-
1
-
-
0344301982
-
Protein folding: A perspective from theory and experiment
-
Dobson CM, Sali A, Karplus M. Protein folding: a perspective from theory and experiment. Angew Chem Int Ed 1998;37:868-893.
-
(1998)
Angew Chem Int Ed
, vol.37
, pp. 868-893
-
-
Dobson, C.M.1
Sali, A.2
Karplus, M.3
-
2
-
-
0032053619
-
Simulations of protein folding and unfolding
-
Brookss CL III. Simulations of protein folding and unfolding. Curr Biol 1998;8:222-226.
-
(1998)
Curr Biol
, vol.8
, pp. 222-226
-
-
Brookss III, C.L.1
-
3
-
-
0036535895
-
Protein folding: The free energy surface
-
Gruebele M. Protein folding: the free energy surface. Curr Opin Struct Biol 2002;12:161-168.
-
(2002)
Curr Opin Struct Biol
, vol.12
, pp. 161-168
-
-
Gruebele, M.1
-
4
-
-
0031059496
-
Theoretical studies of protein folding thermodynamics and kinetics
-
Shakhnovich EI. Theoretical studies of protein folding thermodynamics and kinetics. Curr Opin Struct Biol 1997;7:29-40.
-
(1997)
Curr Opin Struct Biol
, vol.7
, pp. 29-40
-
-
Shakhnovich, E.I.1
-
5
-
-
0037398844
-
Minimalist models for protein folding and design
-
Head-Gordon T, Brown S. Minimalist models for protein folding and design. Curr Opin Struct Biol 2003;13:160-167.
-
(2003)
Curr Opin Struct Biol
, vol.13
, pp. 160-167
-
-
Head-Gordon, T.1
Brown, S.2
-
6
-
-
0031746226
-
A protein engineering analysis of the transition state for protein folding: Simulation in the lattice model
-
Gutin AM, Abkevich VI, Shakhnovich EI. A protein engineering analysis of the transition state for protein folding: simulation in the lattice model. Fold Des 1998;3:183-194.
-
(1998)
Fold Des
, vol.3
, pp. 183-194
-
-
Gutin, A.M.1
Abkevich, V.I.2
Shakhnovich, E.I.3
-
7
-
-
0028270634
-
Kinetics of protein folding: A lattice model study of the requirements of folding to the native state
-
Sali A, Shakhnovich EI, Karplus M. Kinetics of protein folding: a lattice model study of the requirements of folding to the native state. J Mol Biol 1994;235:1614-1636.
-
(1994)
J Mol Biol
, vol.235
, pp. 1614-1636
-
-
Sali, A.1
Shakhnovich, E.I.2
Karplus, M.3
-
8
-
-
0033117927
-
Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models
-
Thirumalai D, Klimov D. Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models. Curr Opin Struct Biol 1999;9:197-207.
-
(1999)
Curr Opin Struct Biol
, vol.9
, pp. 197-207
-
-
Thirumalai, D.1
Klimov, D.2
-
9
-
-
0002689652
-
Thermodynamics of protein folding: A statistical mechanical study of a small beta protein
-
Guo Z, Brooks CL III. Thermodynamics of protein folding: a statistical mechanical study of a small beta protein. Biopolymers 1997;42:745-757.
-
(1997)
Biopolymers
, vol.42
, pp. 745-757
-
-
Guo, Z.1
Brooks III, C.L.2
-
10
-
-
0036785556
-
The origins of symmetry breaking in the folding of proteins with analogous topologies
-
Karanicolas J, Brooks CL III. The origins of symmetry breaking in the folding of proteins with analogous topologies. Protein Sci 2002;11:2351-2361.
-
(2002)
Protein Sci
, vol.11
, pp. 2351-2361
-
-
Karanicolas, J.1
Brooks III, C.L.2
-
11
-
-
0000870658
-
Exploring the space of protein folding Hamiltonians: The balance of forces in a minimalist beta-barrel model
-
Shea J-E, Nochomovitz YD, Guo Z, Brooks CL III. Exploring the space of protein folding Hamiltonians: the balance of forces in a minimalist beta-barrel model. J Chem Phys 1998;109:2895-2903.
-
(1998)
J Chem Phys
, vol.109
, pp. 2895-2903
-
-
Shea, J.-E.1
Nochomovitz, Y.D.2
Guo, Z.3
Brooks III, C.L.4
-
12
-
-
0033607208
-
Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A
-
Shea J-E, Onuchic JN, Brooks CL III. Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A. Proc Natl Acad Sci USA 1999;96:12512-12517.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 12512-12517
-
-
Shea, J.-E.1
Onuchic, J.N.2
Brooks III, C.L.3
-
13
-
-
0034321011
-
Energetic frustration and the nature of the transition state in protein folding
-
Shea J-E, Onuchic JN, Brooks CL III. Energetic frustration and the nature of the transition state in protein folding. J Chem Phys 2000;113:1-9.
-
(2000)
J Chem Phys
, vol.113
, pp. 1-9
-
-
Shea, J.-E.1
Onuchic, J.N.2
Brooks III, C.L.3
-
14
-
-
0034743155
-
From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding
-
Shea J-E, Brooks CL III. From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. Ann Rev Phys Chem 2001;52:499-534.
-
(2001)
Ann Rev Phys Chem
, vol.52
, pp. 499-534
-
-
Shea, J.-E.1
Brooks III, C.L.2
-
15
-
-
0037799371
-
Effects of confinement and crowding on the thermodynamics and kinetics of folding of a minimalist beta-barrel protein
-
Friedel M, Sheeler D, Shea J-E. Effects of confinement and crowding on the thermodynamics and kinetics of folding of a minimalist beta-barrel protein. J Chem Phys 2003;118:8106-8113.
-
(2003)
J Chem Phys
, vol.118
, pp. 8106-8113
-
-
Friedel, M.1
Sheeler, D.2
Shea, J.-E.3
-
16
-
-
0038029818
-
Glass transition in an off-lattice protein model studied by molecular dynamics simulations
-
Baumketner A, Shea J-E, Hiwatari Y. Glass transition in an off-lattice protein model studied by molecular dynamics simulations. Phys Rev E 2003;67:011912.
-
(2003)
Phys Rev E
, vol.67
, pp. 011912
-
-
Baumketner, A.1
Shea, J.-E.2
Hiwatari, Y.3
-
18
-
-
0037459035
-
Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: How adequate is native-centric topological modeling?
-
Kaya, Chan HS. Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: how adequate is native-centric topological modeling? J Mol Biol 2003;326:911-931.
-
(2003)
J Mol Biol
, vol.326
, pp. 911-931
-
-
Kaya1
Chan, H.S.2
-
19
-
-
0037154268
-
Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse
-
Cheung MS, Garcia AE, Onuchic JN. Protein folding mediated by solvation: water expulsion and formation of the hydrophobic core occur after the structural collapse. Proc Natl Acad Sci USA 2002;99:685-690.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 685-690
-
-
Cheung, M.S.1
Garcia, A.E.2
Onuchic, J.N.3
-
20
-
-
0037343134
-
A minimal physically realistic protein-like lattice model: Designing an energy landscape that ensures all-or-none folding to a unique native state
-
Pokarowski P, Kolinski A, Skolnick J. A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native state. Biophys J 2003;84:1518-1526.
-
(2003)
Biophys J
, vol.84
, pp. 1518-1526
-
-
Pokarowski, P.1
Kolinski, A.2
Skolnick, J.3
-
21
-
-
0036217783
-
Long time dynamics of met-enkephalin: Comparison of explicit and implicit solvent models
-
Shen MY, Freed KF. Long time dynamics of met-enkephalin: comparison of explicit and implicit solvent models. Biophys J 2002;82:1791-1808.
-
(2002)
Biophys J
, vol.82
, pp. 1791-1808
-
-
Shen, M.Y.1
Freed, K.F.2
-
22
-
-
0036892356
-
All-atom fast protein folding simulations: The villin headpiece
-
Shen MY, Freed KF. All-atom fast protein folding simulations: the villin headpiece. Proteins 2002;49:439-445.
-
(2002)
Proteins
, vol.49
, pp. 439-445
-
-
Shen, M.Y.1
Freed, K.F.2
-
23
-
-
0035850758
-
Beta-hairpin folding simulations in atomistic detail using an implicit solvent model
-
Zagrovic B, Sorin EJ, Pande VS. Beta-hairpin folding simulations in atomistic detail using an implicit solvent model. J Mol Biol 2001;313:151-169.
-
(2001)
J Mol Biol
, vol.313
, pp. 151-169
-
-
Zagrovic, B.1
Sorin, E.J.2
Pande, V.S.3
-
24
-
-
0032968133
-
Implicit solvent models
-
Roux B, Simonson T. Implicit solvent models. Biophys Chem 1999;78:1-20.
-
(1999)
Biophys Chem
, vol.78
, pp. 1-20
-
-
Roux, B.1
Simonson, T.2
-
25
-
-
0034510764
-
Comparative study of the folding free energy landscape of a three-stranded beta-sheet protein with explicit and implicit solvent models
-
Bursulaya B, Brooks CL III. Comparative study of the folding free energy landscape of a three-stranded beta-sheet protein with explicit and implicit solvent models. J Phys Chem B 2000;104:12378-12383.
-
(2000)
J Phys Chem B
, vol.104
, pp. 12378-12383
-
-
Bursulaya, B.1
Brooks III, C.L.2
-
26
-
-
0037076334
-
Molecular dynamics simulations of protein folding from the transition state
-
Gsponer J, Caflisch A. Molecular dynamics simulations of protein folding from the transition state. Proc Natl Acad Sci USA 2002;99:6719-6724.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 6719-6724
-
-
Gsponer, J.1
Caflisch, A.2
-
27
-
-
0036678831
-
An atomically detailed study of the folding pathways of protein A with the stochastic difference equation
-
Ghosh A, Elber R, Scheraga HA. An atomically detailed study of the folding pathways of protein A with the stochastic difference equation. Proc Natl Acad Sci USA 2002;99:10394-10398.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 10394-10398
-
-
Ghosh, A.1
Elber, R.2
Scheraga, H.A.3
-
28
-
-
0344407048
-
Kinetics of cytochrome C folding: Atomically detailed simulations
-
Cardenas AE, Elber R. Kinetics of cytochrome C folding: atomically detailed simulations. Proteins 2003;51:245-257.
-
(2003)
Proteins
, vol.51
, pp. 245-257
-
-
Cardenas, A.E.1
Elber, R.2
-
29
-
-
0031444104
-
Folding dynamics of the src SH3 domain
-
Grantcharova VP, Baker D. Folding dynamics of the src SH3 domain. Biochemistry 1997;36:15685-15692.
-
(1997)
Biochemistry
, vol.36
, pp. 15685-15692
-
-
Grantcharova, V.P.1
Baker, D.2
-
30
-
-
0031853167
-
Important role of hydrogen bonds in the sturcturally 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 sturcturally 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
-
31
-
-
0032734515
-
Experiment and theory highlight role of native state topology in SH3 folding
-
Riddle DS, Grantcharova VP, Santiago JV, Alm E, Ruczinski I, Baker D. Experiment and theory highlight role of native state topology in SH3 folding. Nat Struct Biol 1999;6:1016-1024.
-
(1999)
Nat Struct Biol
, vol.6
, pp. 1016-1024
-
-
Riddle, D.S.1
Grantcharova, V.P.2
Santiago, J.V.3
Alm, E.4
Ruczinski, I.5
Baker, D.6
-
32
-
-
0028331876
-
Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding transition
-
Viguera AR, Martinez JC, Filimonov VV, Mateo PL, Serrano L. Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding transition. Biochemistry 1994;33:2142-2150.
-
(1994)
Biochemistry
, vol.33
, pp. 2142-2150
-
-
Viguera, A.R.1
Martinez, J.C.2
Filimonov, V.V.3
Mateo, P.L.4
Serrano, L.5
-
33
-
-
0032750509
-
The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved
-
Martinez JC, Serrano L. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nat Struct Biol 1999;6:1010-1016.
-
(1999)
Nat Struct Biol
, vol.6
, pp. 1010-1016
-
-
Martinez, J.C.1
Serrano, L.2
-
34
-
-
0032562182
-
The folding kinetics and thermodynamics of the Fyn-SH3 domain
-
Plaxco KW, Guijarro JI, Morton CJ, Pitkeathly M, Campbell ID, Dobson CM. The folding kinetics and thermodynamics of the Fyn-SH3 domain. Biochemistry 1998;37:2529-2537.
-
(1998)
Biochemistry
, vol.37
, pp. 2529-2537
-
-
Plaxco, K.W.1
Guijarro, J.I.2
Morton, C.J.3
Pitkeathly, M.4
Campbell, I.D.5
Dobson, C.M.6
-
35
-
-
0036172116
-
Hydrophobic core packing in the SH3 domain folding transition state
-
Northey JGB, Di Nardo AA, Davidson AR. Hydrophobic core packing in the SH3 domain folding transition state. J Mol Biol 2002;9:126-130.
-
(2002)
J Mol Biol
, vol.9
, pp. 126-130
-
-
Northey, J.G.B.1
Di Nardo, A.A.2
Davidson, A.R.3
-
36
-
-
0034685604
-
Topological and energetic factors: What determines the structural details of the transition state ensemble and "on route" intermediates for protein folding?: An investigation for small globular proteins
-
Clementi C, Nymeyer H, Onuchic JN. Topological and energetic factors: What determines the structural details of the transition state ensemble and "on route" intermediates for protein folding?: an investigation for small globular proteins. J Mol Biol 2000;298:937-953.
-
(2000)
J Mol Biol
, vol.298
, pp. 937-953
-
-
Clementi, C.1
Nymeyer, H.2
Onuchic, J.N.3
-
37
-
-
0036308818
-
Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics
-
Borreguero JM, Dokholyan NV, Buldyrev SV, Shakhnovich EI, Stanley HE. Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics. J Mol Biol 2002;318:863-876.
-
(2002)
J Mol Biol
, vol.318
, pp. 863-876
-
-
Borreguero, J.M.1
Dokholyan, N.V.2
Buldyrev, S.V.3
Shakhnovich, E.I.4
Stanley, H.E.5
-
38
-
-
0036927818
-
Direct molecular dynamics observation of protein folding transition state ensemble
-
Ding F, Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich EI. Direct molecular dynamics observation of protein folding transition state ensemble. Biophys J 2002;83:3525-3532.
-
(2002)
Biophys J
, vol.83
, pp. 3525-3532
-
-
Ding, F.1
Dokholyan, N.V.2
Buldyrev, S.V.3
Stanley, H.E.4
Shakhnovich, E.I.5
-
40
-
-
0035946940
-
Role of native topology investigated by multiple unfolding simulations of four SH3 domains
-
Gsponer J, Caflisch A. Role of native topology investigated by multiple unfolding simulations of four SH3 domains. J Mol Biol 2001;309:285-298.
-
(2001)
J Mol Biol
, vol.309
, pp. 285-298
-
-
Gsponer, J.1
Caflisch, A.2
-
41
-
-
0345411345
-
Hierarchy of structure loss in MD simulations of src SH3 domain unfolding
-
Tsai J, Levitt M, Baker D. Hierarchy of structure loss in MD simulations of src SH3 domain unfolding. J Mol Biol 1999;291:215-225.
-
(1999)
J Mol Biol
, vol.291
, pp. 215-225
-
-
Tsai, J.1
Levitt, M.2
Baker, D.3
-
42
-
-
0037058992
-
Probing the folding free energy landscape of the src-SH3 protein domain
-
Shea J-E, Onuchic JN, Brooks CL III. Probing the folding free energy landscape of the src-SH3 protein domain. Proc Natl Acad Sci USA 2002;99:16064-16068.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 16064-16068
-
-
Shea, J.-E.1
Onuchic, J.N.2
Brooks III, C.L.3
-
43
-
-
0037974485
-
Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain
-
Guo W, Lampoudi S, Shea J-E. Posttransition state desolvation of the hydrophobic core of the src-SH3 protein domain. Biophys J 2003;85:61-69.
-
(2003)
Biophys J
, vol.85
, pp. 61-69
-
-
Guo, W.1
Lampoudi, S.2
Shea, J.-E.3
-
44
-
-
0033578828
-
Is protein unfolding the reverse of protein folding?: A lattice simulation analysis
-
Dinner AR, Karplus M. Is protein unfolding the reverse of protein folding?: a lattice simulation analysis. J Mol Biol 1999;292:403-419.
-
(1999)
J Mol Biol
, vol.292
, pp. 403-419
-
-
Dinner, A.R.1
Karplus, M.2
-
45
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura J, Impley RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys 1983;79:926-935.
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.3
Impley, R.W.4
Klein, M.L.5
-
46
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan DJ, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comp Chem 1982;4:187-217.
-
(1982)
J Comp Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, D.J.5
Karplus, M.6
-
47
-
-
0000764091
-
Constant-temperature free energy surfaces for physical and chemical processes
-
Boczko EM, Brooks CL III. Constant-temperature free energy surfaces for physical and chemical processes. J Phys Chem 1993;97:4509-4513.
-
(1993)
J Phys Chem
, vol.97
, pp. 4509-4513
-
-
Boczko, E.M.1
Brooks III, C.L.2
-
48
-
-
0032080053
-
Calculations on folding of segment B1 of streptococcal protein G
-
Sheinerman FB, Brooks CL III. Calculations on folding of segment B1 of streptococcal protein G. J Mol Biol 1998;278:439-455.
-
(1998)
J Mol Biol
, vol.278
, pp. 439-455
-
-
Sheinerman, F.B.1
Brooks III, C.L.2
-
49
-
-
0001563395
-
On the transition state for protein folding
-
Du R, Pande VS, Grosberg AY, Tanaka T, Shakhnovich EI. On the transition state for protein folding. J Chem Phys 1998;108:334-350.
-
(1998)
J Chem Phys
, vol.108
, pp. 334-350
-
-
Du, R.1
Pande, V.S.2
Grosberg, A.Y.3
Tanaka, T.4
Shakhnovich, E.I.5
-
51
-
-
0033871567
-
Critical role of beta-hairpin formation in protein G folding
-
McCallister EL, Alm E, Baker D. Critical role of beta-hairpin formation in protein G folding. Nat Struct Biol 2000;7:669-673.
-
(2000)
Nat Struct Biol
, vol.7
, pp. 669-673
-
-
McCallister, E.L.1
Alm, E.2
Baker, D.3
-
52
-
-
0034651984
-
Water penetration and escape in proteins
-
Garcia AE, Hummer G. Water penetration and escape in proteins. Proteins 2000;38:261-272.
-
(2000)
Proteins
, vol.38
, pp. 261-272
-
-
Garcia, A.E.1
Hummer, G.2
-
53
-
-
0028264860
-
Molecular dynamics simulation of protein denaturation: Solvation of the hydrophobic cores and secondary structure of barnase
-
Caflisch A, Karplus M. Molecular dynamics simulation of protein denaturation: solvation of the hydrophobic cores and secondary structure of barnase. Proc Natl Acad Sci USA 1994;91:1746-1750.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, pp. 1746-1750
-
-
Caflisch, A.1
Karplus, M.2
-
54
-
-
0030967896
-
Exploring the folding free energy surface of a three-helix bundle protein
-
Guo Z, Boczko EM, Brooks CL III. Exploring the folding free energy surface of a three-helix bundle protein. Proc Natl Acad Sci USA 1997;94:10161-10166.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 10161-10166
-
-
Guo, Z.1
Boczko, E.M.2
Brooks III, C.L.3
-
55
-
-
0034272188
-
Temperature dependence of hydrophobic interactions: A mean force perspective, effects of water density, and nonadditivity of thermodynamic signatures
-
Shimizu S, Chan HS. Temperature dependence of hydrophobic interactions: a mean force perspective, effects of water density, and nonadditivity of thermodynamic signatures. J Chem Phys 2000;113:4683-4700.
-
(2000)
J Chem Phys
, vol.113
, pp. 4683-4700
-
-
Shimizu, S.1
Chan, H.S.2
-
56
-
-
0036643497
-
Anti-cooperativity and cooperativity in hydrophobic interactions: Three-body free energy landscapes and comparison with implicit-solvent potential functions for proteins
-
Shimizu S, Chan HS. Anti-cooperativity and cooperativity in hydrophobic interactions: three-body free energy landscapes and comparison with implicit-solvent potential functions for proteins. Proteins 2002;48:15-30.
-
(2002)
Proteins
, vol.48
, pp. 15-30
-
-
Shimizu, S.1
Chan, H.S.2
|