-
1
-
-
0002006297
-
Are there pathways for protein folding?
-
Levinthal, C. 1968. Are there pathways for protein folding? J. Chim. Phys. 65:44-45.
-
(1968)
J. Chim. Phys
, vol.65
, pp. 44-45
-
-
Levinthal, C.1
-
3
-
-
0033190538
-
Protein folding from 1961 to 1982
-
Baldwin, R. L. 1999. Protein folding from 1961 to 1982. Nat. Struct. Biol. 6:814-817.
-
(1999)
Nat. Struct. Biol
, vol.6
, pp. 814-817
-
-
Baldwin, R.L.1
-
4
-
-
0033080081
-
Is protein folding hierarchic? II. Folding intermediates and transition states
-
Baldwin, R. L., and G. D. Rose. 1999. Is protein folding hierarchic? II. Folding intermediates and transition states. Trends Biochem. Sci. 24:77-83.
-
(1999)
Trends Biochem. Sci
, vol.24
, pp. 77-83
-
-
Baldwin, R.L.1
Rose, G.D.2
-
5
-
-
25444512161
-
Direct observation of the three-state folding of a single protein molecule
-
Cecconi, C., E. A. Shank, C. Bustamante, and S. Marqusee. 2005. Direct observation of the three-state folding of a single protein molecule. Science. 309:2057-2060.
-
(2005)
Science
, vol.309
, pp. 2057-2060
-
-
Cecconi, C.1
Shank, E.A.2
Bustamante, C.3
Marqusee, S.4
-
6
-
-
0028776642
-
Matching speed and stability
-
Baldwin, R. L. 1994.Matching speed and stability. Nature. 369:183-184.
-
(1994)
Nature
, vol.369
, pp. 183-184
-
-
Baldwin, R.L.1
-
7
-
-
0027313673
-
Pathways of protein folding
-
Matthews, C. R. 1993. Pathways of protein folding. Annu. Rev. Biochem. 62:653-683.
-
(1993)
Annu. Rev. Biochem
, vol.62
, pp. 653-683
-
-
Matthews, C.R.1
-
8
-
-
1842298212
-
From Levinthal to pathways to funnels
-
Dill, K. A., and H. S. Chan. 1997. From Levinthal to pathways to funnels. Nat. Struct. Biol. 4:10-19.
-
(1997)
Nat. Struct. Biol
, vol.4
, pp. 10-19
-
-
Dill, K.A.1
Chan, H.S.2
-
9
-
-
0028947257
-
Funnels, pathways, and the energy landscape of protein folding: A synthesis
-
Bryngelson, J. D., J. N. Onuchic, N. D. Socci, and P. G. Wolynes. 1995. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins. 21:167-195.
-
(1995)
Proteins
, vol.21
, pp. 167-195
-
-
Bryngelson, J.D.1
Onuchic, J.N.2
Socci, N.D.3
Wolynes, P.G.4
-
10
-
-
0026345750
-
Folding of chymotrypsin inhibitor-2. 1. Evidence for a two-state transition
-
Jackson, S. E., and A. R. Fersht. 1991. Folding of chymotrypsin inhibitor-2. 1. Evidence for a two-state transition. Biochemistry. 30:10428-10435.
-
(1991)
Biochemistry
, vol.30
, pp. 10428-10435
-
-
Jackson, S.E.1
Fersht, A.R.2
-
11
-
-
0031815749
-
How do small single-domain proteins fold?
-
Jackson, S. E. 1998. How do small single-domain proteins fold? Fold. Des. 3:R81-R91.
-
(1998)
Fold. Des
, vol.3
-
-
Jackson, S.E.1
-
13
-
-
0035252683
-
Mechanisms of protein folding
-
Grantcharova, V., E. J. Alm, D. Baker, and A. L. Horwich. 2001. Mechanisms of protein folding. Curr. Opin. Struct. Biol. 11:70-82.
-
(2001)
Curr. Opin. Struct. Biol
, vol.11
, pp. 70-82
-
-
Grantcharova, V.1
Alm, E.J.2
Baker, D.3
Horwich, A.L.4
-
14
-
-
0028868995
-
The structure of the transition state for folding of chymotrypsin inhibitor 2 analyzed by protein engineering methods: Evidence for a nucleation-condensation mechanism for protein folding
-
Itzhaki, L. S., D. E. Otzen, and A. R. Fersht. 1995. The structure of the transition state for folding of chymotrypsin inhibitor 2 analyzed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. J. Mol. Biol. 254:260-288.
-
(1995)
J. Mol. Biol
, vol.254
, pp. 260-288
-
-
Itzhaki, L.S.1
Otzen, D.E.2
Fersht, A.R.3
-
15
-
-
0032515105
-
Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain
-
Villegas, V., J. C. Martinez, F. X. Aviles, and L. Serrano. 1998. Structure of the transition state in the folding process of human procarboxypeptidase A2 activation domain. J. Mol. Biol. 283:1027-1036.
-
(1998)
J. Mol. Biol
, vol.283
, pp. 1027-1036
-
-
Villegas, V.1
Martinez, J.C.2
Aviles, F.X.3
Serrano, L.4
-
16
-
-
0032708771
-
Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding
-
Chiti, F., N. Taddei, P. M. White, M. Bucciantini, F. Magherini, M. Stefani, and C. M. Dobson. 1999. Mutational analysis of acylphosphatase suggests the importance of topology and contact order in protein folding. Nat. Struct. Biol. 6:1005-1009.
-
(1999)
Nat. Struct. Biol
, vol.6
, pp. 1005-1009
-
-
Chiti, F.1
Taddei, N.2
White, P.M.3
Bucciantini, M.4
Magherini, F.5
Stefani, M.6
Dobson, C.M.7
-
17
-
-
0033592876
-
From snapshot to movie: Φ analysis of protein folding transition states taken one step further
-
Ternström, T., U. Mayor, M. Akke, and M. Oliveberg. 1999. From snapshot to movie: Φ analysis of protein folding transition states taken one step further. Proc. Natl. Acad. Sci. USA. 96:14854-14859.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 14854-14859
-
-
Ternström, T.1
Mayor, U.2
Akke, M.3
Oliveberg, M.4
-
18
-
-
0033015989
-
The formation of a native-like structure containing eight conserved hydrophobic residues is rate limiting in two-state protein folding of ACBP
-
Kragelund, B. B., P. Osmark, T. B. Neergaard, J. Schiodt, K. Kristiansen, J. Knudsen, and F. M. Poulsen. 1999. The formation of a native-like structure containing eight conserved hydrophobic residues is rate limiting in two-state protein folding of ACBP. Nat. Struct. Biol. 9:594-601.
-
(1999)
Nat. Struct. Biol
, vol.9
, pp. 594-601
-
-
Kragelund, B.B.1
Osmark, P.2
Neergaard, T.B.3
Schiodt, J.4
Kristiansen, K.5
Knudsen, J.6
Poulsen, F.M.7
-
19
-
-
0032750509
-
The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved
-
Martinez, J. C., and L. Serrano. 1999. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nat. Struct. Biol. 6:1010-1016.
-
(1999)
Nat. Struct. Biol
, vol.6
, pp. 1010-1016
-
-
Martinez, J.C.1
Serrano, L.2
-
20
-
-
0032734515
-
Experiment and theory highlight role of native state topology in SH3 folding
-
Riddle, D. S., V. P. Grantcharova, J. V. Santiago, E. Alm, I. Ruczinski, and D. Baker. 1999. Experiment and theory highlight role of native state topology in SH3 folding. Nat. Struct. Biol. 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
-
21
-
-
0032812796
-
Mapping the interactions present in the transition state for unfolding/folding of FKBP12
-
Fulton, K. F., E. R. G. Main, V. Daggett, and S. E. Jackson. 1999. Mapping the interactions present in the transition state for unfolding/folding of FKBP12. J. Mol. Biol. 291:445-461.
-
(1999)
J. Mol. Biol
, vol.291
, pp. 445-461
-
-
Fulton, K.F.1
Main, E.R.G.2
Daggett, V.3
Jackson, S.E.4
-
22
-
-
0034677663
-
The folding of an immunoglobulin-like Greek key protein is defined by a common-core nucleus and regions constrained by topology
-
Hamill, S. J., A. Steward, and J. Clarke. 2000. The folding of an immunoglobulin-like Greek key protein is defined by a common-core nucleus and regions constrained by topology. J. Mol. Biol. 297:165-178.
-
(2000)
J. Mol. Biol
, vol.297
, pp. 165-178
-
-
Hamill, S.J.1
Steward, A.2
Clarke, J.3
-
23
-
-
0034685619
-
A breakdown of symmetry in the folding transition state of protein L
-
Kim, D. E., C. Fisher, and D. Baker. 2000. A breakdown of symmetry in the folding transition state of protein L. J. Mol. Biol. 298:971-984.
-
(2000)
J. Mol. Biol
, vol.298
, pp. 971-984
-
-
Kim, D.E.1
Fisher, C.2
Baker, D.3
-
24
-
-
0033871567
-
Critical role of β-hairpin formation in protein G folding
-
McCallister, E. L., E. Alm, and D. Baker. 2000. Critical role of β-hairpin formation in protein G folding. Nat. Struct. Biol. 7:669-673.
-
(2000)
Nat. Struct. Biol
, vol.7
, pp. 669-673
-
-
McCallister, E.L.1
Alm, E.2
Baker, D.3
-
25
-
-
0035839050
-
The folding mechanism of a β-sheet: The WW domain
-
Jäger, M., H. Nguyen, J. C. Crane, J. W. Kelly, and M. Gruebele. 2001. The folding mechanism of a β-sheet: the WW domain. J. Mol. Biol. 311:373-393.
-
(2001)
J. Mol. Biol
, vol.311
, pp. 373-393
-
-
Jäger, M.1
Nguyen, H.2
Crane, J.C.3
Kelly, J.W.4
Gruebele, M.5
-
26
-
-
0036293485
-
Conformational plasticity in folding of the split β-α-β protein S6: Evidence for burst-phase disruption of the native state
-
Otzen, D. E., and M. Oliveberg. 2002. Conformational plasticity in folding of the split β-α-β protein S6: evidence for burst-phase disruption of the native state. J. Mol. Biol. 317:613-627.
-
(2002)
J. Mol. Biol
, vol.317
, pp. 613-627
-
-
Otzen, D.E.1
Oliveberg, M.2
-
27
-
-
0036172116
-
Hydrophobic core packing in the SH3 domain folding transition state
-
Northey, J. G. B., A. A. Di Nardo, and A. R. Davidson. 2002. Hydrophobic core packing in the SH3 domain folding transition state. Nat. Struct. Biol. 9:126-130.
-
(2002)
Nat. Struct. Biol
, vol.9
, pp. 126-130
-
-
Northey, J.G.B.1
Di Nardo, A.A.2
Davidson, A.R.3
-
28
-
-
0345255608
-
Unifying features in protein-folding mechanisms
-
Gianni, S., N. R. Guydosh, F. Khan, T. D. Caldas, U. Mayor, G. W. N. White, M. L. DeMarco, V. Daggett, and A. R. Fersht. 2004. Unifying features in protein-folding mechanisms. Proc. Natl. Acad. Sci. USA. 100:13286-13291.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 13286-13291
-
-
Gianni, S.1
Guydosh, N.R.2
Khan, F.3
Caldas, T.D.4
Mayor, U.5
White, G.W.N.6
DeMarco, M.L.7
Daggett, V.8
Fersht, A.R.9
-
29
-
-
3042848873
-
Context-dependent contributions of backbone hydrogen bonding to β-sheet folding energetics
-
Deechongkit, S., H. Nguyen, E. T. Powers, P. E. Dawson, M. Gruebele, and J. W. Kelly. 2004. Context-dependent contributions of backbone hydrogen bonding to β-sheet folding energetics. Nature. 430:101-105.
-
(2004)
Nature
, vol.430
, pp. 101-105
-
-
Deechongkit, S.1
Nguyen, H.2
Powers, E.T.3
Dawson, P.E.4
Gruebele, M.5
Kelly, J.W.6
-
30
-
-
2442683149
-
The folding transition state of the cold shock protein is strongly polarized
-
Garcia-Mira, M. M., D. Böhringer, and F. X. Schmid. 2004. The folding transition state of the cold shock protein is strongly polarized. J. Mol. Biol. 339:555-569.
-
(2004)
J. Mol. Biol
, vol.339
, pp. 555-569
-
-
Garcia-Mira, M.M.1
Böhringer, D.2
Schmid, F.X.3
-
31
-
-
27744452242
-
Fine structure analysis of a protein folding transition state; distinguishing between hydrophobic stabilization and specific packing
-
Anil, B., S. Sato, J. H. Cho, and D. P. Raleigh. 2005. Fine structure analysis of a protein folding transition state; distinguishing between hydrophobic stabilization and specific packing. J. Mol. Biol. 354:693-705.
-
(2005)
J. Mol. Biol
, vol.354
, pp. 693-705
-
-
Anil, B.1
Sato, S.2
Cho, J.H.3
Raleigh, D.P.4
-
32
-
-
23044514304
-
Snapshots of a dynamic folding nucleus in zinc-substituted Pseudomonas aeruginosa azurin
-
Wilson, C. J., and P. Wittung-Stafshede. 2005. Snapshots of a dynamic folding nucleus in zinc-substituted Pseudomonas aeruginosa azurin. Biochemistry. 44:10054-10062.
-
(2005)
Biochemistry
, vol.44
, pp. 10054-10062
-
-
Wilson, C.J.1
Wittung-Stafshede, P.2
-
33
-
-
33745606942
-
Φ-analysis at the experimental limits: Mechanism of β-hairpin formation
-
Petrovich, M., A. L. Jonsson, N. Ferguson, V. Daggett, and A. R. Fersht. 2006. Φ-analysis at the experimental limits: mechanism of β-hairpin formation. J. Mol. Biol. 360:865-881.
-
(2006)
J. Mol. Biol
, vol.360
, pp. 865-881
-
-
Petrovich, M.1
Jonsson, A.L.2
Ferguson, N.3
Daggett, V.4
Fersht, A.R.5
-
34
-
-
0024358426
-
Mapping the transition state and pathway of protein folding by protein engineering
-
Matouschek, A., J. T. Kellis, L. Serrano, and A. R. Fersht. 1989. Mapping the transition state and pathway of protein folding by protein engineering. Nature. 340:122-126.
-
(1989)
Nature
, vol.340
, pp. 122-126
-
-
Matouschek, A.1
Kellis, J.T.2
Serrano, L.3
Fersht, A.R.4
-
35
-
-
0034061258
-
Structural analysis of WW domains and design of a WW prototype
-
Macias, M. J., V. Gervais, C. Civera, and H. Oschkinat. 2000. Structural analysis of WW domains and design of a WW prototype. Nat. Struct. Biol. 7:375-379.
-
(2000)
Nat. Struct. Biol
, vol.7
, pp. 375-379
-
-
Macias, M.J.1
Gervais, V.2
Civera, C.3
Oschkinat, H.4
-
36
-
-
0008233581
-
Structural and functional analysis of the mitotic rotamase Pin1 suggests substrate recognition is phosphorylation dependent
-
Ranganathan, R., K. P. Lu, T. Hunter, and J. P. Noel. 1997. Structural and functional analysis of the mitotic rotamase Pin1 suggests substrate recognition is phosphorylation dependent. Cell. 89:875-886.
-
(1997)
Cell
, vol.89
, pp. 875-886
-
-
Ranganathan, R.1
Lu, K.P.2
Hunter, T.3
Noel, J.P.4
-
37
-
-
25644452032
-
Evolutionary information for specifying a protein fold
-
Socolich, M., S. W. Lockless, W. P. Russ, H. Lee, K. H. Gardner, and R. Ranganathan. 2005. Evolutionary information for specifying a protein fold. Nature. 437:512-518.
-
(2005)
Nature
, vol.437
, pp. 512-518
-
-
Socolich, M.1
Lockless, S.W.2
Russ, W.P.3
Lee, H.4
Gardner, K.H.5
Ranganathan, R.6
-
38
-
-
33749341803
-
Design and NMR conformational study of a β-sheet peptide based on betanova and WW domains
-
Fernandez-Escamilla, A. M., S. Ventura, L. Serrano, and M. A. Jimenez. 2006. Design and NMR conformational study of a β-sheet peptide based on betanova and WW domains. Protein Sci. 15:2278-2289.
-
(2006)
Protein Sci
, vol.15
, pp. 2278-2289
-
-
Fernandez-Escamilla, A.M.1
Ventura, S.2
Serrano, L.3
Jimenez, M.A.4
-
39
-
-
0035818563
-
Using flexible loop mimetics to extend Φ-value analysis to secondary structure interactions
-
Ferguson, N., J. R. Pires, F. Toepert, C. M. Johnson, Y. P. Pan, R. Volkmer-Engert, J. Schneider-Mergener, V. Daggett, H. Oschkinat, and A. Fersht. 2002. Using flexible loop mimetics to extend Φ-value analysis to secondary structure interactions. Proc. Natl. Acad. Sci. USA. 98:13008-13013.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 13008-13013
-
-
Ferguson, N.1
Pires, J.R.2
Toepert, F.3
Johnson, C.M.4
Pan, Y.P.5
Volkmer-Engert, R.6
Schneider-Mergener, J.7
Daggett, V.8
Oschkinat, H.9
Fersht, A.10
-
40
-
-
0001071357
-
Tuning the free-energy landscape of a WW domain by temperature, mutation, and truncation
-
Nguyen, H., M. Jäger, A. Moretto, M. Gruebele, and J. W. Kelly. 2003. Tuning the free-energy landscape of a WW domain by temperature, mutation, and truncation. Proc. Natl. Acad. Sci. USA. 100:3948-3953.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 3948-3953
-
-
Nguyen, H.1
Jäger, M.2
Moretto, A.3
Gruebele, M.4
Kelly, J.W.5
-
41
-
-
32344433535
-
β-sheet folding mechanisms from perturbation energetics
-
Deechongkit, S., H. Nguyen, M. Jager, E. T. Powers, M. Gruebele, and J. W. Kelly. 2006. β-sheet folding mechanisms from perturbation energetics. Curr. Opin. Struct. Biol. 16:94-101.
-
(2006)
Curr. Opin. Struct. Biol
, vol.16
, pp. 94-101
-
-
Deechongkit, S.1
Nguyen, H.2
Jager, M.3
Powers, E.T.4
Gruebele, M.5
Kelly, J.W.6
-
42
-
-
33746042979
-
Structure-function- folding relationship in a WW domain
-
Jäger, M., Y. Zhang, J. Bieschke, H. Nguyen, M. Dendle, M. E. Bowman, J. P. Noel, M. Gruebele, and J. W. Kelly. 2006. Structure-function- folding relationship in a WW domain. Proc. Natl. Acad. Sci. USA. 103:10648-10653.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 10648-10653
-
-
Jäger, M.1
Zhang, Y.2
Bieschke, J.3
Nguyen, H.4
Dendle, M.5
Bowman, M.E.6
Noel, J.P.7
Gruebele, M.8
Kelly, J.W.9
-
43
-
-
0033520751
-
Folding free energy surface of a three-stranded β-sheet protein
-
Bursulaya, B. D., and C. L. Brooks III. 1999. Folding free energy surface of a three-stranded β-sheet protein. J. Am. Chem. Soc. 121: 9947-9951.
-
(1999)
J. Am. Chem. Soc
, vol.121
, pp. 9947-9951
-
-
Bursulaya, B.D.1
Brooks III, C.L.2
-
44
-
-
0034718553
-
Folding simulations of a threestranded antiparallel β-sheet peptide
-
Ferrara, P., and A. Caflisch. 2000. Folding simulations of a threestranded antiparallel β-sheet peptide. Proc. Natl. Acad. Sci. USA. 97:10780-10785.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 10780-10785
-
-
Ferrara, P.1
Caflisch, A.2
-
45
-
-
0037159944
-
Determination of the structures of distinct transition state ensembles for a β-sheet peptide with parallel folding pathways
-
Davis, R., C. M. Dobson, and M. Vendruscolo. 2002. Determination of the structures of distinct transition state ensembles for a β-sheet peptide with parallel folding pathways. J. Chem. Phys. 117:9510-9517.
-
(2002)
J. Chem. Phys
, vol.117
, pp. 9510-9517
-
-
Davis, R.1
Dobson, C.M.2
Vendruscolo, M.3
-
46
-
-
1542723482
-
Integrating folding kinetics and protein function: Biphasic kinetics and dual binding specificity in a WW domain
-
Karanicolas, J., and C. L. Brooks III. 2004. Integrating folding kinetics and protein function: biphasic kinetics and dual binding specificity in a WW domain. Proc. Natl. Acad. Sci. USA. 101:3432-3437.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 3432-3437
-
-
Karanicolas, J.1
Brooks III, C.L.2
-
47
-
-
14744267933
-
Analysis of PIN1 WW domain through a simple statistical mechanics model
-
Bruscolini, P., and F. Cecconi. 2005. Analysis of PIN1 WW domain through a simple statistical mechanics model. Biophys. Chem. 115:153-158.
-
(2005)
Biophys. Chem
, vol.115
, pp. 153-158
-
-
Bruscolini, P.1
Cecconi, F.2
-
48
-
-
0029963345
-
Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations
-
Li, A., and V. Daggett. 1996. Identification and characterization of the unfolding transition state of chymotrypsin inhibitor 2 by molecular dynamics simulations. J. Mol. Biol. 257:412-429.
-
(1996)
J. Mol. Biol
, vol.257
, pp. 412-429
-
-
Li, A.1
Daggett, V.2
-
49
-
-
17744395510
-
Sensitivity of the folding/unfolding transition state ensemble of chymotrypsin inhibitor 2 to changes in temperature and solvent
-
Day, R., and V. Daggett. 2005. Sensitivity of the folding/unfolding transition state ensemble of chymotrypsin inhibitor 2 to changes in temperature and solvent. Protein Sci. 14:1242-1252.
-
(2005)
Protein Sci
, vol.14
, pp. 1242-1252
-
-
Day, R.1
Daggett, V.2
-
50
-
-
16344374494
-
Thermal unfolding simulations of a multimeric protein - transition state and unfolding pathways
-
Duan, J., and L. Nilsson. 2005. Thermal unfolding simulations of a multimeric protein - transition state and unfolding pathways. Proteins. 59:170-182.
-
(2005)
Proteins
, vol.59
, pp. 170-182
-
-
Duan, J.1
Nilsson, L.2
-
51
-
-
0035252350
-
Three key residues form a critical contact network in a protein folding transition state
-
Vendruscolo, M., E. Paci, C. M. Dobson, and M. Karplus. 2001. Three key residues form a critical contact network in a protein folding transition state. Nature. 409:641-645.
-
(2001)
Nature
, vol.409
, pp. 641-645
-
-
Vendruscolo, M.1
Paci, E.2
Dobson, C.M.3
Karplus, M.4
-
52
-
-
0036435907
-
Determination of a transition state at atomic resolution from protein engineering data
-
Paci, E., M. Vendruscolo, C. M. Dobson, and M. Karplus. 2002. Determination of a transition state at atomic resolution from protein engineering data. J. Mol. Biol. 324:151-163.
-
(2002)
J. Mol. Biol
, vol.324
, pp. 151-163
-
-
Paci, E.1
Vendruscolo, M.2
Dobson, C.M.3
Karplus, M.4
-
53
-
-
0033613255
-
Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures
-
Alm, E., and D. Baker. 1999. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc. Natl. Acad. Sci. USA. 96:11305-11310.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 11305-11310
-
-
Alm, E.1
Baker, D.2
-
54
-
-
0033613165
-
A simple model for calculating the kinetics of protein folding from three-dimensional structures
-
Muñoz, V., and W. A. Eaton. 1999. A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc. Natl. Acad. Sci. USA. 96:11311-11316.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 11311-11316
-
-
Muñoz, V.1
Eaton, W.A.2
-
55
-
-
0033613131
-
A theoretical search for folding/unfolding nuclei in three-dimensional protein structures
-
Galzitskaya, O. V., and A. V. Finkelstein. 1999. A theoretical search for folding/unfolding nuclei in three-dimensional protein structures. Proc. Natl. Acad. Sci. USA. 96:11299-11304.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 11299-11304
-
-
Galzitskaya, O.V.1
Finkelstein, A.V.2
-
56
-
-
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., H. Nymeyer, and J. N. Onuchic. 2000. 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. 298:937-953.
-
(2000)
J. Mol. Biol
, vol.298
, pp. 937-953
-
-
Clementi, C.1
Nymeyer, H.2
Onuchic, J.N.3
-
57
-
-
0034671177
-
The SH3-fold family: Experimental evidence and prediction of variations in the folding pathways
-
Guerois, R., and L. Serrano. 2000. The SH3-fold family: experimental evidence and prediction of variations in the folding pathways. J. Mol. Biol. 304:967-982.
-
(2000)
J. Mol. Biol
, vol.304
, pp. 967-982
-
-
Guerois, R.1
Serrano, L.2
-
58
-
-
0036384269
-
Simple physical models connect theory and experiment in protein folding kinetics
-
Alm, E., A. V. Morozov, T. Kortemme, and D. Baker. 2002. Simple physical models connect theory and experiment in protein folding kinetics. J. Mol. Biol. 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
-
59
-
-
0242267529
-
Importance of sequence specificity for predicting protein folding pathways: Perturbed Gaussian chain model
-
Kameda, T. 2000. Importance of sequence specificity for predicting protein folding pathways: perturbed Gaussian chain model. Proteins. 53:616-628.
-
(2000)
Proteins
, vol.53
, pp. 616-628
-
-
Kameda, T.1
-
60
-
-
34548098593
-
Estimation of protein folding probability from equilibrium simulations
-
Rao, F., G. Settanni, E. Guarnera, and A. Caflisch. 2005. Estimation of protein folding probability from equilibrium simulations. J. Chem. Phys. 122:184901.
-
(2005)
J. Chem. Phys
, vol.122
, pp. 184901
-
-
Rao, F.1
Settanni, G.2
Guarnera, E.3
Caflisch, A.4
-
61
-
-
14144255497
-
Φ-value analysis by molecular dynamics simulations of reversible folding
-
Settanni, G., F. Rao, and A. Caflisch. 2005. Φ-value analysis by molecular dynamics simulations of reversible folding. Proc. Natl. Acad. Sci. USA. 102:628-633.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 628-633
-
-
Settanni, G.1
Rao, F.2
Caflisch, A.3
-
62
-
-
0001563395
-
On the transition coordinate for protein folding
-
Du, R., V. S. Pande, A. Y. Grosberg, T. Tanaka, and E. S. Shakhnovich. 1998. On the transition coordinate for protein folding. J. Chem. Phys. 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.S.5
-
63
-
-
0842311640
-
From transition paths to transition states and rate coefficients
-
Hummer, G. 2004. From transition paths to transition states and rate coefficients. J. Chem. Phys. 120:516-523.
-
(2004)
J. Chem. Phys
, vol.120
, pp. 516-523
-
-
Hummer, G.1
-
64
-
-
33745744079
-
Kinetic definition of protein folding transition state ensembles and reaction coordinates
-
Snow, C. D., Y. M. Rhee, and V. S. Pande. 2006. Kinetic definition of protein folding transition state ensembles and reaction coordinates. Biophys. J. 91:14-24.
-
(2006)
Biophys. J
, vol.91
, pp. 14-24
-
-
Snow, C.D.1
Rhee, Y.M.2
Pande, V.S.3
-
65
-
-
0036291145
-
Predicting changes in the stability of proteins and protein complexes: A study of more than 1000 mutations
-
Guerois, R., J. E. Nielsen, and L. Serrano. 2002. Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. J. Mol. Biol. 320:369-387.
-
(2002)
J. Mol. Biol
, vol.320
, pp. 369-387
-
-
Guerois, R.1
Nielsen, J.E.2
Serrano, L.3
-
66
-
-
23144436398
-
The FOLDX web server: An online force field
-
Schymkowitz, J., J. Borg, F. Stricher, R. Nys, F. Rousseau, and L. Serrano. 2005. The FOLDX web server: an online force field. Nucleic Acids Res. 33:W382-W388.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Schymkowitz, J.1
Borg, J.2
Stricher, F.3
Nys, R.4
Rousseau, F.5
Serrano, L.6
-
67
-
-
22544454425
-
Φ-values in protein folding kinetics have energetic and structural components
-
Merlo, C., K. A. Dill, and T. R. Weikl. 2005. Φ-values in protein folding kinetics have energetic and structural components. Proc. Natl. Acad. Sci. USA. 102:10171-10175.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 10171-10175
-
-
Merlo, C.1
Dill, K.A.2
Weikl, T.R.3
-
68
-
-
33846026304
-
Transition states in protein folding kinetics: The structural interpretation of Φ-values
-
Weikl, T. R., and K. A. Dill. 2007. Transition states in protein folding kinetics: the structural interpretation of Φ-values. J. Mol. Biol. 365:1578-1586.
-
(2007)
J. Mol. Biol
, vol.365
, pp. 1578-1586
-
-
Weikl, T.R.1
Dill, K.A.2
-
69
-
-
1342268048
-
Cooperativity in two-state protein folding kinetics
-
Weikl, T. R., M. Palassini, and K. A. Dill. 2004. Cooperativity in two-state protein folding kinetics. Protein Sci. 13:822-829.
-
(2004)
Protein Sci
, vol.13
, pp. 822-829
-
-
Weikl, T.R.1
Palassini, M.2
Dill, K.A.3
-
70
-
-
84946031884
-
Procedures for detecting outlying observations in samples
-
Grubbs, F. E. 1969. Procedures for detecting outlying observations in samples. Technometrics. 11:1-21.
-
(1969)
Technometrics
, vol.11
, pp. 1-21
-
-
Grubbs, F.E.1
-
71
-
-
2542599277
-
Φ-value analysis and the nature of protein folding transition states
-
Fersht, A. R., and S. Sato. 2004. Φ-value analysis and the nature of protein folding transition states. Proc. Natl. Acad. Sci. USA. 101:7976-7981.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 7976-7981
-
-
Fersht, A.R.1
Sato, S.2
-
72
-
-
33644541811
-
On the precision of experimentally determined protein folding rates and Φ-values
-
de los Rios, M. A., B. K. Muralidhara, D. Wildes, T. R. Sosnick, S. Marqusee, P. Wittung-Stafshede, K. W. Plaxco, and I. Ruczinski. 2006. On the precision of experimentally determined protein folding rates and Φ-values. Protein Sci. 15:553-563.
-
(2006)
Protein Sci
, vol.15
, pp. 553-563
-
-
de los1
Rios, M.A.2
Muralidhara, B.K.3
Wildes, D.4
Sosnick, T.R.5
Marqusee, S.6
Wittung-Stafshede, P.7
Plaxco, K.W.8
Ruczinski, I.9
-
73
-
-
33749322256
-
Methods for the accurate estimation of confidence intervals on protein folding Φ-values
-
Ruczinski, I., T. R. Sosnick, and K. W. Plaxco. 2006. Methods for the accurate estimation of confidence intervals on protein folding Φ-values. Protein Sci. 15:2257-2264.
-
(2006)
Protein Sci
, vol.15
, pp. 2257-2264
-
-
Ruczinski, I.1
Sosnick, T.R.2
Plaxco, K.W.3
-
74
-
-
0025398721
-
WHAT IF: A molecular modeling and drug design program
-
Vriend, G. 1990. WHAT IF: a molecular modeling and drug design program. J. Mol. Graph. 8:52-56.
-
(1990)
J. Mol. Graph
, vol.8
, pp. 52-56
-
-
Vriend, G.1
-
76
-
-
0030815133
-
Raster3D: Photorealistic molecular graphics
-
Merritt, E. A., and D. J. Bacon. 1997. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277:505-524.
-
(1997)
Methods Enzymol
, vol.277
, pp. 505-524
-
-
Merritt, E.A.1
Bacon, D.J.2
|