-
1
-
-
0030623823
-
Direct evaluation of thermal fluctuations in protein using a single parameter harmonic potential
-
Bahar, I., A. R. Atilgan, and B. Erman. 1997a. Direct evaluation of thermal fluctuations in protein using a single parameter harmonic potential. Fold. Des. 2:173-181.
-
(1997)
Fold. Des.
, vol.2
, pp. 173-181
-
-
Bahar, I.1
Atilgan, A.R.2
Erman, B.3
-
2
-
-
0030729453
-
Efficient characterization of collective motions and inter-residue correlations in proteins by low-resolution simulations
-
Bahar, I., B. Erman, T. Haliloglu, and R. L. Jernigan. 1997b. Efficient characterization of collective motions and inter-residue correlations in proteins by low-resolution simulations. Biochemistry. 36:13512-13523.
-
(1997)
Biochemistry
, vol.36
, pp. 13512-13523
-
-
Bahar, I.1
Erman, B.2
Haliloglu, T.3
Jernigan, R.L.4
-
3
-
-
0030324869
-
Coordination geometry of nonbonded residues in globular proteins
-
Bahar, I., and R. L. Jernigan. 1996. Coordination geometry of nonbonded residues in globular proteins. Fold. Des. 1:357-370.
-
(1996)
Fold. Des.
, vol.1
, pp. 357-370
-
-
Bahar, I.1
Jernigan, R.L.2
-
4
-
-
0031566950
-
Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
-
Bahar, I., and R. L. Jernigan. 1997. Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J. Mol. Biol. 266:195-214.
-
(1997)
J. Mol. Biol.
, vol.266
, pp. 195-214
-
-
Bahar, I.1
Jernigan, R.L.2
-
5
-
-
0030832809
-
Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches
-
Bahar, I., M. Kaplan, and R. L. Jernigan. 1997. Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches. Proteins. 29:292-308.
-
(1997)
Proteins
, vol.29
, pp. 292-308
-
-
Bahar, I.1
Kaplan, M.2
Jernigan, R.L.3
-
6
-
-
0032533396
-
Kinetic steps for α-helix formation
-
Bertsch, R. A., N. Vaidehi, S. I. Chan, and W. A. Goddard, III. 1998. Kinetic steps for α-helix formation. Proteins. 33:343-357.
-
(1998)
Proteins
, vol.33
, pp. 343-357
-
-
Bertsch, R.A.1
Vaidehi, N.2
Chan, S.I.3
Goddard III, W.A.4
-
7
-
-
0003423425
-
-
Wiley and Sons, New York
-
Bird, R. B., C. F. Curtiss, R. C. Armstrong, and O. Hassager. 1987. Dynamics of Polymeric Liquids. Kinetic Theory. Wiley and Sons, New York.
-
(1987)
Dynamics of Polymeric Liquids. Kinetic Theory
-
-
Bird, R.B.1
Curtiss, C.F.2
Armstrong, R.C.3
Hassager, O.4
-
8
-
-
34250173942
-
Conformational equilibria of polypeptides and proteins: The helix-coil transition
-
W.H. Freeman, New York
-
Cantor, C. R., and P. R. Schimmel. 1980. Conformational equilibria of polypeptides and proteins: the helix-coil transition. In Biophysical Chemistry: The Behavior of Biological Macromolecules. W.H. Freeman, New York. 1060-1066.
-
(1980)
Biophysical Chemistry: The Behavior of Biological Macromolecules
, pp. 1060-1066
-
-
Cantor, C.R.1
Schimmel, P.R.2
-
10
-
-
0027367977
-
Helix capping propensities in peptides parallel those in proteins
-
Chakrabartty, A., A. J. Doig, and R. L. Baldwin. 1993. Helix capping propensities in peptides parallel those in proteins. Proc. Natl. Acad. Sci. USA. 90:11332-11336.
-
(1993)
Proc. Natl. Acad. Sci. USA.
, vol.90
, pp. 11332-11336
-
-
Chakrabartty, A.1
Doig, A.J.2
Baldwin, R.L.3
-
11
-
-
0028222235
-
Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions
-
Chakrabartty, A., T. Kortemme, and R. L. Baldwin. 1994. Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions. Protein Sci. 3:843-852.
-
(1994)
Protein Sci.
, vol.3
, pp. 843-852
-
-
Chakrabartty, A.1
Kortemme, T.2
Baldwin, R.L.3
-
12
-
-
0037234367
-
Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide
-
Chowdhury, S., W. Zhang, C. Wu, G. Xiong, and Y. Duan. 2003. Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide. Biopolymers. 68:63-75.
-
(2003)
Biopolymers
, vol.68
, pp. 63-75
-
-
Chowdhury, S.1
Zhang, W.2
Wu, C.3
Xiong, G.4
Duan, Y.5
-
13
-
-
0026205054
-
A molecular dynamics simulation of polyalanine: An analysis of equilibrium motions and helix-coil transitions
-
Daggett, V., P. A. Kollman, and I. D. Kuntz. 1991. A molecular dynamics simulation of polyalanine: an analysis of equilibrium motions and helix-coil transitions. Biopolymers. 31:1115-1134.
-
(1991)
Biopolymers
, vol.31
, pp. 1115-1134
-
-
Daggett, V.1
Kollman, P.A.2
Kuntz, I.D.3
-
14
-
-
0141480850
-
Mechanism for the α-helix to β-hairpin transition
-
Ding, F., J. M. Borreguero, S. V. Buldyrey, H. E. Stanley, and N. V. Dokholyan. 2003. Mechanism for the α-helix to β-hairpin transition. Proteins. 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
-
16
-
-
0037059026
-
Recent advances in helix-coil theory
-
Doig, A. J. 2002. Recent advances in helix-coil theory. Biophys. Chem. 101-102:281-293.
-
(2002)
Biophys. Chem.
, vol.101-102
, pp. 281-293
-
-
Doig, A.J.1
-
18
-
-
0001767031
-
Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations
-
Ferrara, P., J. Apostolakis, and A. Caflisch. 2000. Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulations. J. Phys. Chem. B. 104:5000-5010.
-
(2000)
J. Phys. Chem. B.
, vol.104
, pp. 5000-5010
-
-
Ferrara, P.1
Apostolakis, J.2
Caflisch, A.3
-
20
-
-
0017024625
-
Statistical thermodynamics of random networks
-
Flory, P. J. 1976. Statistical thermodynamics of random networks. Proc. R. Soc. Lond. A. 351:351-380.
-
(1976)
Proc. R. Soc. Lond. A.
, vol.351
, pp. 351-380
-
-
Flory, P.J.1
-
21
-
-
0035255016
-
Identification and ab initio simulations of early folding units in proteins
-
Gilis, D., and M. Rooman. 2001. Identification and ab initio simulations of early folding units in proteins. Proteins. 42:164-176.
-
(2001)
Proteins
, vol.42
, pp. 164-176
-
-
Gilis, D.1
Rooman, M.2
-
22
-
-
0020771265
-
Dynamics of a small globular protein in terms of low-frequency vibrational modes
-
Go, N., T. Noguti, and T. Nishikawa. 1983. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc. Natl. Acad. Sci. USA. 80:3696-3700.
-
(1983)
Proc. Natl. Acad. Sci. USA.
, vol.80
, pp. 3696-3700
-
-
Go, N.1
Noguti, T.2
Nishikawa, T.3
-
23
-
-
0032525271
-
Coarse-grained simulations of conformational dynamics of proteins: Application to apomyoglobin
-
Haliloglu, T., and I. Bahar. 1998. Coarse-grained simulations of conformational dynamics of proteins: application to apomyoglobin. Proteins. 31:271-281.
-
(1998)
Proteins
, vol.31
, pp. 271-281
-
-
Haliloglu, T.1
Bahar, I.2
-
25
-
-
0001075603
-
Finite-size scaling of helix-coil transitions in poly-alanine studied by multicanonical simulations
-
Hansmann, U., and Y. Okamoto. 1999. Finite-size scaling of helix-coil transitions in poly-alanine studied by multicanonical simulations. J. Chem. Phys. 110:1267-1276.
-
(1999)
J. Chem. Phys.
, vol.110
, pp. 1267-1276
-
-
Hansmann, U.1
Okamoto, Y.2
-
27
-
-
0035955148
-
Temperature-dependent helix-coil transition of an alanine-based peptide
-
Huang, C.-Y., J. W. Klemke, Z. Getahun, W. F. DeGrado, and F. Gai. 2001. Temperature-dependent helix-coil transition of an alanine-based peptide. J. Am. Chem. Soc. 123:9235-9238.
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 9235-9238
-
-
Huang, C.-Y.1
Klemke, J.W.2
Getahun, Z.3
Degrado, W.F.4
Gai, F.5
-
28
-
-
0033181019
-
Direct computation of long time processes in peptides and proteins: Reaction path study of the coil-to-helix transition in polyalanine
-
Huo, S., and J. E. Straub. 1999. Direct computation of long time processes in peptides and proteins: reaction path study of the coil-to-helix transition in polyalanine. Proteins. 36:249-261.
-
(1999)
Proteins
, vol.36
, pp. 249-261
-
-
Huo, S.1
Straub, J.E.2
-
30
-
-
0345281586
-
Conformational dynamics of chymotrypsin inhibitor 2 by coarse-grained simulations
-
Kurt, N., and T. Haliloglu. 1999. Conformational dynamics of chymotrypsin inhibitor 2 by coarse-grained simulations. Proteins. 37:454-464.
-
(1999)
Proteins
, vol.37
, pp. 454-464
-
-
Kurt, N.1
Haliloglu, T.2
-
31
-
-
0035029408
-
Conformational dynamics of subtilisin-chymotrypsin inhibitor 2 complex by coarse-grained simulations
-
Kurt, N., and T. Haliloglu. 2001. Conformational dynamics of subtilisin-chymotrypsin inhibitor 2 complex by coarse-grained simulations. J. Biomol. Struct. Dyn. 18:713-731.
-
(2001)
J. Biomol. Struct. Dyn.
, vol.18
, pp. 713-731
-
-
Kurt, N.1
Haliloglu, T.2
-
32
-
-
84985649741
-
Vibrational approach to the dynamics of an α-helix
-
Levy, R. M., and M. Karplus. 1979. Vibrational approach to the dynamics of an α-helix. Biopolymers. 18:2465-2495.
-
(1979)
Biopolymers
, vol.18
, pp. 2465-2495
-
-
Levy, R.M.1
Karplus, M.2
-
33
-
-
0035956901
-
Solvent effects on the energy landscapes and folding kinetics of polyalanine
-
Levy, Y., J. Jortner, and O. M. Becker. 2001. Solvent effects on the energy landscapes and folding kinetics of polyalanine. Proc. Natl. Acad. Sci. USA. 98:2188-2193.
-
(2001)
Proc. Natl. Acad. Sci. USA.
, vol.98
, pp. 2188-2193
-
-
Levy, Y.1
Jortner, J.2
Becker, O.M.3
-
34
-
-
0000333671
-
On the theory of helix-coil transition in polypeptides
-
Lifson, S., and A. Roig. 1961. On the theory of helix-coil transition in polypeptides. J. Chem. Phys. 34:1963-1974.
-
(1961)
J. Chem. Phys.
, vol.34
, pp. 1963-1974
-
-
Lifson, S.1
Roig, A.2
-
35
-
-
5744249209
-
Equation of state calculations by fast computing machines
-
Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. J. Teller. 1953. Equation of state calculations by fast computing machines. J. Chem. Phys. 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.J.5
-
36
-
-
0033687195
-
Helix-coil transitions of aminoacid homo-oligomers in aqueous solution studied by multicanonical simulations
-
Mitsutake, A., and Y. Okamoto. 2000. Helix-coil transitions of aminoacid homo-oligomers in aqueous solution studied by multicanonical simulations. J. Chem. Phys. 112:10638-10647.
-
(2000)
J. Chem. Phys.
, vol.112
, pp. 10638-10647
-
-
Mitsutake, A.1
Okamoto, Y.2
-
37
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal-structures-quasi-chemical approximation
-
Miyazawa, S., and R. Jernigan. 1985. Estimation of effective interresidue contact energies from protein crystal-structures-quasi-chemical approximation. Macromolecules. 18:534-552.
-
(1985)
Macromolecules
, vol.18
, pp. 534-552
-
-
Miyazawa, S.1
Jernigan, R.2
-
38
-
-
0028447768
-
Elucidating the folding problem of helical peptides using empiric parameters
-
Munoz, V., and L. Serrano. 1994. Elucidating the folding problem of helical peptides using empiric parameters. Nat. Struct. Biol. 1:399-409.
-
(1994)
Nat. Struct. Biol.
, vol.1
, pp. 399-409
-
-
Munoz, V.1
Serrano, L.2
-
39
-
-
0031127043
-
Development of the multiple sequence approximation within the AGADIR model of α-helix formation: Comparison with Zimm-Bragg and Lifson-Roig formalisms
-
Munoz, V., and L. Serrano. 1997. Development of the multiple sequence approximation within the AGADIR model of α-helix formation: comparison with Zimm-Bragg and Lifson-Roig formalisms. Biopolymers. 41:495-509.
-
(1997)
Biopolymers
, vol.41
, pp. 495-509
-
-
Munoz, V.1
Serrano, L.2
-
40
-
-
7244253280
-
Solvent effects on the Conformational transition of a model polyalanine peptide
-
Nguyen, H. D., A. J. Marchut, and C. K. Hall. 2004. Solvent effects on the Conformational transition of a model polyalanine peptide. Protein Sci. 13:2909-2924.
-
(2004)
Protein Sci.
, vol.13
, pp. 2909-2924
-
-
Nguyen, H.D.1
Marchut, A.J.2
Hall, C.K.3
-
41
-
-
0029342240
-
Thermodynamics of helix-coil transitions studied by multicanonical algorithms
-
Okamoto, Y., and U, Hansmann. 1995. Thermodynamics of helix-coil transitions studied by multicanonical algorithms. J. Phys. Chem. 99:11276-11287.
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 11276-11287
-
-
Okamoto, Y.1
Hansmann, U.2
-
42
-
-
0033730431
-
The Flory isolated-pair hypothesis is not valid for polypeptide chains: Implications for protein folding
-
Pappu, R. V., R. Srinivasan, and G. D. Rose. 2000. The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding. Proc. Natl. Acad. Sci. USA. 97:12565-12570.
-
(2000)
Proc. Natl. Acad. Sci. USA.
, vol.97
, pp. 12565-12570
-
-
Pappu, R.V.1
Srinivasan, R.2
Rose, G.D.3
-
43
-
-
0000020527
-
Helix-coil stability constants for naturally occurring amino acids in water. IV. Alanine parameters from random poly(hydroxypropylglutamine-co-L- alanine)
-
Platzer, K. A. B., H. Scheraga, R. Andreatt, and V. Anathan. 1972. Helix-coil stability constants for naturally occurring amino acids in water. IV. Alanine parameters from random poly(hydroxypropylglutamine-co-L-alanine). Macromolecules. 5:178-187.
-
(1972)
Macromolecules
, vol.5
, pp. 178-187
-
-
Platzer, K.A.B.1
Scheraga, H.2
Andreatt, R.3
Anathan, V.4
-
44
-
-
0026568185
-
Kinetics of amide proton exchange in helical peptides of varying chain lengths. Interpretation by the Lifson-Roig equation
-
Rohl, C. A., J. M. Scholtz, E. J. York, J. M. Stewart, and R. L. Baldwin. 1992. Kinetics of amide proton exchange in helical peptides of varying chain lengths. Interpretation by the Lifson-Roig equation. Biochemistry. 31:1263-1269.
-
(1992)
Biochemistry
, vol.31
, pp. 1263-1269
-
-
Rohl, C.A.1
Scholtz, J.M.2
York, E.J.3
Stewart, J.M.4
Baldwin, R.L.5
-
45
-
-
0344252790
-
A theory of the linear viscoelastic properties of dilute solutions of coiling polymers
-
Rouse, P. 1953. A theory of the linear viscoelastic properties of dilute solutions of coiling polymers. J. Chem. Phys. 21:1272-1280.
-
(1953)
J. Chem. Phys.
, vol.21
, pp. 1272-1280
-
-
Rouse, P.1
-
46
-
-
33947476272
-
The factors affecting the stability of hydrogen bonded polypeptide structures in solution
-
Schellman, J. A. 1958. The factors affecting the stability of hydrogen bonded polypeptide structures in solution. J. Chem. Phys. 62:1485-1494.
-
(1958)
J. Chem. Phys.
, vol.62
, pp. 1485-1494
-
-
Schellman, J.A.1
-
47
-
-
0026254055
-
Parameters of helix-coil transition theory for alanine-based peptides of varying chain lengths in water
-
Scholtz, J. M., H. Qian, E. S. York, J. M. Stewart, and R. L. Baldwin. 1991. Parameters of helix-coil transition theory for alanine-based peptides of varying chain lengths in water. Biopolymers. 31:1463-1470.
-
(1991)
Biopolymers
, vol.31
, pp. 1463-1470
-
-
Scholtz, J.M.1
Qian, H.2
York, E.S.3
Stewart, J.M.4
Baldwin, R.L.5
-
50
-
-
0030970740
-
Curious structure in "canonical" alanine-based peptides
-
Shirley, W. A., and C. L. Brooks, III. 1997. Curious structure in "canonical" alanine-based peptides. Proteins. 28:59-71.
-
(1997)
Proteins
, vol.28
, pp. 59-71
-
-
Shirley, W.A.1
Brooks III, C.L.2
-
51
-
-
0038767500
-
Monte Carlo approaches to the protein folding problem
-
Skolnick, J., and A. Kolinski. 1999. Monte Carlo approaches to the protein folding problem. Adv. Chem. Phys. 105:203-242.
-
(1999)
Adv. Chem. Phys.
, vol.105
, pp. 203-242
-
-
Skolnick, J.1
Kolinski, A.2
-
52
-
-
0035882559
-
Alpha-helix formation: Discontinuous molecular dynamics on an intermediate-resolution protein model
-
Smith, A. V., and C. K. Hall. 2001. Alpha-helix formation: discontinuous molecular dynamics on an intermediate-resolution protein model. Proteins. 44:344-360.
-
(2001)
Proteins
, vol.44
, pp. 344-360
-
-
Smith, A.V.1
Hall, C.K.2
-
53
-
-
0030006074
-
Molecular dynamics simulations of synthetic peptide folding
-
Sung, S. S., and X. W. Wu. 1996. Molecular dynamics simulations of synthetic peptide folding. Proteins. 25:202-214.
-
(1996)
Proteins
, vol.25
, pp. 202-214
-
-
Sung, S.S.1
Wu, X.W.2
-
54
-
-
0030789351
-
Laser temperature jump study of the helix ↔ coil kinetics of an alanine peptide interpreted with a "kinetic zipper" model. Submillisecond kinetics of protein folding
-
Thompson, P. A., W. A. Eaton, and J. Hofrichter. 1997. Laser temperature jump study of the helix ↔ coil kinetics of an alanine peptide interpreted with a "kinetic zipper" model. Submillisecond kinetics of protein folding. Biochemistry. 36:9200-9210.
-
(1997)
Biochemistry
, vol.36
, pp. 9200-9210
-
-
Thompson, P.A.1
Eaton, W.A.2
Hofrichter, J.3
-
55
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
-
Tirion, M. 1996. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77:1905-1908.
-
(1996)
Phys. Rev. Lett.
, vol.77
, pp. 1905-1908
-
-
Tirion, M.1
-
56
-
-
0029121068
-
Free energy determinants of secondary structure formation. I. Alpha-helices
-
Yang, A. S., and B. Honig. 1995. Free energy determinants of secondary structure formation. I. Alpha-helices. J. Mol. Biol. 252:351-365.
-
(1995)
J. Mol. Biol.
, vol.252
, pp. 351-365
-
-
Yang, A.S.1
Honig, B.2
-
57
-
-
0029887269
-
A microscopic view of helix propagation: N- and C-terminal helix growth in alanine helices
-
Young, W. S., and C. L. Brooks, III. 1996. A microscopic view of helix propagation: N- and C-terminal helix growth in alanine helices. J. Mol. Biol. 259:560-572.
-
(1996)
J. Mol. Biol.
, vol.259
, pp. 560-572
-
-
Young, W.S.1
Brooks III, C.L.2
-
58
-
-
0000668407
-
Theory of the phase transition between helix and random coil in polypeptide chains
-
Zimm, B. H., and J. K. Bragg. 1959. Theory of the phase transition between helix and random coil in polypeptide chains. J. Phys. Chem. 31:526-535.
-
(1959)
J. Phys. Chem.
, vol.31
, pp. 526-535
-
-
Zimm, B.H.1
Bragg, J.K.2
|