-
1
-
-
33646931471
-
Protein folding thermodynamics and dynamics: Where physics, chemistry, and biology meet
-
Shakhnovich E. Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet. Chem Rev 2006;106:1559-1588.
-
(2006)
Chem Rev
, vol.106
, pp. 1559-1588
-
-
Shakhnovich, E.1
-
2
-
-
34347375915
-
The protein folding problem: When will it be solved?
-
Dill KA, Ozkan SB, Weikl TR, Chodera JD, Voelz VA. The protein folding problem: when will it be solved? Curr Opin Struct Biol 2007;17:342-346.
-
(2007)
Curr Opin Struct Biol
, vol.17
, pp. 342-346
-
-
Dill, K.A.1
Ozkan, S.B.2
Weikl, T.R.3
Chodera, J.D.4
Voelz, V.A.5
-
3
-
-
0017842051
-
Studies on protein folding, unfolding and fluctuations by computer simulations. II. A three-dimensional lattice model of lysozyme
-
Ueda Y, Taketomi H, Gö N. Studies on protein folding, unfolding and fluctuations by computer simulations. II. A three-dimensional lattice model of lysozyme. Biopolymers 1978;17:1531-1548.
-
(1978)
Biopolymers
, vol.17
, pp. 1531-1548
-
-
Ueda, Y.1
Taketomi, H.2
Gö, N.3
-
4
-
-
0032502839
-
Contact order transition state placement and the refolding rates of single domain proteins
-
Plaxco KW, Simons KT, Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol 1998;277:985-994.
-
(1998)
J Mol Biol
, vol.277
, pp. 985-994
-
-
Plaxco, K.W.1
Simons, K.T.2
Baker, D.3
-
5
-
-
0028868995
-
The structure of the transitionstate for folding of chymotrypsin inhibitor-2 analyzed by protein engineering methods-evidence for a nucleation-condensation mechanism for protein-folding
-
Itzhaki LS, Otzen DE, Fersht AR. The structure of the transitionstate for folding of chymotrypsin inhibitor-2 analyzed by protein engineering methods-evidence for a nucleation-condensation mechanism for protein-folding. J Mol Biol 1995; 254:260-288.
-
(1995)
J Mol Biol
, vol.254
, pp. 260-288
-
-
Itzhaki, L.S.1
Otzen, D.E.2
Fersht, A.R.3
-
6
-
-
0347753598
-
Energetics of protein thermodynamic cooperativity: Contributions of local and nonlocal interactions
-
Knott M, Kaya H, Chan HS. Energetics of protein thermodynamic cooperativity: contributions of local and nonlocal interactions. Biomacromolecuies 2004; 45:623-632.
-
(2004)
Biomacromolecuies
, vol.45
, pp. 623-632
-
-
Knott, M.1
Kaya, H.2
Chan, H.S.3
-
7
-
-
4644259872
-
Three-body interactions improve the prediction of rate and mechanism in protein folding models
-
Ejtehadi MR, Avail SP, Plotkin SS. Three-body interactions improve the prediction of rate and mechanism in protein folding models. Proc Natl Acad Sci USA 2004;101:15088-15093.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 15088-15093
-
-
Ejtehadi, M.R.1
Avail, S.P.2
Plotkin, S.S.3
-
8
-
-
34247861746
-
Thermodynamics of Go models for protein folding
-
Prieto L, de Sancho D, Rey A. Thermodynamics of Go models for protein folding. J Chem Phys 2005;123:8.
-
(2005)
J Chem Phys
, vol.123
, pp. 8
-
-
Prieto, L.1
De Sancho, D.2
Rey, A.3
-
9
-
-
30344481686
-
Folding pathway dependence on energetic frustration and interaction heterogeneity for a three-dimensional hydrophobic protein model
-
Garcia LG, de Araujo AFP. Folding pathway dependence on energetic frustration and interaction heterogeneity for a three-dimensional hydrophobic protein model. Proteins 2006;62:46-63.
-
(2006)
Proteins
, vol.62
, pp. 46-63
-
-
Garcia, L.G.1
De Araujo, A.F.P.2
-
10
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes A study of more than 1000 mutations
-
Guerois R, Nielsen JE, Serrano L. Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations. J Mol Biol 2002; 320:369-387.
-
(2002)
J Mol Biol
, vol.320
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
11
-
-
0031853167
-
Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain
-
Grantcharova VP, Riddle DS, Santiago JV, Baker D. Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain. Nat Struct Biol 1998;5:714-720.
-
(1998)
Nat Struct Biol
, vol.5
, pp. 714-720
-
-
Grantcharova, V.P.1
Riddle, D.S.2
Santiago, J.V.3
Baker, D.4
-
12
-
-
0031825181
-
Obligatory steps in protein folding and the conformational diversity of the transition state
-
Martinez JC, Pisabarro MT, Serrano L. Obligatory steps in protein folding and the conformational diversity of the transition state. Nat Struct Biol 1998;5:721-729.
-
(1998)
Nat Struct Biol
, vol.5
, pp. 721-729
-
-
Martinez, J.C.1
Pisabarro, M.T.2
Serrano, L.3
-
13
-
-
0029740071
-
Non-native alpha-helical intermediate in the refolding of beta-lactoglobulin, a predominantly betasheet protein
-
Hamada D, Segawa S, Goto Y. Non-native alpha-helical intermediate in the refolding of beta-lactoglobulin, a predominantly betasheet protein. Nat Struct Biol 1996;3:868-873.
-
(1996)
Nat Struct Biol
, vol.3
, pp. 868-873
-
-
Hamada, D.1
Segawa, S.2
Goto, Y.3
-
14
-
-
4143061715
-
Switching two-state to threestate kinetics in the helical protein Im9 via the optimisation of stabilising non-native interactions by design
-
Friel CT, Beddard GS, Radford SE. Switching two-state to threestate kinetics in the helical protein Im9 via the optimisation of stabilising non-native interactions by design. J Mol Biol 2004;342: 261-273.
-
(2004)
J Mol Biol
, vol.342
, pp. 261-273
-
-
Friel, C.T.1
Beddard, G.S.2
Radford, S.E.3
-
15
-
-
28844466085
-
Identification of native and non-native structure in kinetic folding intermediates of apomyoglobin
-
Nishimura C, Dyson HJ, Wright PE. Identification of native and non-native structure in kinetic folding intermediates of apomyoglobin. J Mol Biol 2006;355:139-156.
-
(2006)
J Mol Biol
, vol.355
, pp. 139-156
-
-
Nishimura, C.1
Dyson, H.J.2
Wright, P.E.3
-
16
-
-
0035576033
-
Speeding protein folding beyond the Go model: How a little frustration sometimes helps
-
Plotkin SS. Speeding protein folding beyond the Go model: how a little frustration sometimes helps. Proteins 2001; 45:337-345.
-
(2001)
Proteins
, vol.45
, pp. 337-345
-
-
Plotkin, S.S.1
-
17
-
-
3042677501
-
The effects of nonnative interactions on protein folding rates: Theory and simulation
-
Clementi C, Plotkin SS. The effects of nonnative interactions on protein folding rates: theory and simulation. Protein Sci 2004;13: 1750-1766.
-
(2004)
Protein Sci
, vol.13
, pp. 1750-1766
-
-
Clementi, C.1
Plotkin, S.S.2
-
18
-
-
34447261443
-
The effect of increasing the stability of non-native interactions on the folding landscape of the bacterial immunity protein Im9
-
Morton VL, Friel CT, Allen LR, Paci. E, Radford SE. The effect of increasing the stability of non-native interactions on the folding landscape of the bacterial immunity protein Im9. J Mol Biol 2007; 371:554-568.
-
(2007)
J Mol Biol
, vol.371
, pp. 554-568
-
-
Morton, V.L.1
Friel, C.T.2
Allen, L.R.3
Paci, E.4
Radford, S.E.5
-
19
-
-
38949181862
-
Influence of Go-like interactions on global shapes of energy landscapes in beta-barrel forming model proteins Inherent structure analysis and statistical temperature molecular dynamics simulation
-
Kim J, Keyes T. Influence of Go-like interactions on global shapes of energy landscapes in beta-barrel forming model proteins: Inherent structure analysis and statistical temperature molecular dynamics simulation. J Phys Chem B 2008;112:954-966.
-
(2008)
J Phys Chem B
, vol.112
, pp. 954-966
-
-
Kim, J.1
Keyes, T.2
-
20
-
-
65249121395
-
Analysing the origin of longrange interactions in proteins using lattice models
-
Noivirt-Brik O, Unger R, Horovitz A. Analysing the origin of longrange interactions in proteins using lattice models. BMC Struct Biol 2009;9:4.
-
(2009)
BMC Struct Biol
, vol.9
, pp. 4
-
-
Noivirt-Brik, O.1
Unger, R.2
Horovitz, A.3
-
21
-
-
65649143356
-
Liaison amid disorder non-native interactions may underpin long-range coupling in proteins
-
Chan HS, Zhang ZQ. Liaison amid disorder: non-native interactions may underpin long-range coupling in proteins. J Biol 2009;8:27.
-
(2009)
J Biol
, vol.8
, pp. 27
-
-
Chan, H.S.1
Zhang, Z.Q.2
-
22
-
-
0037093654
-
Native and non-native interactions along protein folding and unfolding pathways
-
Pad E, Vendruscolo M, Karplus M. Native and non-native interactions along protein folding and unfolding pathways. Proteins 2002; 47:379-392.
-
(2002)
Proteins
, vol.47
, pp. 379-392
-
-
Pad, E.1
Vendruscolo, M.2
Karplus, M.3
-
23
-
-
48249138078
-
Theoretical and experimental demonstration of the importance of specific nounative interactions in protein folding
-
Zarrine-Afsar A, Wallin S, Neculai AM, Neudecker P, Howell. PL, Davidson AR, Chan HS. Theoretical and experimental demonstration of the importance of specific nounative interactions in protein folding. Proc Natl Acad Sci USA 2008;105:9999-10004.
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, pp. 9999-10004
-
-
Zarrine-Afsar, A.1
Wallin, S.2
Neculai, A.M.3
Neudecker, P.4
Howell, P.L.5
Davidson, A.R.6
Chan, H.S.7
-
24
-
-
0034112774
-
Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus
-
Li L, Mirny LA, Shakhnovich EI. Kinetics, thermodynamics and evolution of non-native interactions in a protein folding nucleus. Nat Struct Biol 2000; 7:336-342.
-
(2000)
Nat Struct Biol
, vol.7
, pp. 336-342
-
-
Li, L.1
Mirny, L.A.2
Shakhnovich, E.I.3
-
25
-
-
34548778164
-
Temperature-dependent folding pathways of pin1 WW domain: An all-atom, molecular dynamics simulation of a Go model
-
Luo ZL, Ding JD, Zhou YQ. Temperature-dependent folding pathways of pin1 WW domain: an all-atom, molecular dynamics simulation of a Go model. Biophys J 2007;93:2152-2161.
-
(2007)
Biophys J
, vol.93
, pp. 2152-2161
-
-
Luo, Z.L.1
Ding, J.D.2
Zhou, Y.Q.3
-
26
-
-
0043094427
-
Folding of lattice protein chains with modified Go potential
-
Fan K, Wang J, Wang W. Folding of lattice protein chains with modified Go potential. Eur Phys J B 2002;30:381-391.
-
(2002)
Eur Phys J B
, vol.30
, pp. 381-391
-
-
Fan, K.1
Wang, J.2
Wang, W.3
-
27
-
-
0242383943
-
Improved Go-like models demonstrate the robustness of protein folding mechanisms towards nonnative interactions
-
Karanicolas J, Brooks III CL. Improved Go-like models demonstrate the robustness of protein folding mechanisms towards nonnative interactions. J Mol Biol 2003;334:309-325.
-
(2003)
J Mol Biol
, vol.334
, pp. 309-325
-
-
Karanicolas, J.1
Brooks Iii, C.L.2
-
28
-
-
22544446147
-
Balancing energy and entropy: A minimalist model for the characterization of protein folding laudscapes
-
Das P, Matysiak S, Clementi C. Balancing energy and entropy: A minimalist model for the characterization of protein folding laudscapes. Proc Natl Acad Sci USA 2005; 102:10141-10146.
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 10141-10146
-
-
Das, P.1
Matysiak, S.2
Clementi, C.3
-
29
-
-
33745712768
-
Sequence of events in folding mechanism: Beyond the Go model
-
Sutto L, Tiana G, Broglia RA. Sequence of events in folding mechanism: Beyond the Go model. Protein Sci 2006; 15:1638-1652.
-
(2006)
Protein Sci
, vol.15
, pp. 1638-1652
-
-
Sutto, L.1
Tiana, G.2
Broglia, R.A.3
-
30
-
-
0000668407
-
Theory of the phase transition between helix and random coil in polypeptide chains
-
Zimm BH, Bragg JK. Theory of the phase transition between helix and random coil in polypeptide chains. J Chem. Phys 1959;31: 526-535.
-
(1959)
J Chem. Phys
, vol.31
, pp. 526-535
-
-
Zimm, B.H.1
Bragg, J.K.2
-
31
-
-
0000333671
-
On the theory of helix-coil transition in polypeptides
-
Lifson S, Roig A. On the theory of helix-coil transition in polypeptides. J Chem Phys 1961;34:1963-1974.
-
(1961)
J Chem Phys
, vol.34
, pp. 1963-1974
-
-
Lifson, S.1
Roig, A.2
-
32
-
-
0025113815
-
Helix-coil stability constants for the naturally occurring amino acids in water. XXIV. Half-cystine parameters from random poly (hydroxybutylglutamine- co-S-methylthio-L-cysteine)
-
DOI 10.1002/bip.360300113
-
Wojcik J, Altmann KH, Scheraga HA. Helix-coil stability constants for the naturally occurring amino acids in water. XXIV. Half-cystine parameters from random poly(hydroxybutylglutamine-CO-S-methylthio-L-cystdne). Biopolymers 1990;30:121-134. (Pubitemid 20263097)
-
(1990)
Biopolymers
, vol.30
, Issue.1-2
, pp. 121-134
-
-
Wojcik, J.1
Altmann, K.-H.2
Scheraga, H.A.3
-
33
-
-
0026254055
-
Parameters of helix-coil transition theory for alanine-based peptides of varying chain lengths in water
-
Scholtz JM., Qian H, York EJ, Stewart JM, Baldwin RL. Parameters of helix-coil transition theory for alanine-based peptides of varying chain lengths in water. Biopolymers 1991; 31:1463-1470.
-
(1991)
Biopolymers
, vol.31
, pp. 1463-1470
-
-
Scholtz, J.M.1
Qian, H.2
York, E.J.3
Stewart, J.M.4
Baldwin, R.L.5
-
34
-
-
33751391161
-
Helix-coil theories a comparative study for finite length polypeptides
-
Qian H, Schellman JA. Helix-coil theories: a comparative study for finite length polypeptides. J Phys Chem. 1992; 96:3987-3994.
-
(1992)
J Phys Chem.
, vol.96
, pp. 3987-3994
-
-
Qian, H.1
Schellman, J.A.2
-
35
-
-
0000137407
-
The helix-coil kinetics of a heteropeptide
-
Thompson PA, Munoz V, Jas GS, Henry ER, Eaton WA, Hofrichter J. The helix-coil kinetics of a heteropeptide. J Phys Chem B 2000; 104: 378-389.
-
(2000)
J Phys Chem B
, vol.104
, pp. 378-389
-
-
Thompson, P.A.1
Munoz, V.2
Jas, G.S.3
Henry, E.R.4
Eaton, W.A.5
Hofrichter, J.6
-
36
-
-
0033959403
-
Computer simulations of the properties of the alpha(2), and alpha C-2 and alpha D-2 de novo designed helical proteins
-
Sikorski A, Kolinski A, Skolnick J. Computer simulations of the properties of the alpha(2), and alpha C-2 and alpha D-2 de novo designed helical proteins. Proteins 2000;38:17-28.
-
(2000)
Proteins
, vol.38
, pp. 17-28
-
-
Sikorski, A.1
Kolinski, A.2
Skolnick, J.3
-
37
-
-
0037022567
-
Helix formation via conformation diffusion search
-
Huang CY, Getahun Z, Zhu YJ, Klemke JW, DeGrado WF, Gai F. Helix formation via conformation diffusion search. Proc Natl Acad Sci USA 2002;992788-992793
-
(2002)
Proc Natl Acad Sci USA
, pp. 992788-992793
-
-
Huang, C.Y.1
Getahun, Z.2
Zhu, Y.J.3
Klemke, J.W.4
DeGrado, W.F.5
Gai, F.6
-
38
-
-
0037234367
-
Breaking nonnative hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide
-
Chowdhury S, Zhang W, Wu C, Xioug GM, Duan Y. Breaking nonnative hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide. Biopolymers 2003; 68:63-75.
-
(2003)
Biopolymers
, vol.68
, pp. 63-75
-
-
Chowdhury, S.1
Zhang, W.2
Wu, C.3
Xioug, G.M.4
Duan, Y.5
-
39
-
-
0345564821
-
Exploring Flory's isolated-pair hypothesis: Statistical mechanics of helix-coil transitions in polyalanine and the C-peptide from RNase A
-
Ohkubo YZ, Brooks III CL. Exploring Flory's isolated-pair hypothesis: Statistical mechanics of helix-coil transitions in polyalanine and the C-peptide from RNase A. Proc Natl Acad Sci USA 2003; 100:13916-13921.
-
(2003)
Proc Natl Acad Sci USA
, vol.100
, pp. 13916-13921
-
-
Ohkubo, Y.Z.1
Brooks III, C.L.2
-
40
-
-
33947392892
-
Minimum model for the α-helix-ß-hairpin transition in proteins
-
Imamura H, Chen JZY. Minimum model for the α-helix-ß-hairpin transition in proteins. Proteins 2007; 67:459-468.
-
(2007)
Proteins
, vol.67
, pp. 459-468
-
-
Imamura, H.1
Chen, J.Z.Y.2
-
41
-
-
34548314208
-
The helix-coil transition revisited
-
Chen YT, Zhou YQ, Ding JD. The helix-coil transition revisited. Proteins 2007;69:58-68.
-
(2007)
Proteins
, vol.69
, pp. 58-68
-
-
Chen, Y.T.1
Zhou, Y.Q.2
Ding, J.D.3
-
42
-
-
18644371834
-
Inter-diffusion and self-diffusion in polymer mixtures a Monte Carlo study
-
Deutsch HP, Binder K. Inter-diffusion and self-diffusion in polymer mixtures: a Monte Carlo study. J Chem Phys 1991; 94:2294-2304.
-
(1991)
J Chem Phys
, vol.94
, pp. 2294-2304
-
-
Deutsch, H.P.1
Binder, K.2
-
43
-
-
0024071054
-
The bond fluctuation method: A new effective algorithm for the dynamics of polymers in all spatial dimensions
-
Carmesin I, Kremer K. The bond fluctuation method: a new effective algorithm for the dynamics of polymers in all spatial dimensions. Macromolecules 1988; 21:2819-2823.
-
(1988)
Macromolecules
, vol.21
, pp. 2819-2823
-
-
Carmesin, I.1
Kremer, K.2
-
44
-
-
1642409413
-
A coarse-grained model and associated lattice Monte Carlo simulation of the coil-helix transition of a homopolypeptide
-
Chen YF, Zhang Q, Ding JD. A coarse-grained model and associated lattice Monte Carlo simulation of the coil-helix transition of a homopolypeptide. J Chem Phys 2004; 120:3467-3474.
-
(2004)
J Chem Phys
, vol.120
, pp. 3467-3474
-
-
Chen, Y.F.1
Zhang, Q.2
Ding, J.D.3
-
45
-
-
0001194908
-
Discretized model of proteins. I. MonteCarlo study of cooperativity in homopolypeptides
-
Kolinski A, Skolnick J. Discretized model of proteins. I. MonteCarlo study of cooperativity in homopolypeptides. J Chem. Phys 1992; 97:9412-9426.
-
(1992)
J Chem. Phys
, vol.97
, pp. 9412-9426
-
-
Kolinski, A.1
Skolnick, J.2
-
46
-
-
33846096753
-
Monte Carlo calculations on the dynamics of polymers in dilute solution
-
Verdier PH, Stockmayer WH. Monte Carlo calculations on the dynamics of polymers in dilute solution. J Chem. Phys 1962; 36:227-235.
-
(1962)
J Chem. Phys
, vol.36
, pp. 227-235
-
-
Verdier, P.H.1
Stockmayer, W.H.2
-
47
-
-
0000179346
-
Analysis of Monte Carlo results on the kinetics of lattice polymer chains with excluded volume
-
Hilhorst HJ, Deutch JM. Analysis of Monte Carlo results on the kinetics of lattice polymer chains with excluded volume. J Chem Phys 1975; 63:5153-5161.
-
(1975)
J Chem Phys
, vol.63
, pp. 5153-5161
-
-
Hilhorst, H.J.1
Deutch, J.M.2
-
48
-
-
77949895056
-
Dynamic Monte Carlo simulation of the kinetic process for polymer collapse transition
-
Chen YT, Ding JD. Dynamic Monte Carlo simulation of the kinetic process for polymer collapse transition. Acta Polym Sin 12: 1238-1244.
-
Acta Polym Sin
, vol.12
, pp. 1238-1244
-
-
Chen, Y.T.1
Ding, J.D.2
-
49
-
-
43149085052
-
The effect of sequence on the conformational stability of a model heteropolymer in explicit water
-
Patel BA, Debenedetti PG, Stillinger FH, Rossky PJ. The effect of sequence on the conformational stability of a model heteropolymer in explicit water. J Chem Phys 2008; 128:175102.
-
(2008)
J Chem Phys
, vol.128
, pp. 175102
-
-
Patel, B.A.1
Debenedetti, P.G.2
Stillinger, F.H.3
Rossky, P.J.4
-
50
-
-
5744249209
-
Equation of state calculations by fast computing machines
-
Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E. Equation of state calculations by fast computing machines. J Chem Phys 1953; 21:1087-1092.
-
(1953)
J Chem Phys
, vol.21
, pp. 1087-1092
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.H.4
Teller, E.5
-
52
-
-
0000512575
-
Shape asymmetry of random-walks and noureversal random-walks
-
Zifferer G, Olaj OF. Shape asymmetry of random-walks and noureversal random-walks. J Chem Phys 1994;100:636-639.
-
(1994)
J Chem Phys
, vol.100
, pp. 636-639
-
-
Zifferer, G.1
Olaj, O.F.2
-
53
-
-
0000936038
-
The calculation of molecular vibration frequencies
-
Lindemann FA. The calculation of molecular vibration frequencies. Physik Z 1910;11:609-612.
-
(1910)
Physik Z
, vol.11
, pp. 609-612
-
-
Lindemann, F.A.1
-
54
-
-
0031475159
-
Folding thermodynamics of a model threehelix-bundle protein
-
Zhou YQ, Karplus M. Folding thermodynamics of a model threehelix-bundle protein. Proc Natl Acad Sci USA 1997; 94:14429-14432.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 14429-14432
-
-
Zhou, Y.Q.1
Karplus, M.2
-
55
-
-
0000546668
-
Helix-coil transition and 1/f fluctuation in a polypeptide
-
Takano M, Takahashi T, Nagayama K. Helix-coil transition and 1/f fluctuation in a polypeptide. Phys Rev Lett 1998; 80:5691-5694.
-
(1998)
Phys Rev Lett
, vol.80
, pp. 5691-5694
-
-
Takano, M.1
Takahashi, T.2
Nagayama, K.3
-
56
-
-
0001015060
-
Equilibrium thermodynamics of homopolymers and clusters molecular dynamics and Monte Carlo simulations of systems with square-well interactions
-
Zhou YQ, Karplus M, Wichert JM, Hall CK. Equilibrium thermodynamics of homopolymers and clusters: molecular dynamics and Monte Carlo simulations of systems with square-well interactions. J Chem Phys 1997; 107:10691-10708.
-
(1997)
J Chem Phys
, vol.107
, pp. 10691-10708
-
-
Zhou, Y.Q.1
Karplus, M.2
Wichert, J.M.3
Hall, C.K.4
-
57
-
-
0142211225
-
Collapse of homopolymer chains with two fixed terminals
-
Xue B, Wang J, Wang W. Collapse of homopolymer chains with two fixed terminals. J Chem Phys 2003;119:7534-7542.
-
(2003)
J Chem Phys
, vol.119
, pp. 7534-7542
-
-
Xue, B.1
Wang, J.2
Wang, W.3
-
58
-
-
33846207122
-
Coarse-grained model of coil-to-helix kinetics demonstrates the importance of multiple nucleation sites in helix folding
-
van Giessen AE, Straub JE. Coarse-grained model of coil-to-helix kinetics demonstrates the importance of multiple nucleation sites in helix folding. J Chem Theory Comput 2006;2:674-684.
-
(2006)
J Chem Theory Comput
, vol.2
, pp. 674-684
-
-
Van Giessen, A.E.1
Straub, J.E.2
-
59
-
-
2942754061
-
Fs-21 peptides can form both single helix and helix-turn-helix
-
Zhang W, Lei HX, Chowdhury S, Duan Y. Fs-21 peptides can form both single helix and helix-turn-helix. J Phys Chem B 2004;108: 7479-7489.
-
(2004)
J Phys Chem B
, vol.108
, pp. 7479-7489
-
-
Zhang, W.1
Lei, H.X.2
Chowdhury, S.3
Duan, Y.4
-
60
-
-
0038245156
-
The role of alpha-, 3(10)-, and pi-helix in helix -> coil transitions
-
Armen R, Alonso DOV, Daggett V. The role of alpha-, 3(10)-, and pi-helix in helix -> coil transitions. Protein Sci 2003;12:1145-1157.
-
(2003)
Protein Sci
, vol.12
, pp. 1145-1157
-
-
Armen, R.1
Alonso, D.O.V.2
Daggett, V.3
-
61
-
-
0141480850
-
Mechanism for the alpha-helix to beta-hairpin transition
-
Ding F, Borreguero JM, Buldyrey SV, Stanley HE, Dokholyan NV. Mechanism for the alpha-helix to beta-hairpin transition. Proteins 2003; 53:220-228.
-
(2003)
Proteins
, vol.53
, pp. 220-228
-
-
Ding, F.1
Borreguero, J.M.2
Buldyrey, S.V.3
Stanley, H.E.4
Dokholyan, N.V.5
-
62
-
-
33845213187
-
Secondary structure provides a template for the folding of nearby polypeptides
-
Kameda T, Takada S. Secondary structure provides a template for the folding of nearby polypeptides. Proc Natl Acad Sci USA 2006; 103:17765-17770.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, pp. 17765-17770
-
-
Kameda, T.1
Takada, S.2
-
63
-
-
35648949836
-
Importance of metastable states in the free energy landscapes of polypeptide chains
-
Auer S, Miller MA, Krivov SV, Dobson CM, Karplus M, Vendruscolo M. Importance of metastable states in the free energy landscapes of polypeptide chains. Phys Rev Lett 2007;99:178104.
-
(2007)
Phys Rev Lett
, vol.99
, pp. 178104
-
-
Auer, S.1
Miller, M.A.2
Krivov, S.V.3
Dobson, C.M.4
Karplus, M.5
Vendruscolo, M.6
-
64
-
-
44949188455
-
Folding and dimerization of the ionic peptide EAK16-IV
-
Yan ZQ, Wang J, Wang W. Folding and dimerization of the ionic peptide EAK16-IV. Proteins 2008; 72:150-162.
-
(2008)
Proteins
, vol.72
, pp. 150-162
-
-
Yan, Z.Q.1
Wang, J.2
Wang, W.3
-
67
-
-
0001075603
-
Finite-size scaling of helix-coil transitions in poly-alanine studied by multicanonical simulations
-
Hausmann UHE, Okamoto Y. Finite-size scaling of helix-coil transitions in poly-alanine studied by multicanonical simulations. J Chem Phys 1999; 110: 1267-1276.
-
(1999)
J Chem Phys
, vol.110
, pp. 1267-1276
-
-
Hausmann, U.H.E.1
Okamoto, Y.2
-
68
-
-
0033616581
-
Alanine is helix-stabilizing in both template-nucleated and standard peptide helices
-
Rohl CA, Fiori W, Baldwin RL. Alanine is helix-stabilizing in both template-nucleated and standard peptide helices. Proc Natl Acad Sci USA 1999;96:3682-3687.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 3682-3687
-
-
Rohl, C.A.1
Fiori, W.2
Baldwin, R.L.3
|