-
1
-
-
0028024928
-
Specific nucleus as the transition state for protein folding: Evidence from the lattice model
-
Abkevich, V.I., Gutin, A.M., and Shakhnovich, E.I. 1994. Specific nucleus as the transition state for protein folding: Evidence from the lattice model. Biochemistry 22: 10026-10036.
-
(1994)
Biochemistry
, vol.22
, pp. 10026-10036
-
-
Abkevich, V.I.1
Gutin, A.M.2
Shakhnovich, E.I.3
-
2
-
-
0027441950
-
Essential dynamics of proteins
-
Amadei, A., Linssen, A.B.M., and Berendsen, H.J.C. 1993. Essential dynamics of proteins. Proteins 17: 412-425.
-
(1993)
Proteins
, vol.17
, pp. 412-425
-
-
Amadei, A.1
Linssen, A.B.M.2
Berendsen, H.J.C.3
-
3
-
-
0032972986
-
Is protein folding hierarchic? I: Local structure and peptide folding
-
Baldwin, R.L. and Rose, G.D. 1999. Is protein folding hierarchic? I: Local structure and peptide folding. Trends Biochem. Sci. 24: 26-33.
-
(1999)
Trends Biochem. Sci.
, vol.24
, pp. 26-33
-
-
Baldwin, R.L.1
Rose, G.D.2
-
4
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H.J.C., Postma, J.P.M., van Gunsteren, W.F., Di Nola, A., and Haak, J.R. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81: 3684.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Di Nola, A.4
Haak, J.R.5
-
5
-
-
1242346370
-
The missing term in effective pair potentials
-
Berendsen, H.J.C., Grigera, J.R., and Straatsma, T.P. 1987. The missing term in effective pair potentials. J. Phys. Chem. 91: 6269-6271.
-
(1987)
J. Phys. Chem.
, vol.91
, pp. 6269-6271
-
-
Berendsen, H.J.C.1
Grigera, J.R.2
Straatsma, T.P.3
-
6
-
-
0036674529
-
Loop fold structure of proteins: Resolution of Levinthal's paradox
-
Berezovsky, I.N. and Trifonov, E.N. 2002. Loop fold structure of proteins: Resolution of Levinthal's paradox. J. Biomol. Struct. Dyn. 20: 5-6.
-
(2002)
J. Biomol. Struct. Dyn.
, vol.20
, pp. 5-6
-
-
Berezovsky, I.N.1
Trifonov, E.N.2
-
7
-
-
0035576125
-
Protein folding: Looping from hydrophobic nuclei
-
Berezovsky, I.N., Kirzhner, V.M., Kirzhner, A., and Trifonov, E.N. 2001. Protein folding: Looping from hydrophobic nuclei. Proteins 45: 346-350.
-
(2001)
Proteins
, vol.45
, pp. 346-350
-
-
Berezovsky, I.N.1
Kirzhner, V.M.2
Kirzhner, A.3
Trifonov, E.N.4
-
8
-
-
0035576097
-
Reading the three-dimensional structure of a protein from its amino acid sequence
-
Broglia, R.A. and Tiana, G. 2001. Reading the three-dimensional structure of a protein from its amino acid sequence. Proteins 45: 421-427.
-
(2001)
Proteins
, vol.45
, pp. 421-427
-
-
Broglia, R.A.1
Tiana, G.2
-
9
-
-
0026044754
-
Determination of the 3-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 3-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
-
10
-
-
0025906282
-
Polymer principles in protein structure and stability
-
Chan, H.S. and Dill, K. 1991. Polymer principles in protein structure and stability. Annu. Rev. Biophys. Biophys. Chem. 20: 447-490.
-
(1991)
Annu. Rev. Biophys. Biophys. Chem.
, vol.20
, pp. 447-490
-
-
Chan, H.S.1
Dill, K.2
-
11
-
-
0033612756
-
Stability and activity of mesophilic subtilisin e and its thermophilic homolog: Insights from molecular dynamics simulations
-
Colombo, G. and Merz Jr., K.M. 1999. Stability and activity of mesophilic subtilisin e and its thermophilic homolog: Insights from molecular dynamics simulations. J. Am. Chem. Soc. 121: 6895-6903.
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 6895-6903
-
-
Colombo, G.1
Merz Jr., K.M.2
-
12
-
-
0030793767
-
De novo protein design: Fully automated sequence selection
-
Dahiyat, B.I. and Mayo, S.L. 1997. De novo protein design: Fully automated sequence selection. Science 278: 82-87.
-
(1997)
Science
, vol.278
, pp. 82-87
-
-
Dahiyat, B.I.1
Mayo, S.L.2
-
13
-
-
0032584783
-
Reversible peptide folding in solution by molecular dynamics simulation
-
Daura, X., Jaun, B., Seebach, D., van Gunsteren, W.F., and Mark, A.E. 1998. Reversible peptide folding in solution by molecular dynamics simulation. J. Mol. Biol. 280: 925-932.
-
(1998)
J. Mol. Biol.
, vol.280
, pp. 925-932
-
-
Daura, X.1
Jaun, B.2
Seebach, D.3
Van Gunsteren, W.F.4
Mark, A.E.5
-
14
-
-
0034718553
-
Folding simulations of a three-stranded antiparallel β-sheet peptide
-
Ferrara, P. and Caflisch, A. 2000. Folding simulations of a three-stranded antiparallel β-sheet peptide. Proc. Natl. Acad. Sci. 97: 10780-10785.
-
(2000)
Proc. Natl. Acad. Sci.
, vol.97
, pp. 10780-10785
-
-
Ferrara, P.1
Caflisch, A.2
-
16
-
-
0002237761
-
Biomolecules: Where the physics of complexity and simplicity meet
-
Frauenfelder, H. and Wolynes, P.G. 1994. Biomolecules: Where the physics of complexity and simplicity meet. Physics Today 47: 58-64.
-
(1994)
Physics Today
, vol.47
, pp. 58-64
-
-
Frauenfelder, H.1
Wolynes, P.G.2
-
17
-
-
0023746244
-
Conformational sub-states in proteins
-
Frauenfelder, H., Parak, F., and Young, R.D. 1988. Conformational sub-states in proteins. Annu. Rev. Biophys. Biophys. Chem. 17: 451-479.
-
(1988)
Annu. Rev. Biophys. Biophys. Chem.
, vol.17
, pp. 451-479
-
-
Frauenfelder, H.1
Parak, F.2
Young, R.D.3
-
18
-
-
0029558960
-
Conformational pathway of the polypeptide chain of chymotrypsin inhibitor 2 growing from its N-terminus in vitro parallels with the protein folding pathway
-
Gay, G.D., Ruisanz, J., Neira, J.L., Corrales, F.J., Otzen, D.E., Ladurner, A.G., and Fersht, A.R. 1995a. Conformational pathway of the polypeptide chain of chymotrypsin inhibitor 2 growing from its N-terminus in vitro parallels with the protein folding pathway. J. Mol. Biol. 254: 968-979.
-
(1995)
J. Mol. Biol.
, vol.254
, pp. 968-979
-
-
Gay, G.D.1
Ruisanz, J.2
Neira, J.L.3
Corrales, F.J.4
Otzen, D.E.5
Ladurner, A.G.6
Fersht, A.R.7
-
19
-
-
0029053552
-
Folding of a nascent polypeptide chain in vitro, cooperative formation of structure in a protein module
-
Gay, G.D., Ruizsanz, J., Neira, J.L., Itzhaki, L.S., and Fersht, A.R. 1995b. Folding of a nascent polypeptide chain in vitro, cooperative formation of structure in a protein module. Proc. Natl. Acad. Sci. 92: 3683-3686.
-
(1995)
Proc. Natl. Acad. Sci.
, vol.92
, pp. 3683-3686
-
-
Gay, G.D.1
Ruizsanz, J.2
Neira, J.L.3
Itzhaki, L.S.4
Fersht, A.R.5
-
20
-
-
0016812958
-
Theory of reversible denaturation of globular proteins
-
Go, N. 1975. Theory of reversible denaturation of globular proteins. Int. J. Pept. Protein Res. 7: 313-323.
-
(1975)
Int. J. Pept. Protein Res.
, vol.7
, pp. 313-323
-
-
Go, N.1
-
21
-
-
0031853167
-
Important role of hydrogen bonds in the structurally polarized transition state for folding of the src sh3 domain
-
Grantcharova, V., Riddle, D.S., Santiago, J.V., and Baker, D. 1998. Important role of hydrogen bonds in the structurally polarized transition state for folding of the src sh3 domain. Nat. Struct. Biol. 5: 714-720.
-
(1998)
Nat. Struct. Biol.
, vol.5
, pp. 714-720
-
-
Grantcharova, V.1
Riddle, D.S.2
Santiago, J.V.3
Baker, D.4
-
22
-
-
0000388705
-
A linear constraint solver for molecular simulations
-
Hess, B., Bekker, H., Fraaije, J.G.E.M., and Berendsen, H.J.C. 1997. A linear constraint solver for molecular simulations. J. Comp. Chem. 18: 1463-1472.
-
(1997)
J. Comp. Chem.
, vol.18
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Fraaije, J.G.E.M.3
Berendsen, H.J.C.4
-
23
-
-
0027382315
-
Structure of the hydrophobic core in the transition state for folding of chymotrypsin inhibitor 2: A critical test of the protein engineering method of analysis
-
Jackson, S.E., elMasry, N., and Fersht, A.R. 1993. Structure of the hydrophobic core in the transition state for folding of chymotrypsin inhibitor 2: A critical test of the protein engineering method of analysis. Biochemistry 32: 11270-11278.
-
(1993)
Biochemistry
, vol.32
, pp. 11270-11278
-
-
Jackson, S.E.1
ElMasry, N.2
Fersht, A.R.3
-
24
-
-
0347282626
-
Protein folding from a highly disordered denatured state: The folding pathway of chymotrypsin inhibitor 2 at atomic resolution
-
Kazmirski, S.L., Wong, K.B., Freund, S.F., Tan, Y.J., Fersht, A.R., and Daggett, V. 1995. Protein folding from a highly disordered denatured state: The folding pathway of chymotrypsin inhibitor 2 at atomic resolution. J. Mol. Biol. 254: 968-979.
-
(1995)
J. Mol. Biol.
, vol.254
, pp. 968-979
-
-
Kazmirski, S.L.1
Wong, K.B.2
Freund, S.F.3
Tan, Y.J.4
Fersht, A.R.5
Daggett, V.6
-
25
-
-
0034685619
-
A breakdown of symmetry in the folding transition state of protein 1
-
Kim, D.E., Fisher, C., and Baker, D. 2000. A breakdown of symmetry in the folding transition state of protein 1. 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
-
26
-
-
0035830250
-
Dynamics of hierarchical folding on energy landscape of hexapeptides
-
Levy, Y., Jortner, J., and Becker, O.M. 2001. Dynamics of hierarchical folding on energy landscape of hexapeptides. J. Chem. Phys. 115: 10533-10547.
-
(2001)
J. Chem. Phys.
, vol.115
, pp. 10533-10547
-
-
Levy, Y.1
Jortner, J.2
Becker, O.M.3
-
27
-
-
0028143603
-
Characterization of the transition state of protein unfolding by use of molecular dynamics: Chymotrypsin inhibitor 2
-
Li, A. and Daggett, V. 1994. Characterization of the transition state of protein unfolding by use of molecular dynamics: Chymotrypsin inhibitor 2. Proc. Natl. Acad. Sci. 91: 10430-10434.
-
(1994)
Proc. Natl. Acad. Sci.
, vol.91
, pp. 10430-10434
-
-
Li, A.1
Daggett, V.2
-
28
-
-
0033834791
-
Directed evolution of an enantioselective lipase
-
Liebeton, K., Zonta, A., Schimossek, K., Nardini, M., Lang, D., Dijkstra, B.W., and Jaeger, K.E. 2000. Directed evolution of an enantioselective lipase. Chem. Biol. 7: 709-718.
-
(2000)
Chem. Biol.
, vol.7
, pp. 709-718
-
-
Liebeton, K.1
Zonta, A.2
Schimossek, K.3
Nardini, M.4
Lang, D.5
Dijkstra, B.W.6
Jaeger, K.E.7
-
29
-
-
0031825181
-
Obligatory steps in protein folding and the conformational diversity of the transition state
-
Martinez, J., Pisabarro, M., and Serrano, L. 1998. Obligatory steps in protein folding and the conformational diversity of the transition state. Nat. Struct. Biol. 5: 721-729.
-
(1998)
Nat. Struct. Biol.
, vol.5
, pp. 721-729
-
-
Martinez, J.1
Pisabarro, M.2
Serrano, L.3
-
30
-
-
0033871567
-
Critical role of β-hairpin formation in protein G folding
-
McCallister, E.L., Aim, E., and Baker, D. 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
Aim, E.2
Baker, D.3
-
31
-
-
0037375366
-
Prediction of folding rates and transition-state placement from native state geometry
-
Micheletti, C. 2003. Prediction of folding rates and transition-state placement from native state geometry. Proteins 51: 74-84.
-
(2003)
Proteins
, vol.51
, pp. 74-84
-
-
Micheletti, C.1
-
33
-
-
0032574769
-
How evolution makes proteins fold quickly
-
Mimy, L.A., Abkevich, V.L., and Shakhnovich, E.I. 1998. How evolution makes proteins fold quickly. Proc. Natl. Acad. Sci. 95: 4976-4981.
-
(1998)
Proc. Natl. Acad. Sci.
, vol.95
, pp. 4976-4981
-
-
Mimy, L.A.1
Abkevich, V.L.2
Shakhnovich, E.I.3
-
34
-
-
84986440341
-
Settle: An analytical version of the shake and rattle algorithms for rigid water models
-
Miyamoto, S. and Kollman, P.A. 1992. Settle: An analytical version of the shake and rattle algorithms for rigid water models. J. Comp. Chem. 13: 952-962.
-
(1992)
J. Comp. Chem.
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
35
-
-
33845377127
-
Estimation of effective interresidue contact energies from protein crystal structure
-
Miyazawa, S. and Jernigan, R. 1985. Estimation of effective interresidue contact energies from protein crystal structure. Macromolecules 18: 543.
-
(1985)
Macromolecules
, vol.18
, pp. 543
-
-
Miyazawa, S.1
Jernigan, R.2
-
36
-
-
0031552596
-
Hydrogen exchange in chymotrypsin inhibitor 2 probed by mutagenesis
-
Neira, J.L., Itzhaki, L.S., Otzen, D.E., Davis, B., and Fersht, A.R. 1997. Hydrogen exchange in chymotrypsin inhibitor 2 probed by mutagenesis. J. Mol. Biol. 270: 99-110.
-
(1997)
J. Mol. Biol.
, vol.270
, pp. 99-110
-
-
Neira, J.L.1
Itzhaki, L.S.2
Otzen, D.E.3
Davis, B.4
Fersht, A.R.5
-
37
-
-
0029922493
-
Foldons, protein structural modules, and exons
-
Panchenko, A.R., Luthey-Schulten, Z., and Wolynes, P. 1996. Foldons, protein structural modules, and exons. Proc. Natl. Acad. Sci. 93: 2008-2013.
-
(1996)
Proc. Natl. Acad. Sci.
, vol.93
, pp. 2008-2013
-
-
Panchenko, A.R.1
Luthey-Schulten, Z.2
Wolynes, P.3
-
38
-
-
0032502839
-
Contact order, transition state placement and the refolding rates of single domain proteins
-
Plaxco, K.W., Simons, K.T., and Baker, D. 1998. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277: 285-294.
-
(1998)
J. Mol. Biol.
, vol.277
, pp. 285-294
-
-
Plaxco, K.W.1
Simons, K.T.2
Baker, D.3
-
39
-
-
0032734515
-
Experiments and theory highlight role of native state topology in sh3 folding
-
Riddle, D.S., Grantcharova, V.P., Santiago, J.V., Aim, E., Ruczinski, I., and Baker, D. 1999. Experiments 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
Aim, E.4
Ruczinski, I.5
Baker, D.6
-
40
-
-
0028270634
-
Kinetics of protein folding: A lattice model study of the requirements for folding to the native state
-
Sali, A., Shakhnovich, E., and Karplus, M. 1994. Kinetics of protein folding: A lattice model study of the requirements for folding to the native state. J. Mol. Biol. 235: 1614-1636.
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 1614-1636
-
-
Sali, A.1
Shakhnovich, E.2
Karplus, M.3
-
41
-
-
0034743155
-
From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding
-
Shea, J.E. and Brooks III, 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 III, C.L.2
-
42
-
-
0032777649
-
Dissection of the protein GB 1 domain binding site for human IgG Fc fragment
-
Sloan, D.J. and Hellinga, H.W. 1999. Dissection of the protein GB 1 domain binding site for human IgG Fc fragment. Protein Sci. 8: 1643-1648.
-
(1999)
Protein Sci.
, vol.8
, pp. 1643-1648
-
-
Sloan, D.J.1
Hellinga, H.W.2
-
43
-
-
0037038372
-
Absolute comparison of simulated and experimental protein-folding dynamics
-
Snow, C.D., Nguyen, H., Pande, V.S., and Gruebele, M. 2002. Absolute comparison of simulated and experimental protein-folding dynamics. Nature 420: 33-34.
-
(2002)
Nature
, vol.420
, pp. 33-34
-
-
Snow, C.D.1
Nguyen, H.2
Pande, V.S.3
Gruebele, M.4
-
44
-
-
0035932720
-
Hierarchy of events in the folding of model proteins
-
Tiana, G. and Broglia, R.A. 2001a. Hierarchy of events in the folding of model proteins. J. Chem. Phys. 114: 7267.
-
(2001)
J. Chem. Phys.
, vol.114
, pp. 7267
-
-
Tiana, G.1
Broglia, R.A.2
-
45
-
-
0034823503
-
Statistical analysis of native contact formation in the folding of designed model proteins
-
-. 2001b. Statistical analysis of native contact formation in the folding of designed model proteins. J. Chem. Phys. 114: 2503.
-
(2001)
J. Chem. Phys.
, vol.114
, pp. 2503
-
-
-
46
-
-
0000766263
-
Folding and misfolding of designed protein-like folding and mis-folding of designed protein-like chains with mutations
-
Tiana, G., Broglia, R.A., Roman, H.E., Vigezzi, E., and Shaknovich, E. 1998. Folding and misfolding of designed protein-like folding and mis-folding of designed protein-like chains with mutations. J. Chem. Phys. 108: 757.
-
(1998)
J. Chem. Phys.
, vol.108
, pp. 757
-
-
Tiana, G.1
Broglia, R.A.2
Roman, H.E.3
Vigezzi, E.4
Shaknovich, E.5
-
47
-
-
0003624584
-
-
Department of Biophysical Chemistry, BIOSON Research Institute, Nijenborgh, Groningen
-
van der Spoel, D., van Drunen, R., and Berendsen, H.J.C. 1994. Groningen machine for chemical simulations. Department of Biophysical Chemistry, BIOSON Research Institute, Nijenborgh, Groningen.
-
(1994)
Groningen Machine for Chemical Simulations
-
-
Van Der Spoel, D.1
Van Drunen, R.2
Berendsen, H.J.C.3
-
48
-
-
0001486104
-
GROMOS force field
-
(P. von Ragué Schleyer. ed.). Wiley, New York
-
van Gunsteren, W.F., Daura, X., and Mark, A.E. 1998. GROMOS force field. Encyclopedia of computational chemistry (P. von Ragué Schleyer. ed.), Vol. 2, pp. 1211-1216. Wiley, New York.
-
(1998)
Encyclopedia of Computational Chemistry
, vol.2
, pp. 1211-1216
-
-
Van Gunsteren, W.F.1
Daura, X.2
Mark, A.E.3
-
49
-
-
0034130699
-
Hierarchical folding of cytochrome c
-
Yeh, S.R. and Rousseau, D.L. 2000. Hierarchical folding of cytochrome c. Nat. Struct. Biol. 7: 443-445.
-
(2000)
Nat. Struct. Biol.
, vol.7
, pp. 443-445
-
-
Yeh, S.R.1
Rousseau, D.L.2
|