-
1
-
-
0026657433
-
Refined 1.8 Å crystal structure of lambda repressor-operator complex
-
Beamer, L. J., and C. O. Pabo. 1992. Refined 1.8 Å crystal structure of lambda repressor-operator complex. J. Mol. Biol. 227:177-196.
-
(1992)
J. Mol. Biol.
, vol.227
, pp. 177-196
-
-
Beamer, L.J.1
Pabo, C.O.2
-
2
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J. C., J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak. 1984. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684-3690.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
3
-
-
0000764091
-
Constant temperature free energy surfaces for physical and chemical processes
-
Boczko, E. M., and C. L. Brooks 3rd. 1993. Constant temperature free energy surfaces for physical and chemical processes. J. Phys. Chem. 97:4509-4513.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 4509-4513
-
-
Boczko, E.M.1
Brooks III, C.L.2
-
4
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks, B. R., R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. 1983. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 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
-
5
-
-
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
-
6
-
-
0031005061
-
The energy landscape of a fast-folding protein mapped by Ala→Gly substitutions
-
Burton, R. E., G. S. Huang, M. A. Daugherty, T. L. Calderone, and T. G. Oas. 1997. The energy landscape of a fast-folding protein mapped by Ala→Gly substitutions. Nat. Struct. Biol. 4:305-310.
-
(1997)
Nat. Struct. Biol.
, vol.4
, pp. 305-310
-
-
Burton, R.E.1
Huang, G.S.2
Daugherty, M.A.3
Calderone, T.L.4
Oas, T.G.5
-
7
-
-
0032554626
-
Protein folding dynamics: Quantitative comparison between theory and experiment
-
Burton, R. E., J. K. Myers, and T. G. Oas. 1998. Protein folding dynamics: quantitative comparison between theory and experiment. Biochemistry. 37:5337-5343.
-
(1998)
Biochemistry
, vol.37
, pp. 5337-5343
-
-
Burton, R.E.1
Myers, J.K.2
Oas, T.G.3
-
8
-
-
0036870910
-
The range of the contact interactions and the kinetics of the Gō models of proteins
-
Cieplak, M., and T. X. Hoang. 2002. The range of the contact interactions and the kinetics of the Gō models of proteins. Int. J. Mod. Phys. C. 13:1231-1242.
-
(2002)
Int. J. Mod. Phys. C
, vol.13
, pp. 1231-1242
-
-
Cieplak, M.1
Hoang, T.X.2
-
9
-
-
0037459022
-
Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: All-atom representation study of protein L
-
Clementi, C., A. E. Garcia, and J. N. Onuchic. 2003. Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: All-atom representation study of protein L. J. Mol. Biol. 326:933-954.
-
(2003)
J. Mol. Biol.
, vol.326
, pp. 933-954
-
-
Clementi, C.1
Garcia, A.E.2
Onuchic, J.N.3
-
10
-
-
0034705115
-
Now native state topology affects the folding of dihydrofolate reductase and interleukin-1β
-
Clementi, C., P. A. Jennings, and J. N. Onuchic. 2000a. Now native state topology affects the folding of dihydrofolate reductase and interleukin-1β. Proc. Natl. Acad. Sci. USA. 97:5871-5876.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 5871-5876
-
-
Clementi, C.1
Jennings, P.A.2
Onuchic, J.N.3
-
11
-
-
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. 2000b. 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
-
12
-
-
0033624685
-
Fast folding kinetics and mechanisms of protein folding
-
Eaton, W. A., V. Munoz, S. J. Hagen, G. S. Jas, L. J. Lapidus, E. R. Henry, and J. Hofrichter. 2000. Fast folding kinetics and mechanisms of 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
-
13
-
-
33646987405
-
Optimized Monte Carlo data analysis
-
Ferrenberg, A. M., and R. H. Swendsen. 1989. Optimized Monte Carlo data analysis. Phys. Rev. Lett. 63:1195-1198.
-
(1989)
Phys. Rev. Lett.
, vol.63
, pp. 1195-1198
-
-
Ferrenberg, A.M.1
Swendsen, R.H.2
-
16
-
-
0020972782
-
Theoretical studies of protein folding
-
Gō, N. 1983. Theoretical studies of protein folding. Ann. Rev. Biophys. Bioeng. 12:183-210.
-
(1983)
Ann. Rev. Biophys. Bioeng.
, vol.12
, pp. 183-210
-
-
Go, N.1
-
17
-
-
0001022344
-
The fast protein folding problem
-
Gruebele, M. 1999. The fast protein folding problem. Annu. Rev. Phys. Chem. 50:485-516.
-
(1999)
Annu. Rev. Phys. Chem.
, vol.50
, pp. 485-516
-
-
Gruebele, M.1
-
18
-
-
0036535895
-
Protein folding: The free energy surface
-
Gruebele, M. 2002. Protein folding: the free energy surface. Curr. Opin. Struct. Biol. 12:161-168.
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 161-168
-
-
Gruebele, M.1
-
19
-
-
3042713195
-
-
Theoretical Biophysics Group, University of Illinois at Urbana-Champaign, Urbana, IL
-
Gullingsrud, J., and J. Phillips. 2002. PSFGEN User's Guide. Theoretical Biophysics Group, University of Illinois at Urbana-Champaign, Urbana, IL.
-
(2002)
PSFGEN User's Guide
-
-
Gullingsrud, J.1
Phillips, J.2
-
20
-
-
0029964867
-
Diffusion-limited formation in unfolding cytochrome c: Estimating the maximum rate of protein folding
-
Hagen, S. J., J. Hofrichter, A. Szabo, and W. A. Eaton. 1996. Diffusion-limited formation in unfolding cytochrome c: estimating the maximum rate of protein folding. Proc. Natl. Acad. Sci. USA. 93:11615-11617.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 11615-11617
-
-
Hagen, S.J.1
Hofrichter, J.2
Szabo, A.3
Eaton, W.A.4
-
21
-
-
0033557350
-
Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides
-
Hardin, C., Z. Luthey-Schulten, and P. G. Wolynes. 1999. Backbone dynamics, fast folding, and secondary structure formation in helical proteins and peptides. Proteins. 34:281-294.
-
(1999)
Proteins
, vol.34
, pp. 281-294
-
-
Hardin, C.1
Luthey-Schulten, Z.2
Wolynes, P.G.3
-
22
-
-
0037398844
-
Minimalist models for protein folding and design
-
Head-Gordon, T., and S. Brown. 2003. Minimalist models for protein folding and design. Curr. Opin. Struct. Biol. 13:160-167.
-
(2003)
Curr. Opin. Struct. Biol.
, vol.13
, pp. 160-167
-
-
Head-Gordon, T.1
Brown, S.2
-
23
-
-
0029151158
-
Submillisecond folding of monomeric λ repressor
-
Huang, G. S., and T. G. Oas. 1995. Submillisecond folding of monomeric λ repressor. Proc. Natl. Acad. Sci. USA. 92:6878-6882.
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, pp. 6878-6882
-
-
Huang, G.S.1
Oas, T.G.2
-
25
-
-
0042415783
-
NAMD2: Greater scalability for parallel molecular dynamics
-
Kale, L., R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten. 1999. NAMD2: greater scalability for parallel molecular dynamics. J. Comput. Phys. 151:283-312.
-
(1999)
J. Comput. Phys.
, vol.151
, pp. 283-312
-
-
Kale, L.1
Skeel, R.2
Bhandarkar, M.3
Brunner, R.4
Gursoy, A.5
Krawetz, N.6
Phillips, J.7
Shinozaki, A.8
Varadarajan, K.9
Schulten, K.10
-
26
-
-
0036785556
-
The origins of asymmetry in the protein transition states of protein L and protein G
-
Karanicolas, J., and C. L. Brooks 3rd. 2002. The origins of asymmetry in the protein transition states of protein L and protein G. Protein Sci. 11:2351-2361.
-
(2002)
Protein Sci.
, vol.11
, pp. 2351-2361
-
-
Karanicolas, J.1
Brooks III, C.L.2
-
27
-
-
0035850732
-
Roles of native topology and chain-length scaling in protein folding: A simulation study with a Gō-like model
-
Koga, N., and S. Takada. 2001. Roles of native topology and chain-length scaling in protein folding: a simulation study with a Gō-like model. J. Mol. Biol. 313:171-180.
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 171-180
-
-
Koga, N.1
Takada, S.2
-
29
-
-
0000224283
-
CHARMM: The energy function and its parameterization with an overview of the program
-
P. von Raque-Schleyer, editor. John Wiley & Sons, New York
-
MacKerell, A. D., Jr., B. Brooks, C. L. Brooks 3rd, L. Nilsson, B. Roux, Y. Won, and M. Karplus. 1998. CHARMM: the energy function and its parameterization with an overview of the program. In The Encyclopedia of Computational Chemistry, Vol. 1. P. von Raque-Schleyer, editor. John Wiley & Sons, New York. 271-277.
-
(1998)
The Encyclopedia of Computational Chemistry
, vol.1
, pp. 271-277
-
-
MacKerell Jr., A.D.1
Brooks, B.2
Brooks III, C.L.3
Nilsson, L.4
Roux, B.5
Won, Y.6
Karplus, M.7
-
30
-
-
0028574137
-
Contribution of a hydrogen bond/salt bridge network to the stability of secondary and tertiary structure of λ repressor
-
Marqusee, S., and R. T. Sauer. 1994. Contribution of a hydrogen bond/salt bridge network to the stability of secondary and tertiary structure of λ repressor. Protein Sci. 3:2217-2225.
-
(1994)
Protein Sci.
, vol.3
, pp. 2217-2225
-
-
Marqusee, S.1
Sauer, R.T.2
-
31
-
-
0029919190
-
Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term for simulation and threading
-
Miyazawa, S., and R. L. Jernigan. 1996. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term for simulation and threading. J. Mol. Biol. 256:623-644.
-
(1996)
J. Mol. Biol.
, vol.256
, pp. 623-644
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
32
-
-
0035997388
-
Mechanism of fast protein folding
-
Myers, J. K., and T. G. Oas. 2002. Mechanism of fast protein folding. Annu. Rev. Biochem. 71:783-815.
-
(2002)
Annu. Rev. Biochem.
, vol.71
, pp. 783-815
-
-
Myers, J.K.1
Oas, T.G.2
-
35
-
-
0037093654
-
Native and non-native interactions along protein folding and unfolding pathways
-
Paci, E., M. Vendruscolo, and M. Karplus. 2002. Native and non-native interactions along protein folding and unfolding pathways. Proteins. 47:379-392.
-
(2002)
Proteins
, vol.47
, pp. 379-392
-
-
Paci, E.1
Vendruscolo, M.2
Karplus, M.3
-
36
-
-
0035576033
-
Speeding protein folding beyond the Gō model: How a little frustration sometimes helps
-
Plotkin, S. S. 2001. Speeding protein folding beyond the Gō model: How a little frustration sometimes helps. Proteins. 45:337-345.
-
(2001)
Proteins
, vol.45
, pp. 337-345
-
-
Plotkin, S.S.1
-
37
-
-
0036023918
-
Understanding protein folding with energy landscape theory. Part I: Basic concepts
-
Plotkin, S., and J. N. Onuchic. 2002. Understanding protein folding with energy landscape theory. Part I: basic concepts. Q. Rev. Biophys. 35:111-167.
-
(2002)
Q. Rev. Biophys.
, vol.35
, pp. 111-167
-
-
Plotkin, S.1
Onuchic, J.N.2
-
38
-
-
0000227308
-
Variational theory for site resolved protein folding free energy surfaces
-
Portman, J. J., S. Takada, and P. G. Wolynes. 1998. Variational theory for site resolved protein folding free energy surfaces. Phys. Rev. Lett. 81:5237-5240.
-
(1998)
Phys. Rev. Lett.
, vol.81
, pp. 5237-5240
-
-
Portman, J.J.1
Takada, S.2
Wolynes, P.G.3
-
39
-
-
0035868526
-
Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics
-
Portman, J. J., S. Takada, and P. G. Wolynes. 2001. Microscopic theory of protein folding rates. II. Local reaction coordinates and chain dynamics. J. Chem. Phys. 114:5082-5096.
-
(2001)
J. Chem. Phys.
, vol.114
, pp. 5082-5096
-
-
Portman, J.J.1
Takada, S.2
Wolynes, P.G.3
-
40
-
-
0001069331
-
Dynamics of reactions involving diffusive barrier crossing
-
Schulten, K., Z. Schulten, and A. Szabo. 1981. Dynamics of reactions involving diffusive barrier crossing. J. Chem. Phys. 74:4426-4432.
-
(1981)
J. Chem. Phys.
, vol.74
, pp. 4426-4432
-
-
Schulten, K.1
Schulten, Z.2
Szabo, A.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 C. L. Brooks 3rd. 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
-
-
0033607208
-
Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A
-
Shea, J. E., J. N. Onuchic, and C. L. Brooks 3rd. 1999. Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A. Proc. Natl. Acad. Sci. USA. 96:12512-12517.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 12512-12517
-
-
Shea, J.E.1
Onuchic, J.N.2
Brooks III, C.L.3
-
43
-
-
0037143694
-
The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation
-
Shimada, J., and E. I. Shakhnovich. 2002. The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation. Proc. Natl. Acad. Sci. USA. 99:11175-11180.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 11175-11180
-
-
Shimada, J.1
Shakhnovich, E.I.2
-
44
-
-
0000710672
-
Diffusive dynamics of the reaction coordinate for protein folding funnels
-
Socci, N. D., J. N. Onuchic, and P. G. Wolynes. 1996. Diffusive dynamics of the reaction coordinate for protein folding funnels. J. Chem. Phys. 104:5860-5868.
-
(1996)
J. Chem. Phys.
, vol.104
, pp. 5860-5868
-
-
Socci, N.D.1
Onuchic, J.N.2
Wolynes, P.G.3
-
45
-
-
0016696599
-
Studies on protein folding, unfolding and fluctuations by computer simulation I: The effect of specific amino acid sequence represented by the specific inter-unit interactions
-
Taketomi, H., Y. Ueda, and N. Gō. 1975. Studies on protein folding, unfolding and fluctuations by computer simulation I: The effect of specific amino acid sequence represented by the specific inter-unit interactions. Intr. J. Peptide. Res. 7:445-459.
-
(1975)
Intr. J. Peptide. Res.
, vol.7
, pp. 445-459
-
-
Taketomi, H.1
Ueda, Y.2
Go, N.3
-
46
-
-
0342929614
-
Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
-
Torrie, G. M., and J. P. Valleau. 1977. Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling. J. Comput. Phys. 23:187-199.
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 187-199
-
-
Torrie, G.M.1
Valleau, J.P.2
-
47
-
-
22944467757
-
Computer "experiments" on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules
-
Verlet, L. 1967. Computer "experiments" on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 159:98-103.
-
(1967)
Phys. Rev.
, vol.159
, pp. 98-103
-
-
Verlet, L.1
-
48
-
-
0030979740
-
Folding funnels and energy landscapes of larger proteins within the capillarity approximation
-
Wolynes, P. G. 1997. Folding funnels and energy landscapes of larger proteins within the capillarity approximation. Proc. Natl. Acad. Sci. USA. 94:6170-6175.
-
(1997)
Proc. Natl. Acad. Sci. USA
, vol.94
, pp. 6170-6175
-
-
Wolynes, P.G.1
-
50
-
-
0038329308
-
Folding at the speed limit
-
Yang, W. Y., and M. Gruebele. 2003. Folding at the speed limit. Nature. 423:193-197.
-
(2003)
Nature
, vol.423
, pp. 193-197
-
-
Yang, W.Y.1
Gruebele, M.2
-
51
-
-
3042814557
-
Folding λ-repressor at its speed limit
-
Yang, W. Y., and M. Gruebele. 2004. Folding λ-repressor at its speed limit. Biophys. J. 87:596-608.
-
(2004)
Biophys. J.
, vol.87
, pp. 596-608
-
-
Yang, W.Y.1
Gruebele, M.2
-
52
-
-
0033598375
-
Interpreting the folding kinetics of helical proteins
-
Zhou, Y., and M. Karplus. 1999. Interpreting the folding kinetics of helical proteins. Nature. 401:400-403.
-
(1999)
Nature
, vol.401
, pp. 400-403
-
-
Zhou, Y.1
Karplus, M.2
|