-
1
-
-
0030626588
-
The Levinthalparadox: Yesterday and today
-
Karplus, M., The Levinthalparadox: yesterday and today. Fold. Des., 1997. 2(4): p. S69-75.
-
(1997)
Fold. Des
, vol.2
, Issue.4
-
-
Karplus, M.1
-
2
-
-
1842298212
-
From Levinthal to pathways to funnels
-
Dill, K.A. and H.S. Chan, From Levinthal to pathways to funnels. Nat. Struct. Biol., 1997. 4(1): p. 10-19.
-
(1997)
Nat. Struct. Biol
, vol.4
, Issue.1
, pp. 10-19
-
-
Dill, K.A.1
Chan, H.S.2
-
3
-
-
0029973119
-
Direct observation of fast protein folding: The initial collapse of apomyoglobin
-
Ballew, R.M., J. Sabelko, and M. Gruebele, Direct observation of fast protein folding: The initial collapse of apomyoglobin. Proc. Natl. Acad. Sci. USA, 1996. 93: p. 5759-5764.
-
(1996)
Proc. Natl. Acad. Sci. USA
, vol.93
, pp. 5759-5764
-
-
Ballew, R.M.1
Sabelko, J.2
Gruebele, M.3
-
4
-
-
3242883536
-
Rapid mixing methods for exploring the kinetics of protein folding
-
Roder, H., K. Maki, H. Cheng, and M.C. Shastry, Rapid mixing methods for exploring the kinetics of protein folding. Methods, 2004. 34(1): p. 15-27.
-
(2004)
Methods
, vol.34
, Issue.1
, pp. 15-27
-
-
Roder, H.1
Maki, K.2
Cheng, H.3
Shastry, M.C.4
-
5
-
-
33744937937
-
Early events in protein folding explored by rapid mixing methods
-
Roder, H., K. Maki, and H. Cheng, Early events in protein folding explored by rapid mixing methods. Chem. Rev., 2006.106(5): p. 1836-1861.
-
(2006)
Chem. Rev
, vol.106
, Issue.5
, pp. 1836-1861
-
-
Roder, H.1
Maki, K.2
Cheng, H.3
-
6
-
-
0030971246
-
Fluorescence methods for studying kinetics of protein-folding reactions
-
Eftink, M.R. and M.C. Shastry, Fluorescence methods for studying kinetics of protein-folding reactions. Methods Enzymol., 1997. 278: p. 258-286.
-
(1997)
Methods Enzymol
, vol.278
, pp. 258-286
-
-
Eftink, M.R.1
Shastry, M.C.2
-
7
-
-
25444459145
-
NMR spectroscopic characterization of millisecond protein folding by transverse relaxation dispersion measurements
-
Zeeb, M. and J. Baibach, NMR spectroscopic characterization of millisecond protein folding by transverse relaxation dispersion measurements. J. Am. Chem. Soc., 2005. 127(38): p. 13207-13212.
-
(2005)
J. Am. Chem. Soc
, vol.127
, Issue.38
, pp. 13207-13212
-
-
Zeeb, M.1
Baibach, J.2
-
8
-
-
0035926229
-
Time resolved collapse of a folding protein observed with small angle x-ray scattering
-
Pollack, L., M.W. Tate, A.C. Finnefrock, C. Kalidas, S. Trotter, N.C. Darnton, L. Lurio, R.H. Austin, C.A. Batt, S.M. Gruner, and S.G. Mochrie, Time resolved collapse of a folding protein observed with small angle x-ray scattering. Phys. Rev. Lett., 2001. 86(21): p. 4962-4965.
-
(2001)
Phys. Rev. Lett
, vol.86
, Issue.21
, pp. 4962-4965
-
-
Pollack, L.1
Tate, M.W.2
Finnefrock, A.C.3
Kalidas, C.4
Trotter, S.5
Darnton, N.C.6
Lurio, L.7
Austin, R.H.8
Batt, C.A.9
Gruner, S.M.10
Mochrie, S.G.11
-
9
-
-
0033578828
-
Is protein unfolding the reverse of protein folding? A lattice simulation analysis
-
Dinner, A.R. and M. Karplus, Is protein unfolding the reverse of protein folding? A lattice simulation analysis. J. Mol. Biol., 1999. 292(2): p. 403-419.
-
(1999)
J. Mol. Biol
, vol.292
, Issue.2
, pp. 403-419
-
-
Dinner, A.R.1
Karplus, M.2
-
10
-
-
0033515015
-
Stretching lattice models of protein folding
-
Socci, N.D., J.N. Onuchic, and P.G. Wolynes, Stretching lattice models of protein folding. Proc. Natl. Acad. Sci. USA, 1999. 96(5): p. 2031-2035.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, Issue.5
, pp. 2031-2035
-
-
Socci, N.D.1
Onuchic, J.N.2
Wolynes, P.G.3
-
11
-
-
0036928148
-
Validity of Go models: Comparison with a solvent-shielded empirical energy decomposition
-
Paci, E., M. Vendruscolo, and M. Karplus, Validity of Go models: comparison with a solvent-shielded empirical energy decomposition. Biophys. J., 2002. 83(6): p. 3032-3038.
-
(2002)
Biophys. J
, vol.83
, Issue.6
, pp. 3032-3038
-
-
Paci, E.1
Vendruscolo, M.2
Karplus, M.3
-
12
-
-
1342281633
-
The protein folding 'speed limit'
-
Kubelka, J., J. Hofrichter, and W.A. Eaton, The protein folding 'speed limit'. Curr. Opin. Struct. Biol., 2004.14(1): p. 76-88.
-
(2004)
Curr. Opin. Struct. Biol
, vol.14
, Issue.1
, pp. 76-88
-
-
Kubelka, J.1
Hofrichter, J.2
Eaton, W.A.3
-
13
-
-
0037154980
-
Protein folding and unfolding at atomic resolution
-
Fersht, A.R. and V. Daggett, Protein folding and unfolding at atomic resolution. Cell, 2002. 108(4): p. 573-582.
-
(2002)
Cell
, vol.108
, Issue.4
, pp. 573-582
-
-
Fersht, A.R.1
Daggett, V.2
-
14
-
-
1942535023
-
Molecular simulation of the reversible mechanical unfolding of proteins
-
Rathore, N., Q. Yan, and J.J. De Pablo, Molecular simulation of the reversible mechanical unfolding of proteins. J. Chem. Phys., 2004.120(12): p. 5781-5788.
-
(2004)
J. Chem. Phys
, vol.120
, Issue.12
, pp. 5781-5788
-
-
Rathore, N.1
Yan, Q.2
De Pablo, J.J.3
-
15
-
-
0034657550
-
Computer simulations of protein folding by targeted molecular dynamics
-
Ferrara, P, J. Apostolakis, and A. Caflisch, Computer simulations of protein folding by targeted molecular dynamics. Proteins, 2000. 39(3): p. 252-260.
-
(2000)
Proteins
, vol.39
, Issue.3
, pp. 252-260
-
-
Ferrara, P.1
Apostolakis, J.2
Caflisch, A.3
-
16
-
-
0037093874
-
Direct observation of the folding and unfolding of a betahairpin in explicit water through computer simulation
-
Wu, X., S. Wang, and B.R. Brooks, Direct observation of the folding and unfolding of a betahairpin in explicit water through computer simulation. J. Am. Chem. Soc., 2002. 124(19): p. 5282-5283.
-
(2002)
J. Am. Chem. Soc
, vol.124
, Issue.19
, pp. 5282-5283
-
-
Wu, X.1
Wang, S.2
Brooks, B.R.3
-
17
-
-
0034864528
-
Generalized-ensemble algorithms for molecular simulations of biopolymers
-
Mitsutake, A., Y. Sugita, and Y. Okamoto, Generalized-ensemble algorithms for molecular simulations of biopolymers. Biopolymers, 2001. 60(2): p. 96-123.
-
(2001)
Biopolymers
, vol.60
, Issue.2
, pp. 96-123
-
-
Mitsutake, A.1
Sugita, Y.2
Okamoto, Y.3
-
18
-
-
31944443456
-
Free energy surfaces of miniproteins with a betabetaalpha motif: Replica exchange molecular dynamics simulation with an implicit solvation model
-
Jang, S., E. Kim, and Y. Pak, Free energy surfaces of miniproteins with a betabetaalpha motif: replica exchange molecular dynamics simulation with an implicit solvation model. Proteins, 2006. 62(3): p. 6663-6671.
-
(2006)
Proteins
, vol.62
, Issue.3
, pp. 6663-6671
-
-
Jang, S.1
Kim, E.2
Pak, Y.3
-
19
-
-
28644431872
-
Free energy landscape and folding mechanism of a beta-hairpin in explicit water: A replica exchange molecular dynamics study
-
Nguyen, P.H., G. Stock, E. Mittag, C.K. Hu, and M.S. Li, Free energy landscape and folding mechanism of a beta-hairpin in explicit water: a replica exchange molecular dynamics study. Proteins, 2005. 61(4): p. 795-808.
-
(2005)
Proteins
, vol.61
, Issue.4
, pp. 795-808
-
-
Nguyen, P.H.1
Stock, G.2
Mittag, E.3
Hu, C.K.4
Li, M.S.5
-
20
-
-
23944494644
-
Folding cooperativity in a three-stranded beta-sheet model
-
Roe, D.R., V. Hornak, and C. Simmerling, Folding cooperativity in a three-stranded beta-sheet model. J. Mol. Biol., 2005. 352(2): p. 370-381.
-
(2005)
J. Mol. Biol
, vol.352
, Issue.2
, pp. 370-381
-
-
Roe, D.R.1
Hornak, V.2
Simmerling, C.3
-
21
-
-
0344824394
-
Trp-cage: Folding free energy landscape in explicit water
-
Zhou, R., Trp-cage: folding free energy landscape in explicit water. Proc. Natl. Acad. Sci. USA, 2003.100(23): p. 13280-13285.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, Issue.23
, pp. 13280-13285
-
-
Zhou, R.1
-
22
-
-
0032080053
-
-
Sheinerman, F.B. and C.L. Brooks, 3rd, Calculations on folding of segment B1 of streptococcal protein G. J. Mol. Biol., 1998. 278(2): p. 439-456.
-
Sheinerman, F.B. and C.L. Brooks, 3rd, Calculations on folding of segment B1 of streptococcal protein G. J. Mol. Biol., 1998. 278(2): p. 439-456.
-
-
-
-
23
-
-
0037235952
-
Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing
-
Pande, V.S., I. Baker, J. Chapman, S.P. Elmer, S. Khaliq, S.M. Larson, Y.M. Rhee, M.R. Shirts, C.D. Snow, E.J. Sorin, and B. Zagrovic, Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. Biopolymers, 2003. 68(1): p. 91-109.
-
(2003)
Biopolymers
, vol.68
, Issue.1
, pp. 91-109
-
-
Pande, V.S.1
Baker, I.2
Chapman, J.3
Elmer, S.P.4
Khaliq, S.5
Larson, S.M.6
Rhee, Y.M.7
Shirts, M.R.8
Snow, C.D.9
Sorin, E.J.10
Zagrovic, B.11
-
24
-
-
0032842870
-
The fundamentals of protein folding: Bringing together theory and experiment
-
Dobson, C.M. and M. Karplus, The fundamentals of protein folding: bringing together theory and experiment. Curr. Opin. Struct. Biol., 1999. 9(1): p. 92-101.
-
(1999)
Curr. Opin. Struct. Biol
, vol.9
, Issue.1
, pp. 92-101
-
-
Dobson, C.M.1
Karplus, M.2
-
26
-
-
0029653906
-
Models of cooperativity in protein folding
-
Chan, H.S., S. Bromberg, and K.A. Dill, Models of cooperativity in protein folding. Philos. Trans. R. Soc. Lond. B Biol. Sci., 1995. 348(1323): p. 61-70.
-
(1995)
Philos. Trans. R. Soc. Lond. B Biol. Sci
, vol.348
, Issue.1323
, pp. 61-70
-
-
Chan, H.S.1
Bromberg, S.2
Dill, K.A.3
-
27
-
-
0016418420
-
Intermediates in protein folding reactions and the mechanism of protein folding
-
Baldwin, R.L., Intermediates in protein folding reactions and the mechanism of protein folding. Annu. Rev. Biochem., 1975. 44: p. 453-475.
-
(1975)
Annu. Rev. Biochem
, vol.44
, pp. 453-475
-
-
Baldwin, R.L.1
-
28
-
-
0028327236
-
Protein folding dynamics: The diffusion-collision model and experimental data
-
Karplus, M. and D.L. Weaver, Protein folding dynamics: the diffusion-collision model and experimental data. Protein Sci., 1994. 3(4): p. 650-668.
-
(1994)
Protein Sci
, vol.3
, Issue.4
, pp. 650-668
-
-
Karplus, M.1
Weaver, D.L.2
-
29
-
-
0028856785
-
Optimization of rates of protein folding: The nucleation-condensation mechanism and its implications
-
Fersht, A.R., Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications. Proc. Natl. Acad. Sci. USA, 1995. 92(24): p. 10869-10873.
-
(1995)
Proc. Natl. Acad. Sci. USA
, vol.92
, Issue.24
, pp. 10869-10873
-
-
Fersht, A.R.1
-
30
-
-
0037221599
-
Is there a unifying mechanism for protein folding?
-
Daggett, V and A.R. Fersht, Is there a unifying mechanism for protein folding? Trends Biochem. Sci., 2003. 28(1): p. 18-25.
-
(2003)
Trends Biochem. Sci
, vol.28
, Issue.1
, pp. 18-25
-
-
Daggett, V.1
Fersht, A.R.2
-
31
-
-
0030628825
-
Theory of protein folding: The energy landscape perspective
-
Onuchic, J.N., Z. Luthey-Schulten, and P.G. Wolynes, Theory of protein folding: the energy landscape perspective. Annu. Rev. Phys. Chem., 1997. 48: p. 545-600.
-
(1997)
Annu. Rev. Phys. Chem
, vol.48
, pp. 545-600
-
-
Onuchic, J.N.1
Luthey-Schulten, Z.2
Wolynes, P.G.3
-
32
-
-
12944327750
-
-
Wolynes, P.G., Energy landscapes and solved protein-folding problems. Philos. Transact. A Math. Phys. Eng. Sci., 2005. 363(1827): p. 453-464; discussion 464-467.
-
Wolynes, P.G., Energy landscapes and solved protein-folding problems. Philos. Transact. A Math. Phys. Eng. Sci., 2005. 363(1827): p. 453-464; discussion 464-467.
-
-
-
-
33
-
-
0034743155
-
-
Shea, J.E. and C.L. Brooks, 3rd, From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. Annu. Rev. Phys. Chem., 2001. 52: p. 499-535.
-
Shea, J.E. and C.L. Brooks, 3rd, From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. Annu. Rev. Phys. Chem., 2001. 52: p. 499-535.
-
-
-
-
34
-
-
0037686252
-
The present view of the mechanism of protein folding
-
Daggett, V. and A. Fersht, The present view of the mechanism of protein folding. Nat. Rev. Mol. Cell Biol., 2003. 4(6): p. 497-502.
-
(2003)
Nat. Rev. Mol. Cell Biol
, vol.4
, Issue.6
, pp. 497-502
-
-
Daggett, V.1
Fersht, A.2
-
35
-
-
4344612164
-
Replica-exchange extensions of simulated tempering method
-
Mitsutake, A. and Y. Okamoto, Replica-exchange extensions of simulated tempering method. J. Chem. Phys., 2004.121(6): p. 2491-2504.
-
(2004)
J. Chem. Phys
, vol.121
, Issue.6
, pp. 2491-2504
-
-
Mitsutake, A.1
Okamoto, Y.2
-
36
-
-
1942455272
-
Generalized-ensemble algorithms: Enhanced sampling techniques for Monte Carlo and molecular dynamics simulations
-
Okamoto, Y., Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations. J. Mol. Graph. Model., 2004. 22(5): p. 425-439.
-
(2004)
J. Mol. Graph. Model
, vol.22
, Issue.5
, pp. 425-439
-
-
Okamoto, Y.1
-
37
-
-
9244260409
-
-
University of California, San Francisco
-
Case, D.A., et al., AMBER 8. 2004: University of California, San Francisco.
-
(2004)
AMBER 8
-
-
Case, D.A.1
-
38
-
-
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, Charmm-a Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J. Comput. Chem., 1983. 4(2): p. 187-217.
-
(1983)
J. Comput. Chem
, vol.4
, Issue.2
, 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
-
39
-
-
27344454932
-
GROMACS: Fast, flexible, and free
-
Van Der Spoel, D., E. Lindahl, B. Hess, G. Groenhof, A.E. Mark, and H.J. Berendsen, GROMACS: fast, flexible, and free. J. Comput. Chem., 2005. 26(16): p. 1701-1718.
-
(2005)
J. Comput. Chem
, vol.26
, Issue.16
, pp. 1701-1718
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
Berendsen, H.J.6
-
40
-
-
30444448249
-
The GROMOS software for biomolecular simulation: GROMOS05
-
Christen, M., P.H. Hunenberger, D. Bakowies, R. Baron, R. Burgi, D.P. Geerke, T.N. Heinz, M. A. Kastenholz, V. Krautler, C. Oostenbrink, C. Peter, D. Trzesniak, and W.F. van Gunsteren, The GROMOS software for biomolecular simulation: GROMOS05. J. Comput. Chem., 2005. 26(16): p. 1719-1751.
-
(2005)
J. Comput. Chem
, vol.26
, Issue.16
, pp. 1719-1751
-
-
Christen, M.1
Hunenberger, P.H.2
Bakowies, D.3
Baron, R.4
Burgi, R.5
Geerke, D.P.6
Heinz, T.N.7
Kastenholz, M.A.8
Krautler, V.9
Oostenbrink, C.10
Peter, C.11
Trzesniak, D.12
van Gunsteren, W.F.13
-
41
-
-
85069280975
-
-
Tiradorives, J. and W.L. Jorgensen, The Opls Force-Field for Organic and Biomolecular Systems. Abstr. Pap. Am. Chem. S., 1992. 204: p. 43-Comp.
-
Tiradorives, J. and W.L. Jorgensen, The Opls Force-Field for Organic and Biomolecular Systems. Abstr. Pap. Am. Chem. S., 1992. 204: p. 43-Comp.
-
-
-
-
42
-
-
33645408056
-
Balancing solvation and intramolecular interactions: Toward a consistent generalized Born force field
-
Chen, J.H., W.P. Im, and C.L. Brooks, Balancing solvation and intramolecular interactions: Toward a consistent generalized Born force field. J. Amer. Chem. Soc., 2006. 128(11): p. 3728-3736.
-
(2006)
J. Amer. Chem. Soc
, vol.128
, Issue.11
, pp. 3728-3736
-
-
Chen, J.H.1
Im, W.P.2
Brooks, C.L.3
-
43
-
-
14544285906
-
Comparative study of generalized Born models: Born radii and peptide folding
-
Zhu, J., E. Alexov, and B. Honig, Comparative study of generalized Born models: Born radii and peptide folding. J. Phys. Chem. B, 2005. 109(7): p. 3008-3022.
-
(2005)
J. Phys. Chem. B
, vol.109
, Issue.7
, pp. 3008-3022
-
-
Zhu, J.1
Alexov, E.2
Honig, B.3
-
44
-
-
0016996218
-
Conjugate gradient versus steepest descent
-
Allwright, J.C., Conjugate gradient versus steepest descent. J. Optimiz. Theory App., 1976. 20(1): p. 129-134.
-
(1976)
J. Optimiz. Theory App
, vol.20
, Issue.1
, pp. 129-134
-
-
Allwright, J.C.1
-
45
-
-
0029358115
-
Parallel algorithms for hierarchical-clustering
-
Olson, C.F., Parallel algorithms for hierarchical-clustering. Parallel Comput., 1995. 21(8): p. 1313-1325.
-
(1995)
Parallel Comput
, vol.21
, Issue.8
, pp. 1313-1325
-
-
Olson, C.F.1
-
46
-
-
6944235051
-
Hidden complexity of free energy surfaces for peptide (protein) folding
-
Krivov, S.V. and M. Karplus, Hidden complexity of free energy surfaces for peptide (protein) folding. Proc. Natl. Acad. Sci. USA, 2004.101(41): p. 14766-14770.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, Issue.41
, pp. 14766-14770
-
-
Krivov, S.V.1
Karplus, M.2
-
47
-
-
0021755764
-
Solvent accessible surface-area and excluded volume inproteins-analytical equations for overlapping spheres and implications for the hydrophobic effect
-
Richmond, T.J., Solvent accessible surface-area and excluded volume inproteins-analytical equations for overlapping spheres and implications for the hydrophobic effect. J. Mol. Biol., 1984. 178(1): p. 63-89.
-
(1984)
J. Mol. Biol
, vol.178
, Issue.1
, pp. 63-89
-
-
Richmond, T.J.1
-
48
-
-
0033536659
-
Dissecting the stability of a beta-hairpin peptide that folds in water: NMR and molecular dynamics analysis of the beta-turn and beta-strand contributions to folding
-
Griffiths-Jones, S.R., A.J. Maynard, and M.S. Searle, Dissecting the stability of a beta-hairpin peptide that folds in water: NMR and molecular dynamics analysis of the beta-turn and beta-strand contributions to folding. J. Mol. Biol., 1999. 292(5): p. 1051-1069.
-
(1999)
J. Mol. Biol
, vol.292
, Issue.5
, pp. 1051-1069
-
-
Griffiths-Jones, S.R.1
Maynard, A.J.2
Searle, M.S.3
-
49
-
-
0035237233
-
Conformational entropy in protein folding. A guide to estimating conformational entropy via modeling and computation
-
Creamer, T.P., Conformational entropy in protein folding. A guide to estimating conformational entropy via modeling and computation. Methods Mol. Biol., 2001. 168: p. 117-132.
-
(2001)
Methods Mol. Biol
, vol.168
, pp. 117-132
-
-
Creamer, T.P.1
-
50
-
-
10844292652
-
Energy landscape of a small peptide revealed by dihedral angle principal component analysis
-
Mu, Y., P.H. Nguyen, and G. Stock, Energy landscape of a small peptide revealed by dihedral angle principal component analysis. Proteins, 2005. 58(1): p. 45-52.
-
(2005)
Proteins
, vol.58
, Issue.1
, pp. 45-52
-
-
Mu, Y.1
Nguyen, P.H.2
Stock, G.3
-
51
-
-
33645722974
-
Convergence of replica exchange molecular dynamics
-
Zhang, W., C. Wu, and Y. Duan, Convergence of replica exchange molecular dynamics. J. Chem. Phys., 2005.123(15): p. 154105.
-
(2005)
J. Chem. Phys
, vol.123
, Issue.15
, pp. 154105
-
-
Zhang, W.1
Wu, C.2
Duan, Y.3
-
52
-
-
0345133287
-
Folding a protein in a computer: An atomic description of the folding/unfolding of protein A
-
Garcia, A.E. and J.N. Onuchic, Folding a protein in a computer: an atomic description of the folding/unfolding of protein A. Proc. Natl. Acad. Sci. USA, 2003.100(24): p. 13898-13903.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, Issue.24
, pp. 13898-13903
-
-
Garcia, A.E.1
Onuchic, J.N.2
-
53
-
-
0242663237
-
A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
-
Duan, Y., C. Wu, S. Chowdhury, M.C. Lee, G. Xiong, W. Zhang, R. Yang, P. Cieplak, R. Luo, T. Lee, J. Caldwell, J. Wang, and P. Kollman, A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J. Comput. Chem., 2003. 24(16): p. 1999-2012.
-
(2003)
J. Comput. Chem
, vol.24
, Issue.16
, pp. 1999-2012
-
-
Duan, Y.1
Wu, C.2
Chowdhury, S.3
Lee, M.C.4
Xiong, G.5
Zhang, W.6
Yang, R.7
Cieplak, P.8
Luo, R.9
Lee, T.10
Caldwell, J.11
Wang, J.12
Kollman, P.13
-
54
-
-
0347655649
-
CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations
-
Patel, S. and C.L. Brooks, CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations. J. Comput. Chem., 2004. 25(1): p. 1-15.
-
(2004)
J. Comput. Chem
, vol.25
, Issue.1
, pp. 1-15
-
-
Patel, S.1
Brooks, C.L.2
-
55
-
-
4043057278
-
CHARMM fluctuating charge force field for proteins: II-Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model
-
Patel, S., A.D. Mackerell, and C.L. Brooks, CHARMM fluctuating charge force field for proteins: II-Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J. Comput. Chem., 2004. 25(12): p. 1504-1514.
-
(2004)
J. Comput. Chem
, vol.25
, Issue.12
, pp. 1504-1514
-
-
Patel, S.1
Mackerell, A.D.2
Brooks, C.L.3
-
56
-
-
4444282928
-
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets S3AS and S3A6
-
Oostenbrink, C., A. Villa, A.E. Mark, and W.F. van Gunsteren, A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets S3AS and S3A6. J. Comput. Chem., 2004. 25(13): p. 1656-1676.
-
(2004)
J. Comput. Chem
, vol.25
, Issue.13
, pp. 1656-1676
-
-
Oostenbrink, C.1
Villa, A.2
Mark, A.E.3
van Gunsteren, W.F.4
-
57
-
-
21244467488
-
Validation of the S3A6 GROMOS force field
-
Oostenbrink, C., T.A. Soares, N.F. van der Vegt, and W.F. van Gunsteren, Validation of the S3A6 GROMOS force field. Eur. Biophys. J., 2005. 34(4): p. 273-284.
-
(2005)
Eur. Biophys. J
, vol.34
, Issue.4
, pp. 273-284
-
-
Oostenbrink, C.1
Soares, T.A.2
van der Vegt, N.F.3
van Gunsteren, W.F.4
-
58
-
-
85069276355
-
-
Damm, W., T.A. Halgren, R.B. Murphy, A.M. Smondyrev, R.A. Friesner, and W.L. Jorgensen, OPLS-2002: A new version of the OPLS-AA force field. Abstr. Pap. Am. Chem. S., 2002. 224: p. U471-U471.
-
Damm, W., T.A. Halgren, R.B. Murphy, A.M. Smondyrev, R.A. Friesner, and W.L. Jorgensen, OPLS-2002: A new version of the OPLS-AA force field. Abstr. Pap. Am. Chem. S., 2002. 224: p. U471-U471.
-
-
-
-
59
-
-
0038241788
-
-
Mu, Y.G., D.S. Kosov, and G. Stock, Conformational dynamics of trialanine in water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS force fields to NMR and infrared experiments. J. Phys. Chem. B, 2003.107(21): p. 5064-5073.
-
Mu, Y.G., D.S. Kosov, and G. Stock, Conformational dynamics of trialanine in water. 2. Comparison of AMBER, CHARMM, GROMOS, and OPLS force fields to NMR and infrared experiments. J. Phys. Chem. B, 2003.107(21): p. 5064-5073.
-
-
-
-
60
-
-
0024822360
-
A comparison of the Charmm, Amber and Ecepp potentials for peptides. 1. Conformational predictions for the tandemly repeated peptide (asn-ala-asn-pro)9
-
Roterman, I.K., K.D. Gibson, and H.A. Scheraga, A comparison of the Charmm, Amber and Ecepp potentials for peptides. 1. Conformational predictions for the tandemly repeated peptide (asn-ala-asn-pro)9. J. Biomol. Struct. & Dyn., 1989. 7(3): p. 391-419.
-
(1989)
J. Biomol. Struct. & Dyn
, vol.7
, Issue.3
, pp. 391-419
-
-
Roterman, I.K.1
Gibson, K.D.2
Scheraga, H.A.3
-
61
-
-
0024836024
-
A comparison of the Charmm, Amber and Ecepp potentials for peptides. 2. Phi-psi maps for N-acetyl alanine N′methyl amide-comparisons, contrasts and simple experimental tests
-
Roterman, I.K., M.H. Lambert, K.D. Gibson, and H.A. Scheraga, A comparison of the Charmm, Amber and Ecepp potentials for peptides. 2. Phi-psi maps for N-acetyl alanine N′methyl amide-comparisons, contrasts and simple experimental tests. J. Biomol. Struct. & Dyn., 1989. 7(3): p. 421-453.
-
(1989)
J. Biomol. Struct. & Dyn
, vol.7
, Issue.3
, pp. 421-453
-
-
Roterman, I.K.1
Lambert, M.H.2
Gibson, K.D.3
Scheraga, H.A.4
-
62
-
-
0141704162
-
Free energy landscape of protein folding in water: Explicit vs. implicit solvent
-
Zhou, R., Free energy landscape of protein folding in water: explicit vs. implicit solvent. Proteins, 2003. 53(2): p. 148-161.
-
(2003)
Proteins
, vol.53
, Issue.2
, pp. 148-161
-
-
Zhou, R.1
-
63
-
-
0032561237
-
Pathways to a protein folding intermediate observed in a 1 microsecond simulation in aqueous solution
-
Duan, Y. and P.A. Kollman, Pathways to a protein folding intermediate observed in a 1 microsecond simulation in aqueous solution. Science, 1998. 282(5389): p. 740-744.
-
(1998)
Science
, vol.282
, Issue.5389
, pp. 740-744
-
-
Duan, Y.1
Kollman, P.A.2
-
64
-
-
33646940952
-
Numerical- integration of cartesian equations of motion of a system with constraints-molecular-dynamics of N-alkanes
-
Ryckaert, J.P., G. Ciccotti, and H.J.C. Berendsen, Numerical- integration of cartesian equations of motion of a system with constraints-molecular-dynamics of N-alkanes. J. Comput. Phys., 1977. 23(3): p. 327-341.
-
(1977)
J. Comput. Phys
, vol.23
, Issue.3
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
65
-
-
0029878720
-
-
Humphrey, W., A. Dalke, and K. Schulten, VMD: Visual molecular dynamics. J. Mol. Graphics, 1996. 14(1): p. 33-38.
-
Humphrey, W., A. Dalke, and K. Schulten, VMD: Visual molecular dynamics. J. Mol. Graphics, 1996. 14(1): p. 33-38.
-
-
-
-
66
-
-
85069281640
-
-
DeLano, W.L. and J.W. Lam, PyMOL: A communications tool for computational models. Abstr. Pap. Am. Chem. S., 2005. 230: p. U1371-U1372.
-
DeLano, W.L. and J.W. Lam, PyMOL: A communications tool for computational models. Abstr. Pap. Am. Chem. S., 2005. 230: p. U1371-U1372.
-
-
-
-
67
-
-
0029119568
-
Rasmol-biomolecular graphics for all
-
Sayle, R.A. and E.J. Milnerwhite, Rasmol-biomolecular graphics for all. Trends Biochem. Sci., 1995. 20(9): p. 374-376.
-
(1995)
Trends Biochem. Sci
, vol.20
, Issue.9
, pp. 374-376
-
-
Sayle, R.A.1
Milnerwhite, E.J.2
-
68
-
-
0036385794
-
The backbone conformational entropy of protein folding: Experimental measures from atomic force microscopy
-
Thompson, J.B., H.G. Hansma, P.K. Hansma, and K.W. Plaxco, The backbone conformational entropy of protein folding: experimental measures from atomic force microscopy. J. Mol. Biol., 2002. 322(3): p. 645-652.
-
(2002)
J. Mol. Biol
, vol.322
, Issue.3
, pp. 645-652
-
-
Thompson, J.B.1
Hansma, H.G.2
Hansma, P.K.3
Plaxco, K.W.4
-
69
-
-
0028871798
-
Side-chain conformational entropy in protein folding
-
Doig, A.J. and M.J. Sternberg, Side-chain conformational entropy in protein folding. Protein Sci., 1995. 4(11): p. 2247-2251.
-
(1995)
Protein Sci
, vol.4
, Issue.11
, pp. 2247-2251
-
-
Doig, A.J.1
Sternberg, M.J.2
-
70
-
-
0033566618
-
Estimates of the loss of main-chain conformational entropy of different residues on protein folding
-
Pal, D. and P. Chakrabarti, Estimates of the loss of main-chain conformational entropy of different residues on protein folding. Proteins, 1999. 36(3): p. 332-339.
-
(1999)
Proteins
, vol.36
, Issue.3
, pp. 332-339
-
-
Pal, D.1
Chakrabarti, P.2
-
71
-
-
11044221141
-
The role of plastic beta-hairpin and weak hydrophobic core in the stability and unfolding of a full sequence design protein
-
Lei, H.X. and Y. Duan, The role of plastic beta-hairpin and weak hydrophobic core in the stability and unfolding of a full sequence design protein. J. Chem. Phys., 2004. 121(23): p. 12104-12111.
-
(2004)
J. Chem. Phys
, vol.121
, Issue.23
, pp. 12104-12111
-
-
Lei, H.X.1
Duan, Y.2
|