.1
Piana-Agostinetti, S.2
Shaw, D.E.3
Eaton, W.A.4
-
61
-
-
77957572546
-
Challenges in protein-folding simulations
-
Freddolino PL, Harrison CB, Liu Y, Schulten K. Challenges in protein-folding simulations. Nat Phys 2010, 6:751–758. doi:10.1038/nphys1713.
-
(2010)
Nat Phys
, vol.6
, pp. 751-758
-
-
Freddolino, P.L.1
Harrison, C.B.2
Liu, Y.3
Schulten, K.4
-
62
-
-
80055081145
-
How fast-folding proteins fold
-
Lindorff-Larsen K, Piana S, Dror RO, Shaw DE. How fast-folding proteins fold. Science 2011, 334:517–520. doi:10.1126/science.1208351.
-
(2011)
Science
, vol.334
, pp. 517-520
-
-
Lindorff-Larsen, K.1
Piana, S.2
Dror, R.O.3
Shaw, D.E.4
-
63
-
-
84868155171
-
Protein folding kinetics and thermodynamics from atomistic simulation
-
Piana S, Lindorff-Larsen K, Shaw DE. Protein folding kinetics and thermodynamics from atomistic simulation. Proc Natl Acad Sci USA 2012, 109:17845–17850. doi:10.1073/pnas.1201811109.
-
(2012)
Proc Natl Acad Sci USA
, vol.109
, pp. 17845-17850
-
-
Piana, S.1
Lindorff-Larsen, K.2
Shaw, D.E.3
-
64
-
-
70450235210
-
The transition state transit time of WW domain folding is controlled by energy landscape roughness
-
Liu F, Nakaema M, Gruebele M. The transition state transit time of WW domain folding is controlled by energy landscape roughness. J Chem Phys 2009, 131:195101. doi:10.1063/1.3262489.
-
(2009)
J Chem Phys
, vol.131
, pp. 195101
-
-
Liu, F.1
Nakaema, M.2
Gruebele, M.3
-
65
-
-
0024121530
-
Diffusion in a rough potential
-
Zwanzig R. Diffusion in a rough potential. Proc Natl Acad Sci USA 1988, 85:2029–2030.
-
(1988)
Proc Natl Acad Sci USA
, vol.85
, pp. 2029-2030
-
-
Zwanzig, R.1
-
66
-
-
84890518503
-
High-resolution free-energy landscape analysis of -helical protein folding: HP35 and its double mutant
-
Banushkina PV, Krivov SV. High-resolution free-energy landscape analysis of -helical protein folding: HP35 and its double mutant. J Chem Theory Comput 2013, 9:5257–5266. doi:10.1021/ct400651z.
-
(2013)
J Chem Theory Comput
, vol.9
, pp. 5257-5266
-
-
Banushkina, P.V.1
Krivov, S.V.2
-
67
-
-
79952457753
-
The free energy landscape of small molecule unbinding
-
Huang D, Caflisch A. The free energy landscape of small molecule unbinding. PLoS Comput Biol 2011, 7:e1002002. doi:10.1371/journal.pcbi.1002002.
-
(2011)
PLoS Comput Biol
, vol.7
-
-
Huang, D.1
Caflisch, A.2
-
68
-
-
84887801032
-
Modulation of a protein free-energy landscape by circular permutation
-
Radou G, Enciso M, Krivov S, Paci E. Modulation of a protein free-energy landscape by circular permutation. J Phys Chem B 2013, 117:13743–13747. doi:10.1021/jp406818t.
-
(2013)
J Phys Chem B
, vol.117
, pp. 13743-13747
-
-
Radou, G.1
Enciso, M.2
Krivov, S.3
Paci, E.4
-
69
-
-
84964725465
-
Principles and overview of sampling methods for modeling macromolecular structure and dynamics
-
Maximova T, Moffatt R, Ma B, Nussinov R, Shehu A. Principles and overview of sampling methods for modeling macromolecular structure and dynamics. PLoS Comput Biol 2016, 12:e1004619. doi:10.1371/journal.pcbi.1004619.
-
(2016)
PLoS Comput Biol
, vol.12
-
-
Maximova, T.1
Moffatt, R.2
Ma, B.3
Nussinov, R.4
Shehu, A.5
-
70
-
-
0036424048
-
Transition path sampling: throwing ropes over rough mountain passes, in the dark
-
Bolhuis PG, Chandler D, Dellago C, Geissler PL. Transition path sampling: throwing ropes over rough mountain passes, in the dark. Annu Rev Phys Chem 2002, 53:291–318. doi:10.1146/annurev.physchem.53.082301.113146.
-
(2002)
Annu Rev Phys Chem
, vol.53
, pp. 291-318
-
-
Bolhuis, P.G.1
Chandler, D.2
Dellago, C.3
Geissler, P.L.4
-
71
-
-
0342929614
-
Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling
-
Torrie GM, Valleau JP. Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling. J Comput Phys 1977, 23:187–199. doi:10.1016/0021-9991(77)90121-8.
-
(1977)
J Comput Phys
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
72
-
-
84973369671
-
Enhancing important fluctuations: rare events and metadynamics from a conceptual viewpoint
-
Valsson O, Tiwary P, Parrinello M. Enhancing important fluctuations: rare events and metadynamics from a conceptual viewpoint. Annu Rev Phys Chem 2016, 67:159–184. doi:10.1146/annurev-physchem-040215-112229.
-
(2016)
Annu Rev Phys Chem
, vol.67
, pp. 159-184
-
-
Valsson, O.1
Tiwary, P.2
Parrinello, M.3
-
73
-
-
84962482196
-
Spectral gap optimization of order parameters for sampling complex molecular systems
-
Tiwary P, Berne BJ. Spectral gap optimization of order parameters for sampling complex molecular systems. Proc Natl Acad Sci USA 2016, 113:2839–2844. doi:10.1073/pnas.1600917113.
-
(2016)
Proc Natl Acad Sci USA
, vol.113
, pp. 2839-2844
-
-
Tiwary, P.1
Berne, B.J.2
-
74
-
-
24344467850
-
Transition pathways in complex systems: reaction coordinates, isocommittor surfaces, and transition tubes
-
Weinan E, Ren W, Vanden-Eijnden E. Transition pathways in complex systems: reaction coordinates, isocommittor surfaces, and transition tubes. Chem Phys Lett 2005, 413:242–247. doi:10.1016/j.cplett.2005.07.084.
-
(2005)
Chem Phys Lett
, vol.413
, pp. 242-247
-
-
Weinan, E.1
Ren, W.2
Vanden-Eijnden, E.3
-
75
-
-
79952096187
-
Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI
-
Ovchinnikov V, Karplus M, Vanden-Eijnden E. Free energy of conformational transition paths in biomolecules: the string method and its application to myosin VI. J Chem Phys 2011, 134:085103. doi:10.1063/1.3544209.
-
(2011)
J Chem Phys
, vol.134
, pp. 085103
-
-
Ovchinnikov, V.1
Karplus, M.2
Vanden-Eijnden, E.3
-
76
-
-
84963949906
-
Mastering the game of Go with deep neural networks and tree search
-
Silver D, Huang A, Maddison CJ, Guez A, Sifre L, van den Driessche G, Schrittwieser J, Antonoglou I, Panneershelvam V, Lanctot M, et al. Mastering the game of Go with deep neural networks and tree search. Nature 2016, 529:484–489. doi:10.1038/nature16961.
-
(2016)
Nature
, vol.529
, pp. 484-489
-
-
Silver, D.1
Huang, A.2
Maddison, C.J.3
Guez, A.4
Sifre, L.5
van den Driessche, G.6
Schrittwieser, J.7
Antonoglou, I.8
Panneershelvam, V.9
Lanctot, M.10
-
77
-
-
84907028883
-
Mapping brain activity at scale with cluster computing
-
Freeman J, Vladimirov N, Kawashima T, Mu Y, Sofroniew NJ, Bennett DV, Rosen J, Yang CT, Looger LL, Ahrens MB. Mapping brain activity at scale with cluster computing. Nat Methods 2014, 11:941–950. doi:10.1038/nmeth.3041.
-
(2014)
Nat Methods
, vol.11
, pp. 941-950
-
-
Freeman, J.1
Vladimirov, N.2
Kawashima, T.3
Mu, Y.4
Sofroniew, N.J.5
Bennett, D.V.6
Rosen, J.7
Yang, C.T.8
Looger, L.L.9
Ahrens, M.B.10
-
78
-
-
84957072943
-
Variational tensor approach for approximating the rare-event kinetics of macromolecular systems
-
Nüske F, Schneider R, Vitalini F, Noé F. Variational tensor approach for approximating the rare-event kinetics of macromolecular systems. J Chem Phys 2016, 144:054105. doi:10.1063/1.4940774.
-
(2016)
J Chem Phys
, vol.144
, pp. 054105
-
-
Nüske, F.1
Schneider, R.2
Vitalini, F.3
Noé, F.4
-
79
-
-
78649613551
-
Free energy surfaces from single-distance information
-
Schuetz P, Wuttke R, Schuler B, Caflisch A. Free energy surfaces from single-distance information. J Phys Chem B 2010, 114:15227–15235. doi:10.1021/jp1053698.
-
(2010)
J Phys Chem B
, vol.114
, pp. 15227-15235
-
-
Schuetz, P.1
Wuttke, R.2
Schuler, B.3
Caflisch, A.4
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