-
2
-
-
1842298212
-
From levinthal to pathways to funnels
-
Dill K, Chan H. From Levinthal to pathways to funnels. Nat Struct Biol 1997;4:10-19.
-
(1997)
Nat Struct Biol
, vol.4
, pp. 10-19
-
-
Dill, K.1
Chan, H.2
-
3
-
-
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;37:869-893.
-
(1998)
Angew Chem Int Ed
, vol.37
, pp. 869-893
-
-
Dobson, C.M.1
Sali, A.2
Karplus, M.3
-
4
-
-
0032842870
-
The fundamentals of protein folding: Bringing together theory and experiment
-
Dobson CM, Karplus M. The fundamentals of protein folding: bringing together theory and experiment. Curr Opin Struct Biol 1999;9:92-101.
-
(1999)
Curr Opin Struct Biol
, vol.9
, pp. 92-101
-
-
Dobson, C.M.1
Karplus, M.2
-
5
-
-
0033117763
-
Matching theory and experiment in protein folding
-
Alm E, Baker D. Matching theory and experiment in protein folding. Curr Opin Struct Biol 1999;9:189-196.
-
(1999)
Curr Opin Struct Biol
, vol.9
, pp. 189-196
-
-
Alm, E.1
Baker, D.2
-
7
-
-
0028929556
-
Principles of protein folding - A perspective from simple exact models
-
Dill KA, Bromberg S, Yue K, et al. Principles of protein folding - a perspective from simple exact models. Protein Sci 1995;4:561-601.
-
(1995)
Protein Sci
, vol.4
, pp. 561-601
-
-
Dill, K.A.1
Bromberg, S.2
Yue, K.3
-
8
-
-
0025608908
-
Simulations of the folding of a globular protein
-
Skolnick J, Kolinski A. Simulations of the folding of a globular protein. Science 1990;250:1121-1125.
-
(1990)
Science
, vol.250
, pp. 1121-1125
-
-
Skolnick, J.1
Kolinski, A.2
-
9
-
-
0030775114
-
Can protein unfolding simulate protein folding?
-
Finkelstein AV. Can protein unfolding simulate protein folding? Protein Eng 1997;10:843-845.
-
(1997)
Protein Eng
, vol.10
, pp. 843-845
-
-
Finkelstein, A.V.1
-
10
-
-
0029151245
-
First-principles calculation of the folding free energy of a three-helix bundle protein
-
Boczko EM, Brooks III CL. First-principles calculation of the folding free energy of a three-helix bundle protein. Science 1995; 269:393-396.
-
(1995)
Science
, vol.269
, pp. 393-396
-
-
Boczko, E.M.1
Brooks C.L. III2
-
11
-
-
0032080053
-
Calculations on folding of segment B1 of streptococcal protein G
-
Sheinermann FB, Brooks III CL. Calculations on folding of segment B1 of streptococcal protein G. J Mol Biol 1998;278:439-456.
-
(1998)
J Mol Biol
, vol.278
, pp. 439-456
-
-
Sheinermann, F.B.1
Brooks C.L. III2
-
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. Science 1998;282:740-744.
-
(1998)
Science
, vol.282
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
13
-
-
0027794972
-
Targeted molecular dynamics simulation of conformational change: Application to the T ↔ R transition in insulin
-
Schlitter J, Engels M, Krüger P, Jacoby E, Wollmer A. Targeted molecular dynamics simulation of conformational change: Application to the T ↔ R transition in insulin. Mol Simul 1993;10:291-309.
-
(1993)
Mol Simul
, vol.10
, pp. 291-309
-
-
Schlitter, J.1
Engels, M.2
Krüger, P.3
Jacoby, E.4
Wollmer, A.5
-
14
-
-
0242618314
-
Calculation of pathways for the conformational transition between the GTP-and GDP-bound states of the Ha-ras-p21 protein: Calculations with explicit solvent simulations and comparison with calculations in vacuum
-
Diaz J, Wroblowski B, Schlitter J, Engelborghs Y. Calculation of pathways for the conformational transition between the GTP-and GDP-bound states of the Ha-ras-p21 protein: calculations with explicit solvent simulations and comparison with calculations in vacuum. Proteins 1997;28:434-451.
-
(1997)
Proteins
, vol.28
, pp. 434-451
-
-
Diaz, J.1
Wroblowski, B.2
Schlitter, J.3
Engelborghs, Y.4
-
15
-
-
0030711616
-
Molecular switch in signal transduction: Reaction paths of the conformational changes in ras p21
-
Ma J, Karplus M. Molecular switch in signal transduction: reaction paths of the conformational changes in ras p21. Proc Natl Acad Sci USA 1997;94:11905-11910.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 11905-11910
-
-
Ma, J.1
Karplus, M.2
-
16
-
-
0001568871
-
Calculation of conformational transitions and barriers in solvated systems: Application to the alanine dipeptide in water
-
Apostolakis J, Ferrara P, Caflisch A. Calculation of conformational transitions and barriers in solvated systems: application to the alanine dipeptide in water. J Chem Phys 1999;110:2099-2108.
-
(1999)
J Chem Phys
, vol.110
, pp. 2099-2108
-
-
Apostolakis, J.1
Ferrara, P.2
Caflisch, A.3
-
17
-
-
0026345750
-
Folding of chymotrypsin inhibitor 2. 1. Evidence for a two-state transition
-
Jackson SE, Fersht AR. Folding of chymotrypsin inhibitor 2. 1. evidence for a two-state transition. Biochemistry 1991;30:10248-10435.
-
(1991)
Biochemistry
, vol.30
, pp. 10248-10435
-
-
Jackson, S.E.1
Fersht, A.R.2
-
18
-
-
0028868995
-
The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: Evidence for a nucleation-condensation mechanism for protein folding
-
Itzhaki LS, Otzen DE, Fersht AR. The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed 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
-
19
-
-
0029963345
-
Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations
-
Li A, Daggett V. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J Mol Biol 1996;257:412-429.
-
(1996)
J Mol Biol
, vol.257
, pp. 412-429
-
-
Li, A.1
Daggett, V.2
-
20
-
-
0031465967
-
"New view" of protein folding reconciled with the old through multiple unfolding simulations
-
Lazaridis T, Karplus M. "New view" of protein folding reconciled with the old through multiple unfolding simulations. Science 1997;278:1928-1931.
-
(1997)
Science
, vol.278
, pp. 1928-1931
-
-
Lazaridis, T.1
Karplus, M.2
-
21
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4: 187-217.
-
(1983)
J Comput Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
22
-
-
0000036869
-
Simulation of activation free energies in molecular systems
-
Neria E, Fischer S, Karplus M. Simulation of activation free energies in molecular systems. J Chem Phys 1996;105:1902-1921.
-
(1996)
J Chem Phys
, vol.105
, pp. 1902-1921
-
-
Neria, E.1
Fischer, S.2
Karplus, M.3
-
23
-
-
0033135638
-
Effective energy function for proteins in solution
-
Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins 1999;35:133-152.
-
(1999)
Proteins
, vol.35
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
24
-
-
0022596727
-
Solvation energy in protein folding and binding
-
Eisenberg D, McLachlan AD. Solvation energy in protein folding and binding. Nature 1986;319:199-203.
-
(1986)
Nature
, vol.319
, pp. 199-203
-
-
Eisenberg, D.1
McLachlan, A.D.2
-
26
-
-
0029970351
-
An efficient mean solvation force model for use molecular dynamics simulations of proteins in aqueous solution
-
Fraternali F, van Gunsteren WF. An efficient mean solvation force model for use molecular dynamics simulations of proteins in aqueous solution. J Mol Biol 1996;256:939-948.
-
(1996)
J Mol Biol
, vol.256
, pp. 939-948
-
-
Fraternali, F.1
Van Gunsteren, W.F.2
-
27
-
-
36149010019
-
Some studies concerning rotating axes and polyatomic molecules
-
Eckart C. Some studies concerning rotating axes and polyatomic molecules. Phys Rev 1935;47:552-558.
-
(1935)
Phys Rev
, vol.47
, pp. 552-558
-
-
Eckart, C.1
-
28
-
-
0033531973
-
Forced unfolding of fibronectin type 3 modules: An analysis by biased molecular dynamics simulations
-
Paci E, Karplus M. Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations. J Mol Biol 1999;288:441-459.
-
(1999)
J Mol Biol
, vol.288
, pp. 441-459
-
-
Paci, E.1
Karplus, M.2
-
29
-
-
0001160648
-
Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems
-
Marchi M, Ballone P. Adiabatic bias molecular dynamics: a method to navigate the conformational space of complex molecular systems. J Chem Phys 1999;110:3697-3702.
-
(1999)
J Chem Phys
, vol.110
, pp. 3697-3702
-
-
Marchi, M.1
Ballone, P.2
-
30
-
-
0008863560
-
Some factors in the interpretation of protein denaturation
-
Kauzmann W. Some factors in the interpretation of protein denaturation. Adv Protein Chem 1959;14:1-64.
-
(1959)
Adv Protein Chem
, vol.14
, pp. 1-64
-
-
Kauzmann, W.1
-
31
-
-
0032544002
-
The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation
-
Duan Y, Wang L, Kollman PA. The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation. Proc Natl Acad Sci USA 1998;95: 9897-9902.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 9897-9902
-
-
Duan, Y.1
Wang, L.2
Kollman, P.A.3
-
32
-
-
0030626588
-
The levinthal paradox: Yesterday and today
-
Karplus M. The Levinthal paradox: yesterday and today. Folding and Design 1997;2:S69-S75.
-
(1997)
Folding and Design
, vol.2
-
-
Karplus, M.1
-
33
-
-
0029124248
-
Molten globule and protein folding
-
Ptitsyn OB. Molten globule and protein folding. Advan Protein Chem 1995;47:83-230.
-
(1995)
Advan Protein Chem
, vol.47
, pp. 83-230
-
-
Ptitsyn, O.B.1
-
34
-
-
0022423920
-
Theory for the folding and stability of globular proteins
-
Dill KA. Theory for the folding and stability of globular proteins. Biochemistry 1985;24:1501-1509.
-
(1985)
Biochemistry
, vol.24
, pp. 1501-1509
-
-
Dill, K.A.1
-
35
-
-
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
-
36
-
-
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
-
37
-
-
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
-
38
-
-
18344391877
-
Protein structures and optimal folding from a geometrical variational principle
-
Micheletti C, Banavar JR, Maritan A, Seno F. Protein structures and optimal folding from a geometrical variational principle. Phys Rev Lett 1999;82:3372-3375.
-
(1999)
Phys Rev Lett
, vol.82
, pp. 3372-3375
-
-
Micheletti, C.1
Banavar, J.R.2
Maritan, A.3
Seno, F.4
-
39
-
-
0020997912
-
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
-
40
-
-
0026244229
-
Molscript, a program to produce both detailed and schematic plots of protein structures
-
Kraulis P. Molscript, a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 1991;24: 946-950.
-
(1991)
J Appl Crystallogr
, vol.24
, pp. 946-950
-
-
Kraulis, P.1
|