-
1
-
-
11844289547
-
Protein folding and the organization of the protein topology universe
-
Lindorff-Larsen, K., Rogen, P., Paci, E., Vendruscolo, M., and Dobson, C. M. (2005) Protein folding and the organization of the protein topology universe, Trends Biochem. Sci. 30, 13-19.
-
(2005)
Trends Biochem. Sci.
, vol.30
, pp. 13-19
-
-
Lindorff-Larsen, K.1
Rogen, P.2
Paci, E.3
Vendruscolo, M.4
Dobson, C.M.5
-
3
-
-
1342281633
-
The protein folding 'speed limit'
-
Kubelka, J., Hofrichter, J., and Eaton, W. A. (2004) The protein folding 'speed limit', Curr. Opin. Struct. Biol. 14, 76-88.
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, pp. 76-88
-
-
Kubelka, J.1
Hofrichter, J.2
Eaton, W.A.3
-
4
-
-
0034743155
-
From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding
-
Shea, J. E., and Brooks, C. L. (2001) From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding, Annu. Rev. Phys. Chem. 52, 499-535.
-
(2001)
Annu. Rev. Phys. Chem.
, vol.52
, pp. 499-535
-
-
Shea, J.E.1
Brooks, C.L.2
-
5
-
-
0037221599
-
Is there a unifying mechanism for protein folding?
-
Daggett, V., and Fersht, A. R. (2003) Is there a unifying mechanism for protein folding? Trends Biochem. Sci. 28, 18-25.
-
(2003)
Trends Biochem. Sci.
, vol.28
, pp. 18-25
-
-
Daggett, V.1
Fersht, A.R.2
-
6
-
-
0034383950
-
Protein folding: Progress made and promises ahead
-
Radford, S. E. (2000) Protein folding: progress made and promises ahead, Trends Biochem. Sci. 25, 611-618.
-
(2000)
Trends Biochem. Sci.
, vol.25
, pp. 611-618
-
-
Radford, S.E.1
-
7
-
-
0033624685
-
Fast kinetics and mechanisms in protein folding
-
Eaton, W. A., Munoz, V., Hagen, S. J., Jas, G. S., Lapidus, L. J., Henry, E. R., and Hofrichter, J. (2000) Fast kinetics and mechanisms in protein folding, Annu. Rev. Biophys. Biomol. Struct. 29, 327-359.
-
(2000)
Annu. Rev. Biophys. Biomol. Struct.
, vol.29
, pp. 327-359
-
-
Eaton, W.A.1
Munoz, V.2
Hagen, S.J.3
Jas, G.S.4
Lapidus, L.J.5
Henry, E.R.6
Hofrichter, J.7
-
8
-
-
0020024242
-
Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding
-
Kim, P. S., and Baldwin, R. L. (1982) Specific intermediates in the folding reactions of small proteins and the mechanism of protein folding, Annu. Rev. Biochem. 51, 459-489.
-
(1982)
Annu. Rev. Biochem.
, vol.51
, pp. 459-489
-
-
Kim, P.S.1
Baldwin, R.L.2
-
9
-
-
0016671420
-
Model of myoglobin self-organization
-
Ptitsyn, O. B., and Rashin, A. A. (1975) Model of myoglobin self-organization, Biophys. Chem. 3, 1-20.
-
(1975)
Biophys. Chem.
, vol.3
, pp. 1-20
-
-
Ptitsyn, O.B.1
Rashin, A.A.2
-
10
-
-
0028327236
-
Protein-folding dynamics - The diffusion-collision model and experimental-data
-
Karplus, M., and Weaver, D. L. (1994) Protein-folding dynamics - the diffusion-collision model and experimental-data, Protein Sci. 3, 650-668.
-
(1994)
Protein Sci.
, vol.3
, pp. 650-668
-
-
Karplus, M.1
Weaver, D.L.2
-
11
-
-
0025345415
-
Intermediates in the folding reactions of small proteins
-
Kim, P. S., and Baldwin, R. L. (1990) Intermediates in the folding reactions of small proteins, Annu. Rev. Biochem. 59, 631-660.
-
(1990)
Annu. Rev. Biochem.
, vol.59
, pp. 631-660
-
-
Kim, P.S.1
Baldwin, R.L.2
-
12
-
-
0008863560
-
Some factors in the interpretation of protein denaturation
-
Kauzmann, W. (1959) Some factors in the interpretation of protein denaturation, Adv. Protein Chem. 14, 1-63.
-
(1959)
Adv. Protein Chem.
, vol.14
, pp. 1-63
-
-
Kauzmann, W.1
-
13
-
-
0024391879
-
How does protein folding get started
-
Baldwin, R. L. (1989) How does protein folding get started, Trends Biochem. Sci. 14, 291-294.
-
(1989)
Trends Biochem. Sci.
, vol.14
, pp. 291-294
-
-
Baldwin, R.L.1
-
14
-
-
0014718113
-
Protein denaturation, Part C
-
Tanford, C. (1970) Protein denaturation, Part C, Adv. Protein Chem. 21, 1-95.
-
(1970)
Adv. Protein Chem.
, vol.21
, pp. 1-95
-
-
Tanford, C.1
-
15
-
-
0031043161
-
Nucleation mechanisms in protein folding
-
Fersht, A. R. (1997) Nucleation mechanisms in protein folding, Curr. Opin. Struct. Biol. 7, 3-9.
-
(1997)
Curr. Opin. Struct. Biol.
, vol.7
, pp. 3-9
-
-
Fersht, A.R.1
-
16
-
-
0036280655
-
Molecular dynamics simulations of the protein unfolding/folding reaction
-
Daggett, V. (2002) Molecular dynamics simulations of the protein unfolding/folding reaction, Acc. Chem. Res. 35, 422-429.
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 422-429
-
-
Daggett, V.1
-
17
-
-
0345255608
-
Unifying features in protein-folding mechanisms
-
Gianni, S., Guydosh, N. R., Khan, F., Caldas, T. D., Mayor, U., White, G. W. N., DeMarco, M. L., Daggett, V., and Fersht, A. R. (2003) Unifying features in protein-folding mechanisms, Proc. Natl. Acad. Sci. U.S.A. 100, 13286-13291.
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, 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
-
18
-
-
0030789351
-
Laser temperature jump study of the helix-coil kinetics of an alanine peptide interpretted as a 'kinetic zipper' model
-
Thompson, P. A., Eaton, W. A., and Hofrichter, J. (1997) Laser temperature jump study of the helix-coil kinetics of an alanine peptide interpretted as a 'kinetic zipper' model, Biochemistry 36, 9200-9210.
-
(1997)
Biochemistry
, vol.36
, pp. 9200-9210
-
-
Thompson, P.A.1
Eaton, W.A.2
Hofrichter, J.3
-
19
-
-
0030046906
-
Fast Events in Protein Folding: Helix Melting and Formation in a Small Peptide
-
Williams, S., Causgrove, T. P., Gilmanshin, R., Fang, K. S., Callender, R. H., Woodruff, W. H., and Dyer, R. B. (1996) Fast Events in Protein Folding: Helix Melting and Formation in a Small Peptide, Biochemistry 35, 691-697.
-
(1996)
Biochemistry
, vol.35
, pp. 691-697
-
-
Williams, S.1
Causgrove, T.P.2
Gilmanshin, R.3
Fang, K.S.4
Callender, R.H.5
Woodruff, W.H.6
Dyer, R.B.7
-
20
-
-
6344230036
-
Length dependent helix-coil transition kinetics of nine alanine-based peptides
-
Wang, T., Zhu, Y. J., Getahun, Z., Du, D. G., Huang, C. Y., DeGrado, W. F., and Gai, F. (2004) Length dependent helix-coil transition kinetics of nine alanine-based peptides, J. Phys. Chem. B 108, 15301-15310.
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 15301-15310
-
-
Wang, T.1
Zhu, Y.J.2
Getahun, Z.3
Du, D.G.4
Huang, C.Y.5
DeGrado, W.F.6
Gai, F.7
-
21
-
-
0037022567
-
Helix formation via conformation diffusion search
-
Huang, C.-Y., Getahun, Z., Zhu, Y., Klemke, J. W., DeGrado, W. F., and Gai, F. (2002) Helix formation via conformation diffusion search, Proc. Natl. Acad. Sci. U.S.A. 99, 2788-2793.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 2788-2793
-
-
Huang, C.-Y.1
Getahun, Z.2
Zhu, Y.3
Klemke, J.W.4
DeGrado, W.F.5
Gai, F.6
-
22
-
-
0026525048
-
Molecular dynamics simulations of helix denaturation
-
Daggett, V., and Levitt, M. (1992) Molecular dynamics simulations of helix denaturation, J. Mol. Biol. 223, 1121-1138.
-
(1992)
J. Mol. Biol.
, vol.223
, pp. 1121-1138
-
-
Daggett, V.1
Levitt, M.2
-
23
-
-
0037234367
-
Breaking non-native hydrophobic clusters is the rate-limiting step in the folding of an alanine-based peptide
-
Chowdhury, S., Zhang, W., Wu, C., Xiong, G., and Duan, Y. (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
-
24
-
-
0001767031
-
Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulation
-
Ferrara, P., Apostolakis, J., and Caflisch, A. (2000) Thermodynamics and kinetics of folding of two model peptides investigated by molecular dynamics simulation, 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
-
25
-
-
0037022662
-
Alpha-helical stabilisation by side chain shielding of backbone hydrogen bonds
-
Garcia, A. E., and Sanbonmatsu, K. Y. (2002) Alpha-helical stabilisation by side chain shielding of backbone hydrogen bonds, Proc. Natl. Acad. Sci. U.S.A. 99, 2782-2787.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 2782-2787
-
-
Garcia, A.E.1
Sanbonmatsu, K.Y.2
-
26
-
-
18844361915
-
Helix-coil transition of alanine peptides in water: Force field dependence on the folded and unfolded structures
-
Gnanakaran, S., and Garcia, A. E. (2005) Helix-coil transition of alanine peptides in water: Force field dependence on the folded and unfolded structures, Proteins 59, 773-782.
-
(2005)
Proteins
, vol.59
, pp. 773-782
-
-
Gnanakaran, S.1
Garcia, A.E.2
-
27
-
-
18744415073
-
Simulations of the pressure and temperature unfolding of an alpha-helical peptide
-
Paschek, D., Gnanakaran, S., and Garcia, A. E. (2005) Simulations of the pressure and temperature unfolding of an alpha-helical peptide, Proc. Natl. Acad. Sci. U.S.A. 102, 6754-6770.
-
(2005)
Proc. Natl. Acad. Sci. U.S.A.
, vol.102
, pp. 6754-6770
-
-
Paschek, D.1
Gnanakaran, S.2
Garcia, A.E.3
-
28
-
-
0344702698
-
Simulation of the folding equilibrium of alpha-helical peptides: A comparison of the generalized Born approximation with explicit solvent
-
Nymeyer, H., and Garcia, A. E. (2003) Simulation of the folding equilibrium of alpha-helical peptides: A comparison of the generalized Born approximation with explicit solvent, Proc. Natl. Acad. Sci. U.S.A. 100, 13934-13939.
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 13934-13939
-
-
Nymeyer, H.1
Garcia, A.E.2
-
29
-
-
20544435097
-
Exploring the helix-coil transition via all-atom equibrium ensemble simulations
-
Sorin, E. J., and Pande, V. S. (2005) Exploring the helix-coil transition via all-atom equibrium ensemble simulations, Biophys. J. 88, 2472-2493.
-
(2005)
Biophys. J.
, vol.88
, pp. 2472-2493
-
-
Sorin, E.J.1
Pande, V.S.2
-
30
-
-
0031472252
-
Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: Description of the folding pathway
-
Bond, C. J., Wong, K. B., Clarke, J., Fersht, A. R., and Daggett, V. (1997) Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: Description of the folding pathway, Proc. Natl. Acad. Sci. U.S.A. 94, 13409-13413.
-
(1997)
Proc. Natl. Acad. Sci. U.S.A.
, vol.94
, pp. 13409-13413
-
-
Bond, C.J.1
Wong, K.B.2
Clarke, J.3
Fersht, A.R.4
Daggett, V.5
-
31
-
-
0034628913
-
Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding
-
Wong, K. B., Clarke, J., Bond, C. J., Neira, J. L., Freund, S. M. V., Fersht, A. R., and Daggett, V. (2000) Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding, J. Mol. Biol. 296, 1257-1282.
-
(2000)
J. Mol. Biol.
, vol.296
, pp. 1257-1282
-
-
Wong, K.B.1
Clarke, J.2
Bond, C.J.3
Neira, J.L.4
Freund, S.M.V.5
Fersht, A.R.6
Daggett, V.7
-
32
-
-
0034602807
-
Staphylococcal protein A: Unfolding pathways, unfolded states, and differences between the B and E domains
-
Alonso, D. O. V., and Daggett, V. (2000) Staphylococcal protein A: Unfolding pathways, unfolded states, and differences between the B and E domains, Proc. Natl. Acad. Sci. U.S.A. 97, 133-138.
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 133-138
-
-
Alonso, D.O.V.1
Daggett, V.2
-
33
-
-
0026550397
-
The folding of an enzyme 4. Structure of an intermediate in the refolding of barnase analyzed by a protein engineering procedure
-
Matouschek, A., Serrano, L., and Fersht, A. R. (1992) The folding of an enzyme 4. Structure of an intermediate in the refolding of barnase analyzed by a protein engineering procedure, J. Mol. Biol. 224, 819-835.
-
(1992)
J. Mol. Biol.
, vol.224
, pp. 819-835
-
-
Matouschek, A.1
Serrano, L.2
Fersht, A.R.3
-
34
-
-
0028168139
-
Extrapolation to water of kinetic and equilibrium data for the unfolding of barnase in urea solutions
-
Matouschek, A., Matthews, J. M., Johnson, C. M., and Fersht, A. R. (1994) Extrapolation to water of kinetic and equilibrium data for the unfolding of barnase in urea solutions, Protein Eng. 7, 1089-1095.
-
(1994)
Protein Eng.
, vol.7
, pp. 1089-1095
-
-
Matouschek, A.1
Matthews, J.M.2
Johnson, C.M.3
Fersht, A.R.4
-
35
-
-
0026579572
-
The folding of an enzyme 3. Structure of the transition-state for unfolding of barnase analyzed by a protein engineering procedure
-
Serrano, L., Matouschek, A., and Fersht, A. R. (1992) The folding of an enzyme 3. Structure of the transition-state for unfolding of barnase analyzed by a protein engineering procedure, J. Mol. Biol. 224, 805-818.
-
(1992)
J. Mol. Biol.
, vol.224
, pp. 805-818
-
-
Serrano, L.1
Matouschek, A.2
Fersht, A.R.3
-
36
-
-
0027163998
-
Protein-folding and stability - The pathway of folding of Barnase
-
Fersht, A. R. (1993) Protein-folding and stability - the pathway of folding of Barnase, FEBS Lett. 325, 5-16.
-
(1993)
FEBS Lett.
, vol.325
, pp. 5-16
-
-
Fersht, A.R.1
-
37
-
-
0028806684
-
A Comparison of the pH, urea, and temperature-denatured states of barnase by heteronuclear NMR - Implications for the initiation of protein-folding
-
Arcus, V. L., Vuilleumier, S., Freund, S. M. V., Bycroff, M., and Fersht, A. R. (1995) A Comparison of the pH, urea, and temperature-denatured states of barnase by heteronuclear NMR - Implications for the initiation of protein-folding, J. Mol. Biol. 254, 305-321.
-
(1995)
J. Mol. Biol.
, vol.254
, pp. 305-321
-
-
Arcus, V.L.1
Vuilleumier, S.2
Freund, S.M.V.3
Bycroff, M.4
Fersht, A.R.5
-
38
-
-
0141457507
-
The kinetic pathway of folding of barnase
-
Khan, F., Chuang, J. I., Gianni, S., and Fersht, A. R. (2003) The kinetic pathway of folding of barnase, J. Mol. Biol. 333, 169-186.
-
(2003)
J. Mol. Biol.
, vol.333
, pp. 169-186
-
-
Khan, F.1
Chuang, J.I.2
Gianni, S.3
Fersht, A.R.4
-
39
-
-
0033134665
-
Structural details of urea binding to barnase: A molecular dynamics analysis
-
Caflisch, A., and Karplus, M. (1999) Structural details of urea binding to barnase: a molecular dynamics analysis, Struct. Fold. Des. 7, 477-488.
-
(1999)
Struct. Fold. Des.
, vol.7
, pp. 477-488
-
-
Caflisch, A.1
Karplus, M.2
-
40
-
-
0029124153
-
Acid and thermal-denaturation of barnase investigated by molecular-dynamics simulations
-
Caflisch, A., and Karplus, M. (1995) Acid and thermal-denaturation of barnase investigated by molecular-dynamics simulations, J. Mol. Biol. 252, 672-708.
-
(1995)
J. Mol. Biol.
, vol.252
, pp. 672-708
-
-
Caflisch, A.1
Karplus, M.2
-
41
-
-
0028264860
-
Molecular-dynamics simulation of protein denaturation - Solvation of the hydrophobic cores and secondary structure of barnase
-
Caflisch, A., and Karplus, M. (1994) Molecular-dynamics simulation of protein denaturation - solvation of the hydrophobic cores and secondary structure of barnase, Proc. Natl. Acad. Sci. U.S.A. 91, 1746-1750.
-
(1994)
Proc. Natl. Acad. Sci. U.S.A.
, vol.91
, pp. 1746-1750
-
-
Caflisch, A.1
Karplus, M.2
-
42
-
-
0030939289
-
Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea
-
TiradoRives, J., Orozco, M., and Jorgensen, W. L. (1997) Molecular dynamics simulations of the unfolding of barnase in water and 8 M aqueous urea, Biochemistry 36, 7313-7329.
-
(1997)
Biochemistry
, vol.36
, pp. 7313-7329
-
-
TiradoRives, J.1
Orozco, M.2
Jorgensen, W.L.3
-
43
-
-
0032579189
-
Molecular dynamics simulation of the unfolding of barnase: Characterization of the major intermediate
-
Li, A. J., and Daggett, V. (1998) Molecular dynamics simulation of the unfolding of barnase: Characterization of the major intermediate, J. Mol. Biol. 275, 677-694.
-
(1998)
J. Mol. Biol.
, vol.275
, pp. 677-694
-
-
Li, A.J.1
Daggett, V.2
-
44
-
-
0032539209
-
Combined molecular dynamics and phi value analysis of structure-reactivity relationships in the transition state and unfolding pathway of barnase: Structural basis of Hammond and anti-Hammond effects
-
Daggett, V., Li, A., and Fersht, A. R. (1998) Combined molecular dynamics and phi value analysis of structure-reactivity relationships in the transition state and unfolding pathway of barnase: Structural basis of Hammond and anti-Hammond effects, J. Am. Chem. Soc. 120, 12740-12754.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 12740-12754
-
-
Daggett, V.1
Li, A.2
Fersht, A.R.3
-
45
-
-
0031717907
-
A study of the interactions between an IgG-binding domain based on the B domain of staphylococcal protein A and rabbit IgC
-
Brown, N. L., Bottomley, S. P., Scawen, M. D., and Gore, M. G. (1998) A study of the interactions between an IgG-binding domain based on the B domain of staphylococcal protein A and rabbit IgC, Mol. Biotechnol. 10, 9-16.
-
(1998)
Mol. Biotechnol.
, vol.10
, pp. 9-16
-
-
Brown, N.L.1
Bottomley, S.P.2
Scawen, M.D.3
Gore, M.G.4
-
46
-
-
0017673298
-
Interaction of protein-A and Fc-fragment of rabbit immunoglobulin-G as probed by complement-fixation and NMR-studies
-
Wright, C., Willan, K. J., Sjodahl, J., Burton, D. R., and Dwek, R. A. (1977) Interaction of protein-A and Fc-fragment of rabbit immunoglobulin-G as probed by complement-fixation and NMR-studies, Biochem. J. 167, 661-668.
-
(1977)
Biochem. J.
, vol.167
, pp. 661-668
-
-
Wright, C.1
Willan, K.J.2
Sjodahl, J.3
Burton, D.R.4
Dwek, R.A.5
-
47
-
-
2342525803
-
Latest folding game results: Protein A barely frustrates computationalists
-
Wolynes, P. G. (2004) Latest folding game results: Protein A barely frustrates computationalists, Proc. Natl. Acad. Sci. U.S.A. 101, 6837-6838.
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 6837-6838
-
-
Wolynes, P.G.1
-
48
-
-
0036678831
-
An atomically detailed study of the folding pathways of protein A with the stochastic difference equation
-
Ghosh, A., Elber, R., and Scheraga, H. A. (2002) An atomically detailed study of the folding pathways of protein A with the stochastic difference equation, Proc. Natl. Acad. Sci. U.S.A. 99, 10394-10398.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 10394-10398
-
-
Ghosh, A.1
Elber, R.2
Scheraga, H.A.3
-
49
-
-
0345133287
-
Folding a protein in a computer: An atomic description of the folding/unfolding of protein A
-
Garcia, A. E., and Onuchic, J. N. (2003) Folding a protein in a computer: An atomic description of the folding/unfolding of protein A, Proc. Natl. Acad. Sci. U.S.A. 100, 13898-13903.
-
(2003)
Proc. Natl. Acad. Sci. U.S.A.
, vol.100
, pp. 13898-13903
-
-
Garcia, A.E.1
Onuchic, J.N.2
-
50
-
-
0028608099
-
The stability and unfolding of an Igg binding-protein based upon the B-domain of protein-A from Staphylococcus-aureus probed by tryptophan substitution and fluorescence spectroscopy
-
Bottomley, S. P., Popplewell, A. G., Scawen, M., Wan, T., Sutton, B. J., and Gore, M. G. (1994) The stability and unfolding of an Igg binding-protein based upon the B-domain of protein-A from Staphylococcus-aureus probed by tryptophan substitution and fluorescence spectroscopy, Protein Eng. 7, 1463-1470.
-
(1994)
Protein Eng.
, vol.7
, pp. 1463-1470
-
-
Bottomley, S.P.1
Popplewell, A.G.2
Scawen, M.3
Wan, T.4
Sutton, B.J.5
Gore, M.G.6
-
51
-
-
0030755502
-
Absence of a stable intermediate on the folding pathway of protein A
-
Bai, Y. W., Karimi, A., Dyson, H. J., and Wright, P. E. (1997) Absence of a stable intermediate on the folding pathway of protein A, Protein Sci. 6, 1449-1457.
-
(1997)
Protein Sci.
, vol.6
, pp. 1449-1457
-
-
Bai, Y.W.1
Karimi, A.2
Dyson, H.J.3
Wright, P.E.4
-
52
-
-
0029151245
-
First-principles calculation of the folding free-energy of a 3-helix bundle protein
-
Boczko, E. M., and Brooks, C. L. (1995) First-principles calculation of the folding free-energy of a 3-helix bundle protein, Science 269, 393-396.
-
(1995)
Science
, vol.269
, pp. 393-396
-
-
Boczko, E.M.1
Brooks, C.L.2
-
53
-
-
0030967896
-
Exploring the folding free energy surface of a three-helix bundle protein
-
Guo, Z. Y., Brooks, C. L., and Boczko, E. M. (1997) Exploring the folding free energy surface of a three-helix bundle protein, Proc. Natl. Acad. Sci. U.S.A. 94, 10161-10166.
-
(1997)
Proc. Natl. Acad. Sci. U.S.A.
, vol.94
, pp. 10161-10166
-
-
Guo, Z.Y.1
Brooks, C.L.2
Boczko, E.M.3
-
54
-
-
0031475159
-
Folding thermodynamics of a model three-helix-bundle protein
-
Zhou, Y. Q., and Karplus, M. (1997) Folding thermodynamics of a model three-helix-bundle protein, Proc. Natl. Acad. Sci. U.S.A. 94, 14429-14432.
-
(1997)
Proc. Natl. Acad. Sci. U.S.A.
, vol.94
, pp. 14429-14432
-
-
Zhou, Y.Q.1
Karplus, M.2
-
55
-
-
2342449128
-
Testing protein-folding simulations by experiment: B domain of protein A
-
Sato, S., Religa, T. L., Daggett, V., and Fersht, A. R. (2004) Testing protein-folding simulations by experiment: B domain of protein A, Proc. Natl. Acad. Sci. U.S.A. 101, 6952-6956.
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 6952-6956
-
-
Sato, S.1
Religa, T.L.2
Daggett, V.3
Fersht, A.R.4
-
56
-
-
0029906640
-
Solution structure of the E-domain of staphylococcal protein A
-
Starovasnik, M. A., Skelton, N. J., Oconnell, M. P., Kelley, R. F., Reilly, D., and Fairbrother, W. J. (1996) Solution structure of the E-domain of staphylococcal protein A, Biochemistry 35, 15558-15569.
-
(1996)
Biochemistry
, vol.35
, pp. 15558-15569
-
-
Starovasnik, M.A.1
Skelton, N.J.2
Oconnell, M.P.3
Kelley, R.F.4
Reilly, D.5
Fairbrother, W.J.6
-
57
-
-
0026044754
-
Determination of the three-dimensional solution structure of barnase using nuclear magnetic resonance spectroscopy
-
Bycroft, M., Ludvigsen, S., Fersht, A. R., and Poulsen, F. M. (1991) Determination of the three-dimensional solution structure of barnase using nuclear magnetic resonance spectroscopy, Biochemistry 30, 8697-8701.
-
(1991)
Biochemistry
, vol.30
, pp. 8697-8701
-
-
Bycroft, M.1
Ludvigsen, S.2
Fersht, A.R.3
Poulsen, F.M.4
-
58
-
-
0029633167
-
Potential-energy function and parameters for simulations of the molecular-dynamics of proteins and nucleic-acids in solution
-
Levitt, M., Hirshberg, M., Sharon, R., and Daggett, V. (1995) Potential-energy function and parameters for simulations of the molecular-dynamics of proteins and nucleic-acids in solution, Comput. Phys. Commun. 91, 215-231.
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 215-231
-
-
Levitt, M.1
Hirshberg, M.2
Sharon, R.3
Daggett, V.4
-
59
-
-
0000125216
-
Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution
-
Levitt, M., Hirshberg, M., Sharon, R., Laidig, K. E., and Daggett, V. (1997) Calibration and testing of a water model for simulation of the molecular dynamics of proteins and nucleic acids in solution, J. Phys. Chem. B 101, 5051-5061.
-
(1997)
J. Phys. Chem. B
, vol.101
, pp. 5051-5061
-
-
Levitt, M.1
Hirshberg, M.2
Sharon, R.3
Laidig, K.E.4
Daggett, V.5
-
60
-
-
0003661377
-
-
Hemisphere Publishing Corp.: Washington, DC
-
Haar, L., Gallagher, J. S., and Kell, G. S. (1984) NBS/NRC Steam Tables: Thermodynamic and Transport Properties and Computer Programs for Vapor and Liquid States of Water in SI Units, pp 271-276, Hemisphere Publishing Corp.: Washington, DC.
-
(1984)
NBS/NRC Steam Tables: Thermodynamic and Transport Properties and Computer Programs for Vapor and Liquid States of Water in SI Units
, pp. 271-276
-
-
Haar, L.1
Gallagher, J.S.2
Kell, G.S.3
-
61
-
-
0009979659
-
Precise representation of volume properties of water at one atmosphere
-
Kell, G. S. (1967) Precise representation of volume properties of water at one atmosphere, J. Chem. Eng. Data 12, 66-69.
-
(1967)
J. Chem. Eng. Data
, vol.12
, pp. 66-69
-
-
Kell, G.S.1
-
62
-
-
4444221565
-
UCSF chimera - A visualization system for exploratory research and analysis
-
Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., and Ferrin, T. E. (2004) UCSF chimera - A visualization system for exploratory research and analysis, J. Comput. Chem. 25, 1605-1612.
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
63
-
-
0031808074
-
A helix propensity scale based on experimental studies of peptides and proteins
-
Pace, C. N., and Scholtz, J. M. (1998) A helix propensity scale based on experimental studies of peptides and proteins, Biophys. J. 75, 422-427.
-
(1998)
Biophys. J.
, vol.75
, pp. 422-427
-
-
Pace, C.N.1
Scholtz, J.M.2
-
64
-
-
0028222235
-
Helix propensities of the amino-acids measured in alanine-based peptides without helix-stabilizing side-chain interactions
-
Chakrabartty, A., Kortemme, T., and Baldwin, R. L. (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
-
65
-
-
0034649410
-
Transitions from alpha to pi helix observed in molecular dynamics simulations of synthetic peptides
-
Lee, K. H., Benson, D. R., and Kuczera, K. (2000) Transitions from alpha to pi helix observed in molecular dynamics simulations of synthetic peptides, Biochemistry 39, 13737-13747.
-
(2000)
Biochemistry
, vol.39
, pp. 13737-13747
-
-
Lee, K.H.1
Benson, D.R.2
Kuczera, K.3
-
66
-
-
0038245156
-
The role of alpha-, 3(10)-, and pi-helix in helix → coil transitions
-
Armen, R., Alonso, D. O. V., and Daggett, V. (2003) The role of alpha-, 3(10)-, and pi-helix in helix → coil transitions, Protein Sci. 12, 1145-1157.
-
(2003)
Protein Sci.
, vol.12
, pp. 1145-1157
-
-
Armen, R.1
Alonso, D.O.V.2
Daggett, V.3
-
67
-
-
0031564662
-
Estimating the relative populations of 3(10)-helix and alpha-helix in Ala-rich peptides: A hydrogen exchange and high field NMR study
-
Millhauser, G. L., Stenland, C. J., Hanson, P., Bolin, K. A., and vandeVen, F. J. M. (1997) Estimating the relative populations of 3(10)-helix and alpha-helix in Ala-rich peptides: A hydrogen exchange and high field NMR study, J. Mol. Biol. 267, 963-974.
-
(1997)
J. Mol. Biol.
, vol.267
, pp. 963-974
-
-
Millhauser, G.L.1
Stenland, C.J.2
Hanson, P.3
Bolin, K.A.4
VandeVen, F.J.M.5
-
68
-
-
0038054912
-
Force field influence on the observation of pi-helical protein structures in molecular dynamics simulations
-
Feig, M., MacKerell, A. D., and Brooks, C. L. (2003) Force field influence on the observation of pi-helical protein structures in molecular dynamics simulations, J. Phys. Chem. B 107, 2831-2836.
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 2831-2836
-
-
Feig, M.1
MacKerell, A.D.2
Brooks, C.L.3
-
69
-
-
0000180763
-
Temperature-dependence of the hydrophobic interaction in protein folding
-
Baldwin, R. L. (1986) Temperature-dependence of the hydrophobic interaction in protein folding, Proc. Natl. Acad. Sci. U.S.A. 83, 8069-8072.
-
(1986)
Proc. Natl. Acad. Sci. U.S.A.
, vol.83
, pp. 8069-8072
-
-
Baldwin, R.L.1
-
70
-
-
0025253106
-
Relative helix-forming tendencies of nonpolar amino-acids
-
Padmanabhan, S., Marqusee, S., Ridgeway, T., Laue, T. M., and Baldwin, R. L. (1990) Relative helix-forming tendencies of nonpolar amino-acids. Nature 344, 268-270.
-
(1990)
Nature
, vol.344
, pp. 268-270
-
-
Padmanabhan, S.1
Marqusee, S.2
Ridgeway, T.3
Laue, T.M.4
Baldwin, R.L.5
-
71
-
-
0037456298
-
The complete folding pathway of a protein from nanoseconds to microseconds
-
Mayor, U., Guydosh, N. R., Johnson, C. M., Grossmann, J. G., Sato, S., Jas, G. S., Freund, S. M. V., Alonso, D. O. V., Daggett, V., and Fersht, A. R. (2003) The complete folding pathway of a protein from nanoseconds to microseconds, Nature 421, 863-867.
-
(2003)
Nature
, vol.421
, pp. 863-867
-
-
Mayor, U.1
Guydosh, N.R.2
Johnson, C.M.3
Grossmann, J.G.4
Sato, S.5
Jas, G.S.6
Freund, S.M.V.7
Alonso, D.O.V.8
Daggett, V.9
Fersht, A.R.10
-
72
-
-
0034610360
-
Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation
-
Mayor, U., Johnson, C. M., Daggett, V., and Fersht, A. R. (2000) Protein folding and unfolding in microseconds to nanoseconds by experiment and simulation, Proc. Natl. Acad. Sci. U.S.A. 97, 13518-13522.
-
(2000)
Proc. Natl. Acad. Sci. U.S.A.
, vol.97
, pp. 13518-13522
-
-
Mayor, U.1
Johnson, C.M.2
Daggett, V.3
Fersht, A.R.4
-
73
-
-
20544462511
-
Simulation and experiment conspire to reveal cryptic intermediates and a slide from the nucleation-condensation to framework mechanism of folding
-
White, G. W. N., Gianni, S., Grossmann, J. G., Jemth, P., Fersht, A. R., and Daggett, V. (2005) Simulation and experiment conspire to reveal cryptic intermediates and a slide from the nucleation-condensation to framework mechanism of folding, J. Mol. Biol. 350, 757-775.
-
(2005)
J. Mol. Biol.
, vol.350
, pp. 757-775
-
-
White, G.W.N.1
Gianni, S.2
Grossmann, J.G.3
Jemth, P.4
Fersht, A.R.5
Daggett, V.6
-
74
-
-
0020997912
-
Dictionary of protein secondary structure-pattern-recognition of hydrogen-bonded and geometrical features
-
Kabsch, W., and Sander, C. (1983) Dictionary of protein secondary structure-pattern-recognition of hydrogen-bonded and geometrical features, Biopolymers 22, 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
|