-
1
-
-
0034613172
-
Dynamically Controlled Protein Tunneling Paths in Photosynthetic Reaction Centers
-
Balabin, L. A.; Onuchic, J. N. Dynamically Controlled Protein Tunneling Paths in Photosynthetic Reaction Centers. Science 2000, 290, 114-117.
-
(2000)
Science
, vol.290
, pp. 114-117
-
-
Balabin, L.A.1
Onuchic, J.N.2
-
2
-
-
0034864528
-
Generalized-ensemble algorithms for molecular simulations of biopolymers
-
Mitsutake, A.; Sugita, Y.; Okamoto, Y. Generalized-ensemble algorithms for molecular simulations of biopolymers. Biopolymers 2001, 60(2), 96-123.
-
(2001)
Biopolymers
, vol.60
, Issue.2
, pp. 96-123
-
-
Mitsutake, A.1
Sugita, Y.2
Okamoto, Y.3
-
3
-
-
0000106469
-
Multicanonical algorithms for first-order phase transitions
-
Berg, B. A.; Neuhaus, T. Multicanonical algorithms for first-order phase transitions. Phys. Lett. 1991, 267 (2), 249-53.
-
(1991)
Phys. Lett
, vol.267
, Issue.2
, pp. 249-253
-
-
Berg, B.A.1
Neuhaus, T.2
-
4
-
-
4243613377
-
Multicanonical ensemble: A new approach to simulate first-order phase transitions
-
Berg, B. A.; Neuhaus, T. Multicanonical ensemble: A new approach to simulate first-order phase transitions. Phys. Rev. Lett. 1992, 68 (1), 9-12.
-
(1992)
Phys. Rev. Lett
, vol.68
, Issue.1
, pp. 9-12
-
-
Berg, B.A.1
Neuhaus, T.2
-
5
-
-
84953648015
-
New approach to Monte Carlo calculations of the free energy: Method of expanded ensembles
-
Lyubartsev, A. P.; Martinovski, A. A.; Shevkunov, S. V.; Vorontsov-Velyaminov, P. N. New approach to Monte Carlo calculations of the free energy: Method of expanded ensembles. J. Chem. Phys. 1992, 96 (3), 1776-83.
-
(1992)
J. Chem. Phys
, vol.96
, Issue.3
, pp. 1776-1783
-
-
Lyubartsev, A.P.1
Martinovski, A.A.2
Shevkunov, S.V.3
Vorontsov-Velyaminov, P.N.4
-
6
-
-
33644899039
-
Simulated tempering: A new Monte Carlo scheme
-
Marinari, E.; Parisi, G. Simulated tempering: A new Monte Carlo scheme. Europhys. Lett. 1992, 19, 451-58.
-
(1992)
Europhys. Lett
, vol.19
, pp. 451-458
-
-
Marinari, E.1
Parisi, G.2
-
7
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 1999, 314, 141-51.
-
(1999)
Chem. Phys. Lett
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
8
-
-
0000888146
-
Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape
-
Sugita, Y.; Okamoto, Y. Replica-exchange multicanonical algorithm and multicanonical replica-exchange method for simulating systems with rough energy landscape. Chem. Phys. Lett. 2000, 329, 261-70.
-
(2000)
Chem. Phys. Lett
, vol.329
, pp. 261-270
-
-
Sugita, Y.1
Okamoto, Y.2
-
9
-
-
0034294024
-
Multidimensional replica-exchange method for free-energy calculations
-
Sugita, Y.; Kitao, A.; Okamoto, Y. Multidimensional replica-exchange method for free-energy calculations. J. Chem. Phys. 2000, 113 (15), 6042-51.
-
(2000)
J. Chem. Phys
, vol.113
, Issue.15
, pp. 6042-6051
-
-
Sugita, Y.1
Kitao, A.2
Okamoto, Y.3
-
10
-
-
0001007392
-
Replica-exchange molecular dynamics simulation for supercooled liquids
-
5B, 5473-6
-
Yamamoto, R.; Kob, W. Replica-exchange molecular dynamics simulation for supercooled liquids. Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top. 2000, 61 (5B), 5473-6.
-
(2000)
Phys. Rev. E: Stat. Phys., Plasmas, Fluids, Relat. Interdiscip. Top
, vol.61
-
-
Yamamoto, R.1
Kob, W.2
-
11
-
-
0000551750
-
Replica-exchange Monte Carlo method for the isobaric-isothermal ensemble
-
Okabe, T.; Kawata, M.; Okamoto, Y.; Mikami, M. Replica-exchange Monte Carlo method for the isobaric-isothermal ensemble. Chem. Phys. Lett. 2001, 335, 435-9.
-
(2001)
Chem. Phys. Lett
, vol.335
, pp. 435-439
-
-
Okabe, T.1
Kawata, M.2
Okamoto, Y.3
Mikami, M.4
-
12
-
-
0036467163
-
Structure of Metenkephalin in explicit aqueous solution using replica exchange molecular dynamics
-
Sanbonmatsu, K. Y.; Garcia, A. E. Structure of Metenkephalin in explicit aqueous solution using replica exchange molecular dynamics. Proteins 2002, 46 (2), 225-34.
-
(2002)
Proteins
, vol.46
, Issue.2
, pp. 225-234
-
-
Sanbonmatsu, K.Y.1
Garcia, A.E.2
-
13
-
-
0000597634
-
Domain-wall free energy of spin-glass models: Numerical model and boundary conditions
-
Hukushima, K. Domain-wall free energy of spin-glass models: numerical model and boundary conditions. Phys. Rev. E.: Stat., Nonlinear, Soft Matter Phys. 1999, 60 (4), 3606-3614.
-
(1999)
Phys. Rev. E.: Stat., Nonlinear, Soft Matter Phys
, vol.60
, Issue.4
, pp. 3606-3614
-
-
Hukushima, K.1
-
14
-
-
0034275016
-
Comparison of three Monte Carlo conformational search strategies for a protein-like homopolymer model: Folding thermodynamics and identification of low-energy structures
-
Gront, D.; Kolinski, A.; Skolnick, J. Comparison of three Monte Carlo conformational search strategies for a protein-like homopolymer model: Folding thermodynamics and identification of low-energy structures. J. Chem. Phys. 2000, 113 (12), 5065-71.
-
(2000)
J. Chem. Phys
, vol.113
, Issue.12
, pp. 5065-5071
-
-
Gront, D.1
Kolinski, A.2
Skolnick, J.3
-
15
-
-
0030516672
-
Exchange Monte Carlo method and application to spin glass simulations
-
Hukushima, K.; Nemoto, K. Exchange Monte Carlo method and application to spin glass simulations. J. Phys. Soc. Jpn. 1996, 65 (4), 1604-8.
-
(1996)
J. Phys. Soc. Jpn
, vol.65
, Issue.4
, pp. 1604-1608
-
-
Hukushima, K.1
Nemoto, K.2
-
16
-
-
0037157317
-
On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
-
Fukunishi, H.; Watanabe, O.; Takada, S. On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction. J. Chem. Phys. 2002, 116 (20), 9058-67.
-
(2002)
J. Chem. Phys
, vol.116
, Issue.20
, pp. 9058-9067
-
-
Fukunishi, H.1
Watanabe, O.2
Takada, S.3
-
17
-
-
21444439271
-
Molecular dynamics simulations of DNA dimers based on replica-exchange umbrella sampling II: Free energy analysis
-
Murata, K.; Sugita, Y.; Okamoto, Y. Molecular dynamics simulations of DNA dimers based on replica-exchange umbrella sampling II: Free energy analysis. J. Theor. Comput. Chem. 2005, 4, 433-448.
-
(2005)
J. Theor. Comput. Chem
, vol.4
, pp. 433-448
-
-
Murata, K.1
Sugita, Y.2
Okamoto, Y.3
-
18
-
-
20544464457
-
How well can simulation predict protein folding kinetics and thermodynamics
-
Snow, C. D.; Sorin, E. J.; Rhee, Y. M.; Pande, V. How well can simulation predict protein folding kinetics and thermodynamics. Annu. Rev. Biophys. Biomol. Struct. 2005, 34, 43.
-
(2005)
Annu. Rev. Biophys. Biomol. Struct
, vol.34
, pp. 43
-
-
Snow, C.D.1
Sorin, E.J.2
Rhee, Y.M.3
Pande, V.4
-
19
-
-
0041874658
-
The interplay between protein dynamics and frustration of nonbonded interactions as revealed by molecular dynamics simulations
-
Tavernelli, I.; Di Iorio, E. E. The interplay between protein dynamics and frustration of nonbonded interactions as revealed by molecular dynamics simulations. Chem. Phys. Lett. 2001, 345, 287-294.
-
(2001)
Chem. Phys. Lett
, vol.345
, pp. 287-294
-
-
Tavernelli, I.1
Di Iorio, E.E.2
-
20
-
-
0002466234
-
The physics of protein folding
-
Wolynes, P. G.; Eaton, W. A. The physics of protein folding. Phys. World 1999, 12, 39-44.
-
(1999)
Phys. World
, vol.12
, pp. 39-44
-
-
Wolynes, P.G.1
Eaton, W.A.2
-
21
-
-
0028947257
-
Funnels, pathways, and the energy landscape of protein folding: A synthesis
-
Bryngelson, J. D.; Onuchic, J. N.; Socci, N. D.; Wolynes, P. G. Funnels, pathways, and the energy landscape of protein folding: A synthesis. Proteins 1995, 21 (3), 167-95.
-
(1995)
Proteins
, vol.21
, Issue.3
, pp. 167-195
-
-
Bryngelson, J.D.1
Onuchic, J.N.2
Socci, N.D.3
Wolynes, P.G.4
-
22
-
-
0000594925
-
The multiple-minima problem in the conformational analysis of molecules. Deformation of the potential energy hypersurface by the diffusion equation method
-
Piela, L.; Kostrowicki, J.; Scheraga, H. A. The multiple-minima problem in the conformational analysis of molecules. Deformation of the potential energy hypersurface by the diffusion equation method. J. Chem. Phys. 1989, 93, 3339-3346.
-
(1989)
J. Chem. Phys
, vol.93
, pp. 3339-3346
-
-
Piela, L.1
Kostrowicki, J.2
Scheraga, H.A.3
-
23
-
-
0001031118
-
Application of the diffusion equation method for global optimization to oligopeptides
-
Kostrowicki, J.; Scheraga, H. A. Application of the diffusion equation method for global optimization to oligopeptides. J. Chem. Phys. 1992, 96, 7442-7449.
-
(1992)
J. Chem. Phys
, vol.96
, pp. 7442-7449
-
-
Kostrowicki, J.1
Scheraga, H.A.2
-
24
-
-
0642285282
-
Reproducible protein folding with the stochastic tunneling method
-
Schug, A.; Herges, T.; Wenzel, W. Reproducible protein folding with the stochastic tunneling method. Phys. Rev. Lett. 2003, 91 (15), 158102.
-
(2003)
Phys. Rev. Lett
, vol.91
, Issue.15
, pp. 158102
-
-
Schug, A.1
Herges, T.2
Wenzel, W.3
-
25
-
-
0032932375
-
A potential smoothing algorithm accurately predicts transmembrane helix packing
-
Pappu, R. V.; Marshall, G. R.; Ponder, J. W. A potential smoothing algorithm accurately predicts transmembrane helix packing. Nat. Struct. Mol. Biol. 1999, 6(1), 50-55.
-
(1999)
Nat. Struct. Mol. Biol
, vol.6
, Issue.1
, pp. 50-55
-
-
Pappu, R.V.1
Marshall, G.R.2
Ponder, J.W.3
-
26
-
-
2442629457
-
Calnexin, calreticulin and ERp57: Teammates in glycoprotein folding
-
Ellgaard, L.; Frickel, E.-M. Calnexin, calreticulin and ERp57: teammates in glycoprotein folding. Cell Biochem. Biophys. 2003, 39, 223-248.
-
(2003)
Cell Biochem. Biophys
, vol.39
, pp. 223-248
-
-
Ellgaard, L.1
Frickel, E.-M.2
-
27
-
-
0036387164
-
NMR structures of 36 and 73-residue fragments of the calreticulin P-domain
-
Ellgaard, L.; Bettendorff, P.; Braun, D.; Herrmann, T.; Fiorito, F.; Jelesarov, I.; Guntert, P.; Helenius, A.; Wuthrich, K. NMR structures of 36 and 73-residue fragments of the calreticulin P-domain. J. Mol. Biol. 2002, 322 (4), 773-84.
-
(2002)
J. Mol. Biol
, vol.322
, Issue.4
, pp. 773-784
-
-
Ellgaard, L.1
Bettendorff, P.2
Braun, D.3
Herrmann, T.4
Fiorito, F.5
Jelesarov, I.6
Guntert, P.7
Helenius, A.8
Wuthrich, K.9
-
28
-
-
0035846853
-
Three-dimensional structure topology of the calreticulin P-domain based on NMR assignment
-
Ellgaard, L.; Riek, R.; Braun, D.; Herrmann, T.; Helenius, A.; Wuthrich, K. Three-dimensional structure topology of the calreticulin P-domain based on NMR assignment. FEBS Lett. 2001, 488 (1-2), 69-73.
-
(2001)
FEBS Lett
, vol.488
, Issue.1-2
, pp. 69-73
-
-
Ellgaard, L.1
Riek, R.2
Braun, D.3
Herrmann, T.4
Helenius, A.5
Wuthrich, K.6
-
29
-
-
0035853075
-
NMR structure of the calreticulin P-domain
-
Ellgaard, L.; Riek, R.; Herrmann, T.; Guntert, P.; Braun, D.; Helenius, A.; Wuthrich, K. NMR structure of the calreticulin P-domain. Proc. Natl. Acad. Sci. U.S.A. 2001, 98 (6), 3133-8.
-
(2001)
Proc. Natl. Acad. Sci. U.S.A
, vol.98
, Issue.6
, pp. 3133-3138
-
-
Ellgaard, L.1
Riek, R.2
Herrmann, T.3
Guntert, P.4
Braun, D.5
Helenius, A.6
Wuthrich, K.7
-
30
-
-
0029633168
-
GROMACS: A message-passing parallel molecular dynamics implementation
-
Berendsen, H. J. C.; van der Spoel, D.; van Drunen, R. GROMACS: A message-passing parallel molecular dynamics implementation. Comput. Phys. Commun. 1995, 91, 43-56.
-
(1995)
Comput. Phys. Commun
, vol.91
, pp. 43-56
-
-
Berendsen, H.J.C.1
van der Spoel, D.2
van Drunen, R.3
-
31
-
-
0035789518
-
GROMACS 3.0: A package for molecular simulation and trajectory analysis
-
Lindahl, E.; Hess, B.; van der Spoel, D. GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Model. 2001, 7, 306-17.
-
(2001)
J. Mol. Model
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
van der Spoel, D.3
-
32
-
-
0003544049
-
-
vdf Hochschulverlag AG an der ETH Zurich, BIOMOS b.v. Zurich Groningen: Zurich, Switzerland; Groningen, Netherlands
-
van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular simulation: The GROMOS96 manual and user guide; vdf Hochschulverlag AG an der ETH Zurich, BIOMOS b.v. Zurich Groningen: Zurich, Switzerland; Groningen, Netherlands, 1996.
-
(1996)
Biomolecular simulation: The GROMOS96 manual and user guide
-
-
van Gunsteren, W.F.1
Billeter, S.R.2
Eising, A.A.3
Hünenberger, P.H.4
Krüger, P.5
Mark, A.E.6
Scott, W.R.P.7
Tironi, I.G.8
-
33
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Di Nola, A.; Haak, J. R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 1984, 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
Di Nola, A.4
Haak, J.R.5
-
34
-
-
0000388705
-
A linear constraint colver for molecular simulations
-
Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. LINCS: A linear constraint colver for molecular simulations. J. Comput. Chem. 1997, 18, 1463-72.
-
(1997)
J. Comput. Chem
, vol.18
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.J.C.3
Fraaije, J.G.E.4
LINCS, M.5
-
35
-
-
84986440341
-
An analytical version of the SHAKE and RATTLE algorithms for rigid water models
-
Miyamoto, S.; Kollman, P. A. SETTLE: An analytical version of the SHAKE and RATTLE algorithms for rigid water models. J. Comput. Chem. 1992, 13, 952-62.
-
(1992)
J. Comput. Chem
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.2
SETTLE, A.3
-
36
-
-
4544369164
-
A generalized reaction field method for molecular dynamics simulations
-
Tironi, I. G.; Sperb, R.; Smith, P. E.; van Gunsteren, W. F. A generalized reaction field method for molecular dynamics simulations. J. Chem. Phys. 1995, 102, 5451-5459.
-
(1995)
J. Chem. Phys
, vol.102
, pp. 5451-5459
-
-
Tironi, I.G.1
Sperb, R.2
Smith, P.E.3
van Gunsteren, W.F.4
-
37
-
-
2242491482
-
Consistent dielectric properties of the simple point charge and extended simple point charge water models at 277 and 300 K
-
Smith, P. E.; van Gunsteren, W. F. Consistent dielectric properties of the simple point charge and extended simple point charge water models at 277 and 300 K. J. Chem. Phys. 1994, 100 (4), 3169-74.
-
(1994)
J. Chem. Phys
, vol.100
, Issue.4
, pp. 3169-3174
-
-
Smith, P.E.1
van Gunsteren, W.F.2
-
38
-
-
1242346370
-
The missing term in effective pair potentials
-
Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. The missing term in effective pair potentials. J. Chem. Phys. 1987, 91 (24), 6269-71.
-
(1987)
J. Chem. Phys
, vol.91
, Issue.24
, pp. 6269-6271
-
-
Berendsen, H.J.C.1
Grigera, J.R.2
Straatsma, T.P.3
-
39
-
-
84986519238
-
The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
-
Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J. Comput. Chem. 1992, 13 (8), 1011-21.
-
(1992)
J. Comput. Chem
, vol.13
, Issue.8
, pp. 1011-1021
-
-
Kumar, S.1
Bouzida, D.2
Swendsen, R.H.3
Kollman, P.A.4
Rosenberg, J.M.5
-
40
-
-
84986497803
-
Multidimensional free-energy calculations using the weighted histogram analysis method
-
Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A. Multidimensional free-energy calculations using the weighted histogram analysis method. J. Comput. Chem. 1995, 16 (11), 1339-50.
-
(1995)
J. Comput. Chem
, vol.16
, Issue.11
, pp. 1339-1350
-
-
Kumar, S.1
Rosenberg, J.M.2
Bouzida, D.3
Swendsen, R.H.4
Kollman, P.A.5
-
41
-
-
0000764091
-
Constant-temperature free energy surfaces for physical and chemical processes
-
Boczko, E. M.; Brooks, C. L., III. Constant-temperature free energy surfaces for physical and chemical processes. J. Phys. Chem. 1993, 97 (17), 4509-13.
-
(1993)
J. Phys. Chem
, vol.97
, Issue.17
, pp. 4509-4513
-
-
Boczko, E.M.1
Brooks III, C.L.2
-
42
-
-
0141707867
-
Protein dynamics, thermal stability, and free-energy landscapes: A molecular dynamics investigation
-
Tavernelli, I.; Cotesta, S.; Di Iorio, E. E. Protein dynamics, thermal stability, and free-energy landscapes: a molecular dynamics investigation. Biophys. J. 2003, 85 (4), 2641-9.
-
(2003)
Biophys. J
, vol.85
, Issue.4
, pp. 2641-2649
-
-
Tavernelli, I.1
Cotesta, S.2
Di Iorio, E.E.3
-
43
-
-
0033556236
-
Peptide folding: When simulation meets experiment
-
Daura, X.; Gademann, K.; Jaun, B.; Seebach, D.; van Gunsteren, W. F.; Mark, A. E. Peptide folding: When simulation meets experiment. Angew. Chem., Int. Ed. 1999, 38, 236-40.
-
(1999)
Angew. Chem., Int. Ed
, vol.38
, pp. 236-240
-
-
Daura, X.1
Gademann, K.2
Jaun, B.3
Seebach, D.4
van Gunsteren, W.F.5
Mark, A.E.6
-
44
-
-
0141976331
-
Replica-exchange method using the generalized effective potential
-
Jang, S.; Shin, S.; Pak, Y. Replica-exchange method using the generalized effective potential. Phys. Rev. Lett. 2003, 91 (5), 058305.
-
(2003)
Phys. Rev. Lett
, vol.91
, Issue.5
, pp. 058305
-
-
Jang, S.1
Shin, S.2
Pak, Y.3
-
45
-
-
0034806777
-
The beta-peptide hairpin in solution: Conformational study of a beta-hexapeptide in methanol by NMR spectroscopy and MD simulation
-
Daura, X.; Gademann, K.; Schafer, H.; Jaun, B.; Seebach, D.; van Gunsteren, W. F. The beta-peptide hairpin in solution: conformational study of a beta-hexapeptide in methanol by NMR spectroscopy and MD simulation. J. Am. Chem. Soc. 2001, 123 (10), 2393-404.
-
(2001)
J. Am. Chem. Soc
, vol.123
, Issue.10
, pp. 2393-2404
-
-
Daura, X.1
Gademann, K.2
Schafer, H.3
Jaun, B.4
Seebach, D.5
van Gunsteren, W.F.6
-
46
-
-
0020997912
-
Dictionary of secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
-
Kabsch, W.; Sander, C. Dictionary of secondary structure: Pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22, 2577-2637.
-
(1983)
Biopolymers
, vol.22
, pp. 2577-2637
-
-
Kabsch, W.1
Sander, C.2
|