-
1
-
-
0000668407
-
Theory of phase transition between helix and random coil in polypeptide chains
-
Zimm BH, Bragg JK. Theory of phase transition between helix and random coil in polypeptide chains. J Chem Phys 1959;31:526.
-
(1959)
J Chem Phys
, vol.31
, pp. 526
-
-
Zimm, B.H.1
Bragg, J.K.2
-
2
-
-
33751391161
-
Helix-coil theories: A comparative study for finit length polypeptides
-
Qian H, Schellman J. Helix-coil theories: a comparative study for finit length polypeptides. J Phys Chem 1992;96:3987.
-
(1992)
J Phys Chem
, vol.96
, pp. 3987
-
-
Qian, H.1
Schellman, J.2
-
4
-
-
0026209013
-
The helical s constant for alanine in water derived from template-nucleated helices
-
Kemp DS, Boyd JG, Muendel CC. The helical s constant for alanine in water derived from template-nucleated helices. Nature 1991;352:451.
-
(1991)
Nature
, vol.352
, pp. 451
-
-
Kemp, D.S.1
Boyd, J.G.2
Muendel, C.C.3
-
5
-
-
0028222235
-
Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions
-
Chakrabartty A, Kortemme T, Baldwin RL. Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci 1994;3:843.
-
(1994)
Protein Sci
, vol.3
, pp. 843
-
-
Chakrabartty, A.1
Kortemme, T.2
Baldwin, R.L.3
-
6
-
-
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.
-
(1991)
Biopolymers
, vol.31
, pp. 1463
-
-
Scholtz, J.M.1
Qian, H.2
York, E.J.3
Stewart, J.M.4
Baldwin, R.L.5
-
7
-
-
0025113815
-
Helix-coil stability constants for the naturally occuring amino acids in water. XXIV. half-cystine parameters from random poly (hydroxybutlglutamineco-s-methylthio-l-cysteine)
-
Wójcik J, Altmann KH, Scheraga HA. Helix-coil stability constants for the naturally occuring amino acids in water. xxiv. half-cystine parameters from random poly (hydroxybutlglutamineco-s-methylthio-l-cysteine). Biopolymers 1990;30:121.
-
(1990)
Biopolymers
, vol.30
, pp. 121
-
-
Wójcik, J.1
Altmann, K.H.2
Scheraga, H.A.3
-
8
-
-
0028847038
-
Thermodynamic parameters for the helix-coil transition of oligopeptides: Molecular dynamics simulation with the peptide growth method
-
Wang L, O'Connell T, Tropsha A, Hermans J. Thermodynamic parameters for the helix-coil transition of oligopeptides: molecular dynamics simulation with the peptide growth method. Proc Natl Acad Sci USA 1995;92:10924.
-
(1995)
Proc Natl Acad Sci USA
, vol.92
, pp. 10924
-
-
Wang, L.1
O'Connell, T.2
Tropsha, A.3
Hermans, J.4
-
9
-
-
0029887269
-
A microscopic view of helix propagation: N and c-terminal helix growth in alanine helices
-
Young WS, Brooks CL III. A microscopic view of helix propagation: N and c-terminal helix growth in alanine helices. J Mol Biol 1996;259:260.
-
(1996)
J Mol Biol
, vol.259
, pp. 260
-
-
Young, W.S.1
Brooks C.L. III2
-
10
-
-
0026525048
-
Molecular dynamics simulations of helix denaturation
-
Daggett V, Levitt M. Molecular dynamics simulations of helix denaturation. J Mol Biol 1992;223:1121.
-
(1992)
J Mol Biol
, vol.223
, pp. 1121
-
-
Daggett, V.1
Levitt, M.2
-
11
-
-
0031587288
-
Kinetics of peptide folding: Computer simulations of SYPFDV and peptide variants in water
-
Mohanty D, Elber R, Thirumalai D, Beglov D, Roux B. Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. J Mol Biol 1997;272:423.
-
(1997)
J Mol Biol
, vol.272
, pp. 423
-
-
Mohanty, D.1
Elber, R.2
Thirumalai, D.3
Beglov, D.4
Roux, B.5
-
12
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution
-
Duan Y, Kollman PA. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Proc Natl Acad Sci USA 1998;282:740.
-
(1998)
Proc Natl Acad Sci USA
, vol.282
, pp. 740
-
-
Duan, Y.1
Kollman, P.A.2
-
13
-
-
0001842441
-
Adding backbone to protein folding: Why proteins are polypeptides
-
Honig B, Cohen FE. Adding backbone to protein folding: why proteins are polypeptides. Fold Des 1996;1:R17-R20.
-
(1996)
Fold Des
, vol.1
-
-
Honig, B.1
Cohen, F.E.2
-
14
-
-
0032424129
-
Virtual atom representation of hydrogen bonds in minimal off-lattice models of α-helices: Effect on stability, cooperativity and kinetics
-
Klimov DK, Betancourt MR, Virtual atom representation of hydrogen bonds in minimal off-lattice models of α-helices: effect on stability, cooperativity and kinetics. Thirumalai D. Fold Des 1998;3:481-496.
-
(1998)
Thirumalai D. Fold Des
, vol.3
, pp. 481-496
-
-
Klimov, D.K.1
Betancourt, M.R.2
-
15
-
-
33645675171
-
Comparison of lattice Monte Carlo dynamics and Brownian dynamics folding pathways of α-helical hairpins
-
Rey J, Skolnick J. Comparison of lattice Monte Carlo dynamics and Brownian dynamics folding pathways of α-helical hairpins. Chem Phys 1991;158:199.
-
(1991)
Chem Phys
, vol.158
, pp. 199
-
-
Rey, J.1
Skolnick, J.2
-
16
-
-
0026643094
-
The nature of folded states in globular proteins
-
Honeycutt JD, Thirumalai D. The nature of folded states in globular proteins. Biopolymers 1992;32:695.
-
(1992)
Biopolymers
, vol.32
, pp. 695
-
-
Honeycutt, J.D.1
Thirumalai, D.2
-
17
-
-
0030601851
-
Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein
-
Guo Z, Thirumalai D. Kinetics and thermodynamics of folding of a de novo designed four-helix bundle protein. J Mol Biol 1996;263: 323.
-
(1996)
J Mol Biol
, vol.263
, pp. 323
-
-
Guo, Z.1
Thirumalai, D.2
-
18
-
-
0027080909
-
Atomic solvation parameters applied to molecular dynamics of proteins in solution
-
Wesson L, Eisenberg D. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci 1992;1: 227.
-
(1992)
Protein Sci
, vol.1
, pp. 227
-
-
Wesson, L.1
Eisenberg, D.2
-
19
-
-
0031256658
-
The maxflux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body system at finite temperature
-
Huo S, Straub JE. The maxflux algorithm for calculating variationally optimized reaction paths for conformational transitions in many body system at finite temperature. J Chem Phys 1997;107: 5000.
-
(1997)
J Chem Phys
, vol.107
, pp. 5000
-
-
Huo, S.1
Straub, J.E.2
-
20
-
-
0017251893
-
Protein-folding dynamics
-
Karplus M, Weaver DL. Protein-folding dynamics. Nature 1976; 260:404.
-
(1976)
Nature
, vol.260
, pp. 404
-
-
Karplus, M.1
Weaver, D.L.2
-
21
-
-
84985656311
-
Diffusion-collision model for protein folding
-
Karplus M, Weaver DL. Diffusion-collision model for protein folding. Biopolymers 1979;18:1421.
-
(1979)
Biopolymers
, vol.18
, pp. 1421
-
-
Karplus, M.1
Weaver, D.L.2
-
22
-
-
0024391879
-
How does protein folding get started?
-
Baldwin RL. How does protein folding get started? Trends Biochem Sci 1989;14:291.
-
(1989)
Trends Biochem Sci
, vol.14
, pp. 291
-
-
Baldwin, R.L.1
-
23
-
-
0026205054
-
A molecular dynamics simulations of polyalanine: An analysis of equilibrium motions and helix-coil transitions
-
Daggett V, Kollman PA, Kuntz ID. A molecular dynamics simulations of polyalanine: an analysis of equilibrium motions and helix-coil transitions. Biopolymers 1991;31:1115.
-
(1991)
Biopolymers
, vol.31
, pp. 1115
-
-
Daggett, V.1
Kollman, P.A.2
Kuntz, I.D.3
-
24
-
-
0344557043
-
Molecular dynamics and monte carlo simulations favor the alpha-helical form for alanine-based peptides in water
-
Tirado-Rives J, Maxwell DS, Jorgensen WL. Molecular dynamics and Monte Carlo simulations favor the alpha-helical form for alanine-based peptides in water. J Am Chem Soc 1993; 115:11590.
-
(1993)
J Am Chem Soc
, vol.115
, pp. 11590
-
-
Tirado-Rives, J.1
Maxwell, D.S.2
Jorgensen, W.L.3
-
26
-
-
0028317634
-
10 helix versus α-helix: A molecular dynamics study of conformational preferences of aib and alanine
-
10 helix versus α-helix: a molecular dynamics study of conformational preferences of aib and alanine. J Am Chem Soc 1994;116:11915.
-
(1994)
J Am Chem Soc
, vol.116
, pp. 11915
-
-
Zhang, L.1
Hermans, J.2
-
27
-
-
0028921182
-
10-helix along the thermodynamic folding pathway
-
10-helix along the thermodynamic folding pathway. Biochemistry 1995;34:3873.
-
(1995)
Biochemistry
, vol.34
, pp. 3873
-
-
Millhauser, G.L.1
-
29
-
-
84986512474
-
CHARMM: A program for macromolecular energy minimization and dynamics calculations
-
Brooks BR, Bruccoleri R, Olafson B, States D, Swaninathan S, Karplus M. CHARMM: a program for macromolecular energy minimization and dynamics calculations. J Comp Chem 1983;4: 187.
-
(1983)
J Comp Chem
, vol.4
, pp. 187
-
-
Brooks, B.R.1
Bruccoleri, R.2
Olafson, B.3
States, D.4
Swaninathan, S.5
Karplus, M.6
-
30
-
-
0030006074
-
Molecular dynamics simulations of synthetic peptide folding
-
Sung S, Wu X. Molecular dynamics simulations of synthetic peptide folding. Proteins 1996;25:202.
-
(1996)
Proteins
, vol.25
, pp. 202
-
-
Sung, S.1
Wu, X.2
-
31
-
-
0027955787
-
Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
-
Abagyan R, Totrov M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol 1994;235:983.
-
(1994)
J Mol Biol
, vol.235
, pp. 983
-
-
Abagyan, R.1
Totrov, M.2
-
32
-
-
0345246954
-
-
Molecular Simulations, Inc
-
Molecular Simulations, Inc. (1997).
-
(1997)
-
-
-
34
-
-
0000055722
-
Diffusion-controlled reactions: A variational formula for the optimum reaction coordinate
-
Berkowitz M, Morgan JD, McCammon JA, Northrup SH. Diffusion-controlled reactions: a variational formula for the optimum reaction coordinate. J Chem Phys 1983;79:5563.
-
(1983)
J Chem Phys
, vol.79
, pp. 5563
-
-
Berkowitz, M.1
Morgan, J.D.2
McCammon, J.A.3
Northrup, S.H.4
-
35
-
-
84987058840
-
Self-avoiding walk between two fixed points as a tool to calculate reaction paths in large molecular systems
-
Czerminski R, Elber R. Self-avoiding walk between two fixed points as a tool to calculate reaction paths in large molecular systems. Int J Quant Chem 1990;24:167.
-
(1990)
Int J Quant Chem
, vol.24
, pp. 167
-
-
Czerminski, R.1
Elber, R.2
-
37
-
-
0028835443
-
Nucleation mechanism for protein-folding and theoretical predictions for hydrogen-exchange labeling experiments
-
Guo Z, Thirumalai D. Nucleation mechanism for protein-folding and theoretical predictions for hydrogen-exchange labeling experiments. Biopolymers 1994;35:137.
-
(1994)
Biopolymers
, vol.35
, pp. 137
-
-
Guo, Z.1
Thirumalai, D.2
-
38
-
-
0031285905
-
Kinetics partitioning mechanism as a unifying theme in the folding of biomolecules
-
Thirumalai D, Klimov DK, Woodson SA. Kinetics partitioning mechanism as a unifying theme in the folding of biomolecules. Theor Chem Ace 1997;1:23.
-
(1997)
Theor Chem Ace
, vol.1
, pp. 23
-
-
Thirumalai, D.1
Klimov, D.K.2
Woodson, S.A.3
-
39
-
-
0030970740
-
Curious structure in canonical alanine-based peptides
-
Shirley WA, Brooks CL III. Curious structure in canonical alanine-based peptides. Proteins 1997;28:59.
-
(1997)
Proteins
, vol.28
, pp. 59
-
-
Shirley, W.A.1
Brooks C.L. III2
|