-
1
-
-
0031815749
-
How do small single-domain proteins fold?
-
Jackson SE. How do small single-domain proteins fold? Fold Des 1998;3:R81-R91.
-
(1998)
Fold des
, vol.3
-
-
Jackson, S.E.1
-
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
-
-
0034687123
-
Topology, stability, sequence, and length: Defining the determinants of two-state protein folding kinetics
-
Plaxco KW, Simons KT, Ruczinski I, Baker D. Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics. Biochemistry 2000;39:11177-11183.
-
(2000)
Biochemistry
, vol.39
, pp. 11177-11183
-
-
Plaxco, K.W.1
Simons, K.T.2
Ruczinski, I.3
Baker, D.4
-
6
-
-
0035967862
-
Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: Application of long-range order to folding rate prediction
-
Gromiha MM, Selvaraj S. Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding rate prediction. J Mol Biol 2001;310:27-32.
-
(2001)
J Mol Biol
, vol.310
, pp. 27-32
-
-
Gromiha, M.M.1
Selvaraj, S.2
-
7
-
-
0037133574
-
How the folding rate constant of simple, single-domain proteins depends on the number of native contacts
-
Makarov DE, Keller CA, Plaxco KW, Metiu H. How the folding rate constant of simple, single-domain proteins depends on the number of native contacts. Proc Natl Acad Sci U S A 2002;99:3535-3539.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 3535-3539
-
-
Makarov, D.E.1
Keller, C.A.2
Plaxco, K.W.3
Metiu, H.4
-
8
-
-
0037215268
-
The topomore search model: A simple, quantitative theory of two-state protein folding kinetics
-
Makarov DE, Plaxco KW. The topomore search model: a simple, quantitative theory of two-state protein folding kinetics. Protein Sci 2003;12:17-26.
-
(2003)
Protein Sci
, vol.12
, pp. 17-26
-
-
Makarov, D.E.1
Plaxco, K.W.2
-
9
-
-
0036215854
-
Folding rate prediction using total contact distance
-
Zhou H, Zhou Y. Folding rate prediction using total contact distance. Biophys J 2002;82:458-463.
-
(2002)
Biophys J
, vol.82
, pp. 458-463
-
-
Zhou, H.1
Zhou, Y.2
-
10
-
-
0037375366
-
Prediction of folding rates and transition-state placement from native-state geometry
-
Micheletti C. Prediction of folding rates and transition-state placement from native-state geometry. Proteins 2003;51:74-84.
-
(2003)
Proteins
, vol.51
, pp. 74-84
-
-
Micheletti, C.1
-
11
-
-
0037432567
-
Local secondary structure content predicts folding rates for simple, two-state proteins
-
Gong HP, Isom DG, Srinivasan R, Rose GD. Local secondary structure content predicts folding rates for simple, two-state proteins. J Mol Biol 2003;327:1149-1154.
-
(2003)
J Mol Biol
, vol.327
, pp. 1149-1154
-
-
Gong, H.P.1
Isom, D.G.2
Srinivasan, R.3
Rose, G.D.4
-
12
-
-
0041089466
-
Effect of preformed correct tertiary interactions on rapid two-state tendamistat folding: Evidence for hairpins as initiation sites for β-sheet formation
-
Schönbrunner N, Pappenberger G, Scharf M, Engels J, Kiefhaber T. Effect of preformed correct tertiary interactions on rapid two-state tendamistat folding: evidence for hairpins as initiation sites for β-sheet formation. Biochemistry 1997;36:9057-9065.
-
(1997)
Biochemistry
, vol.36
, pp. 9057-9065
-
-
Schönbrunner, N.1
Pappenberger, G.2
Scharf, M.3
Engels, J.4
Kiefhaber, T.5
-
13
-
-
0032474460
-
Folding of circular and permuted chymotrypsin inhibitor 2: Retention of the folding nucleus
-
Otzen DE, Fersht AR. Folding of circular and permuted chymotrypsin inhibitor 2: retention of the folding nucleus. Biochemistry 1998;37:8139-8146.
-
(1998)
Biochemistry
, vol.37
, pp. 8139-8146
-
-
Otzen, D.E.1
Fersht, A.R.2
-
15
-
-
0035906728
-
Rescuing a destabilized protein fold through backbone cyclization
-
Camarero JA, Fushman D, Sato S, Giriat I, Cowburn D, Raleigh DP, Muir TW. Rescuing a destabilized protein fold through backbone cyclization. J Mol Biol 2001;308:1045-1062.
-
(2001)
J Mol Biol
, vol.308
, pp. 1045-1062
-
-
Camarero, J.A.1
Fushman, D.2
Sato, S.3
Giriat, I.4
Cowburn, D.5
Raleigh, D.P.6
Muir, T.W.7
-
16
-
-
0000381972
-
Protein core assembly processes
-
Fiebig KM, Dill KA. Protein core assembly processes. J Chem Phys 1993;98:3475-3487.
-
(1993)
J Chem Phys
, vol.98
, pp. 3475-3487
-
-
Fiebig, K.M.1
Dill, K.A.2
-
18
-
-
0033613165
-
A simple model for calculating the kinetics of protein folding from three dimensional structures
-
Muñoz V, Eaton WA. A simple model for calculating the kinetics of protein folding from three dimensional structures. Proc Natl Acad Sci U S A 1999;96:11311-11316.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 11311-11316
-
-
Muñoz, V.1
Eaton, W.A.2
-
19
-
-
0037166875
-
Exact solution of the Munoz-Eaton model for protein folding
-
Bruscolini P, Pelizzola A. Exact solution of the Munoz-Eaton model for protein folding. Phys Rev Lett 2002;88:258101.
-
(2002)
Phys Rev Lett
, vol.88
, pp. 258101
-
-
Bruscolini, P.1
Pelizzola, A.2
-
20
-
-
0033613255
-
Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
-
Alm E, Baker D. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc Natl Acad Sci U S A 1999;96:11305-11310.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 11305-11310
-
-
Alm, E.1
Baker, D.2
-
21
-
-
0036384269
-
Simple physical models connect theory and experiment in protein folding kinetics
-
Alm E, Morozov AV, Kortemme T, Baker D. Simple physical models connect theory and experiment in protein folding kinetics. J Mol Biol 2002;322:463-476.
-
(2002)
J Mol Biol
, vol.322
, pp. 463-476
-
-
Alm, E.1
Morozov, A.V.2
Kortemme, T.3
Baker, D.4
-
22
-
-
0033613131
-
A theoretical search for folding/unfolding nuclei in three-dimensional protein structures
-
Galzitskaya OV, Finkelstein AV. A theoretical search for folding/unfolding nuclei in three-dimensional protein structures. Proc Natl Acad Sci U S A 1999;96:11299-11304.
-
(1999)
Proc Natl Acad Sci U S A
, vol.96
, pp. 11299-11304
-
-
Galzitskaya, O.V.1
Finkelstein, A.V.2
-
23
-
-
0033521194
-
First principles prediction of protein folding rates
-
Debe DA, Goddard WA. First principles prediction of protein folding rates. J Mol Biol 1999;294:619-625.
-
(1999)
J Mol Biol
, vol.294
, pp. 619-625
-
-
Debe, D.A.1
Goddard, W.A.2
-
24
-
-
0034671177
-
The SH3-fold family: Experimental evidence and prediction of variations in the folding pathways
-
Guerois R, Serrano L. The SH3-fold family: experimental evidence and prediction of variations in the folding pathways. J Mol Biol 2000;304:967-982.
-
(2000)
J Mol Biol
, vol.304
, pp. 967-982
-
-
Guerois, R.1
Serrano, L.2
-
25
-
-
0034685604
-
Topological and energetic factors: What determines the structural details of the transition state ensemble and en-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 en-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
-
26
-
-
0034319711
-
Sequencing of folding events in Go-type proteins
-
Hoang TX, Cieplak M. Sequencing of folding events in Go-type proteins. J Chem Phys 2000;113:8319-8328.
-
(2000)
J Chem Phys
, vol.113
, pp. 8319-8328
-
-
Hoang, T.X.1
Cieplak, M.2
-
27
-
-
0035818481
-
Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations
-
Li L, Shakhnovich EI. Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations. Proc Natl Acad Sci U S A 2001;98:13014-13018.
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, pp. 13014-13018
-
-
Li, L.1
Shakhnovich, E.I.2
-
28
-
-
0035868476
-
Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach
-
Portman JJ, Takada S, Wolynes PG. Microscopic theory of protein folding rates. I. Fine structure of the free energy profile and folding routes from a variational approach. J Chem Phys 2001;114: 5069-5081.
-
(2001)
J Chem Phys
, vol.114
, pp. 5069-5081
-
-
Portman, J.J.1
Takada, S.2
Wolynes, P.G.3
-
29
-
-
0242267529
-
Importance of sequence specificity for predicting protein folding pathways: Perturbed Gaussian chain model
-
Kameda T. Importance of sequence specificity for predicting protein folding pathways: perturbed Gaussian chain model. Proteins 2003;53:616-628.
-
(2003)
Proteins
, vol.53
, pp. 616-628
-
-
Kameda, T.1
-
30
-
-
0036295960
-
Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains
-
Klimov DK, Thirumalai D. Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains. J Mol Biol 2002;317:721-737.
-
(2002)
J Mol Biol
, vol.317
, pp. 721-737
-
-
Klimov, D.K.1
Thirumalai, D.2
-
31
-
-
0037062047
-
Energy landscape and native-state structure of proteins - A simplified model
-
Flammini A, Banavar JR, Maritan A. Energy landscape and native-state structure of proteins - a simplified model. Europhys Lett 2002;58:623-629.
-
(2002)
Europhys Lett
, vol.58
, pp. 623-629
-
-
Flammini, A.1
Banavar, J.R.2
Maritan, A.3
-
32
-
-
0038630483
-
Folding rates and low-entropy-loss routes of two-state proteins
-
Weikl TR, Dill KA. Folding rates and low-entropy-loss routes of two-state proteins. J Mol Biol 2003;329:585-598.
-
(2003)
J Mol Biol
, vol.329
, pp. 585-598
-
-
Weikl, T.R.1
Dill, K.A.2
-
33
-
-
0041825363
-
Folding kinetics of two-state proteins: Effect of circularization, permutation, and crosslinks
-
Weikl TR, Dill KA. Folding kinetics of two-state proteins: effect of circularization, permutation, and crosslinks. J Mol Biol 2003;332: 953-963.
-
(2003)
J Mol Biol
, vol.332
, pp. 953-963
-
-
Weikl, T.R.1
Dill, K.A.2
-
34
-
-
24644460584
-
Loop-closure events during protein folding: Rationalizing the shape of Φ-value distributions
-
Weikl TR. Loop-closure events during protein folding: Rationalizing the shape of Φ-value distributions. Proteins 2005;60:701-711.
-
(2005)
Proteins
, vol.60
, pp. 701-711
-
-
Weikl, T.R.1
-
35
-
-
19444371858
-
A critical assessment of the topomer search model of protein folding using a continuum explicit-chain model with extensive conformational sampling
-
Wallin S, Chan HS. A critical assessment of the topomer search model of protein folding using a continuum explicit-chain model with extensive conformational sampling. Protein Sci 2005;14:1643-1660.
-
(2005)
Protein Sci
, vol.14
, pp. 1643-1660
-
-
Wallin, S.1
Chan, H.S.2
-
36
-
-
3843114319
-
Intramolecular reaction in polycondensations. I. The theory of linear systems
-
Jacobson H, Stockmayer WH. Intramolecular reaction in polycondensations. I. The theory of linear systems. J Chem Phys 1950;18: 1600-1606.
-
(1950)
J Chem Phys
, vol.18
, pp. 1600-1606
-
-
Jacobson, H.1
Stockmayer, W.H.2
-
37
-
-
0001193711
-
The effects of internal constraints on the configurations of chain molecules
-
Chan HS, Dill KA. The effects of internal constraints on the configurations of chain molecules. J Chem Phys 1990;92:3118-3135.
-
(1990)
J Chem Phys
, vol.92
, pp. 3118-3135
-
-
Chan, H.S.1
Dill, K.A.2
-
38
-
-
0028941444
-
Theoretical predictions of folding pathways by using the proximity rule, with applications to bovine pancreatic trypsin inhibitor
-
Camacho CJ, Thirumalai D. Theoretical predictions of folding pathways by using the proximity rule, with applications to bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci U S A 1995;92: 1277-1281.
-
(1995)
Proc Natl Acad Sci U S A
, vol.92
, pp. 1277-1281
-
-
Camacho, C.J.1
Thirumalai, D.2
-
39
-
-
0042235294
-
Effect of backbone cyclization on protein folding stability: Chain entropies of both the unfolded and the folded states are restricted
-
Zhou H-X. Effect of backbone cyclization on protein folding stability: chain entropies of both the unfolded and the folded states are restricted. J Mol Biol 2003;332:257-264.
-
(2003)
J Mol Biol
, vol.332
, pp. 257-264
-
-
Zhou, H.-X.1
-
40
-
-
1242338901
-
Loops, linkages, rings, catenanes, cages, and crowders: Entropy-based strategies for stabilizing proteins
-
Zhou H-X. Loops, linkages, rings, catenanes, cages, and crowders: entropy-based strategies for stabilizing proteins. Ace Chem Res 2004;37:123-130.
-
(2004)
Ace Chem Res
, vol.37
, pp. 123-130
-
-
Zhou, H.-X.1
-
41
-
-
0042510944
-
Contact order revisited: Influence of protein size on the folding rate
-
Ivankov DN, Garbuzynskiy SO, Alm E, Plaxco KW, Baker D, Finkelstein AV. Contact order revisited: influence of protein size on the folding rate. Protein Sci 2003;12:2057-2062.
-
(2003)
Protein Sci
, vol.12
, pp. 2057-2062
-
-
Ivankov, D.N.1
Garbuzynskiy, S.O.2
Alm, E.3
Plaxco, K.W.4
Baker, D.5
Finkelstein, A.V.6
-
42
-
-
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
-
43
-
-
0034604105
-
A surprising simplicity to protein folding
-
Baker D. A surprising simplicity to protein folding. Nature 2000;405:39-42.
-
(2000)
Nature
, vol.405
, pp. 39-42
-
-
Baker, D.1
-
44
-
-
0030601788
-
Microsecond protein folding through a compact transition state
-
Burton RE, Huang GS, Daugherty MA, Fullbright PW, Oas TG. Microsecond protein folding through a compact transition state. J Mol Biol 1996;263:311-322.
-
(1996)
J Mol Biol
, vol.263
, pp. 311-322
-
-
Burton, R.E.1
Huang, G.S.2
Daugherty, M.A.3
Fullbright, P.W.4
Oas, T.G.5
-
45
-
-
0038329308
-
Folding at the speed limit
-
Yang WY, Gruebele M. Folding at the speed limit. Nature 2003;423:193-197.
-
(2003)
Nature
, vol.423
, pp. 193-197
-
-
Yang, W.Y.1
Gruebele, M.2
-
46
-
-
0029760326
-
Different folding transition states may result in the same native structure
-
Viguera AR, Serrano L, Wilmanns M. Different folding transition states may result in the same native structure. Nat Struct Biol 1996;3:874-880.
-
(1996)
Nat Struct Biol
, vol.3
, pp. 874-880
-
-
Viguera, A.R.1
Serrano, L.2
Wilmanns, M.3
-
47
-
-
0035824886
-
Folding of circular permutants with decreased contact order: General trend balanced by protein stability
-
Lindberg MO, Tangrot J, Otzen DE, Dolgikh DA, Finkelstein AV, Oliveberg M. Folding of circular permutants with decreased contact order: general trend balanced by protein stability. J Mol Biol 2001;314:891-900.
-
(2001)
J Mol Biol
, vol.314
, pp. 891-900
-
-
Lindberg, M.O.1
Tangrot, J.2
Otzen, D.E.3
Dolgikh, D.A.4
Finkelstein, A.V.5
Oliveberg, M.6
-
48
-
-
0036829967
-
Complete change of the protein folding transition state upon circular permutation
-
Lindberg M, Tangrot J, Oliveberg M. Complete change of the protein folding transition state upon circular permutation. Nat Struct Biol 2001;9:818-822.
-
(2001)
Nat Struct Biol
, vol.9
, pp. 818-822
-
-
Lindberg, M.1
Tangrot, J.2
Oliveberg, M.3
-
49
-
-
0036678120
-
Experimental evaluation of topological parameters determining protein-folding rates
-
Miller EJ, Fischer KF, Marqusee S. Experimental evaluation of topological parameters determining protein-folding rates. Proc Natl Acad Sci U S A 2002;99:10359-10363.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 10359-10363
-
-
Miller, E.J.1
Fischer, K.F.2
Marqusee, S.3
|