-
1
-
-
21244469736
-
Molecular dynamics study of water penetration in staphylococcal nuclease
-
Damjanović, A., García-Moreno, B., Lattman, E.E., García, A.E.: Molecular dynamics study of water penetration in staphylococcal nuclease. Proteins 60, 433-449 (2005)
-
(2005)
Proteins
, vol.60
, pp. 433-449
-
-
Damjanović, A.1
García-Moreno, B.2
Lattman, E.E.3
García, A.E.4
-
2
-
-
38849176920
-
A multiscale model for kinetics of formation and disintegration of spherical micelles
-
Mohan, G., Kopelevich, D.I.: A multiscale model for kinetics of formation and disintegration of spherical micelles. J. Chem. Phys. 128, 044905 (2008)
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 044905
-
-
Mohan, G.1
Kopelevich, D.I.2
-
3
-
-
27144516347
-
Coarse nonlinear dynamics and metastability of filling-emptying transitions: Water in carbon nanotubes
-
Sriraman, S., Kevrekidis, I.G., Hummer, G.: Coarse nonlinear dynamics and metastability of filling-emptying transitions: water in carbon nanotubes. Phys. Rev. Lett. 95, 130603 (2005)
-
(2005)
Phys. Rev. Lett.
, vol.95
, pp. 130603
-
-
Sriraman, S.1
Kevrekidis, I.G.2
Hummer, G.3
-
4
-
-
27344455346
-
Reproducible polypeptide folding and structure prediction using molecular dynamics simulations
-
Seibert, M.M., Patriksson, A., Hess, B., van der Spoel, D.: Reproducible polypeptide folding and structure prediction using molecular dynamics simulations. J. Mol. Biol. 354, 173-83 (2005)
-
(2005)
J. Mol. Biol.
, vol.354
, pp. 173-183
-
-
Seibert, M.M.1
Patriksson, A.2
Hess, B.3
Van Der Spoel, D.4
-
5
-
-
33745184030
-
Protein folding kinetics and thermodynamics from atomistic simulations
-
van der Spoel, D., Seibert, M.M.: Protein folding kinetics and thermodynamics from atomistic simulations. Phys. Rev. Lett. 96, 238102 (2006)
-
(2006)
Phys. Rev. Lett.
, vol.96
, pp. 238102
-
-
Van Der Spoel, D.1
Seibert, M.M.2
-
7
-
-
34249930405
-
Protein-folding dynamics: Overview of molecular simulation techniques
-
Scheraga, H.A., Khalili, M., Liwo, A.: Protein-folding dynamics: overview of molecular simulation techniques. Annu. Rev. Phys. Chem. 58, 57-83 (2007)
-
(2007)
Annu. Rev. Phys. Chem.
, vol.58
, pp. 57-83
-
-
Scheraga, H.A.1
Khalili, M.2
Liwo, A.3
-
8
-
-
0033600716
-
Submillisecond unfolding kinetics of apomyoglobin and its pH 4 intermediate
-
Jamin, M., Yeh, S., Rousseau, D.L., Baldwin, R.L.: Submillisecond unfolding kinetics of apomyoglobin and its pH 4 intermediate. J. Mol. Biol. 292, 731-740 (1999)
-
(1999)
J. Mol. Biol.
, vol.292
, pp. 731-740
-
-
Jamin, M.1
Yeh, S.2
Rousseau, D.L.3
Baldwin, R.L.4
-
9
-
-
33646472558
-
Pressure denaturation of apomyoglobin: A molecular dynamics simulation study
-
McCarthy, A.N., Grigera, J.R.: Pressure denaturation of apomyoglobin: a molecular dynamics simulation study. Biochim. Biophys. Acta. 1764, 506-515 (2006)
-
(2006)
Biochim. Biophys. Acta.
, vol.1764
, pp. 506-515
-
-
McCarthy, A.N.1
Grigera, J.R.2
-
10
-
-
0031932824
-
Structural and dynamic characterization of partially folded states of apomyoglobin and implications for protein folding
-
Eliezer, D., Yao, J., Dyson, H.J., Wright, P.E.: Structural and dynamic characterization of partially folded states of apomyoglobin and implications for protein folding. Nat. Struct. Biol. 5, 148-155 (1998)
-
(1998)
Nat. Struct. Biol.
, vol.5
, pp. 148-155
-
-
Eliezer, D.1
Yao, J.2
Dyson, H.J.3
Wright, P.E.4
-
11
-
-
0036291143
-
High pressure NMR reveals that apomyoglobin is an equilibrium mixture from the native to the unfolded
-
Kitahara, R., Yamada, H., Akasaka, K., Wright, P.E.: High pressure NMR reveals that apomyoglobin is an equilibrium mixture from the native to the unfolded. J. Mol. Biol. 320, 311-319 (2002)
-
(2002)
J. Mol. Biol.
, vol.320
, pp. 311-319
-
-
Kitahara, R.1
Yamada, H.2
Akasaka, K.3
Wright, P.E.4
-
12
-
-
0030933329
-
Modeling unfolded states of proteins and peptides. II. Backbone solvent accessibility
-
Creamer, T.P., Srinivasan, R., Rose, G.D.: Modeling unfolded states of proteins and peptides. II. Backbone solvent accessibility. Biochemistry 36, 2832-2835 (1997)
-
(1997)
Biochemistry
, vol.36
, pp. 2832-2835
-
-
Creamer, T.P.1
Srinivasan, R.2
Rose, G.D.3
-
13
-
-
33845923182
-
BPPred: A Web-based computational tool for predicting biophysical parameters of proteins
-
Geierhaas, C.D., Nickson, A.A., Lindorff-Larsen, K., Clarke, J., Vendruscolo, M.: BPPred: a Web-based computational tool for predicting biophysical parameters of proteins. Protein Sci. 16, 125-134 (2007)
-
(2007)
Protein Sci.
, vol.16
, pp. 125-134
-
-
Geierhaas, C.D.1
Nickson, A.A.2
Lindorff-Larsen, K.3
Clarke, J.4
Vendruscolo, M.5
-
14
-
-
0028820703
-
Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding
-
Myers, J.K., Pace, C.N., Scholtz, J.M.: Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding. Protein Sci. 4, 2138-2148 (1995)
-
(1995)
Protein Sci.
, vol.4
, pp. 2138-2148
-
-
Myers, J.K.1
Pace, C.N.2
Scholtz, J.M.3
-
15
-
-
0017802519
-
Solvent denaturation
-
Schellman, J.A.: Solvent denaturation. Biopolymers 17, 1305-1322 (1978)
-
(1978)
Biopolymers
, vol.17
, pp. 1305-1322
-
-
Schellman, J.A.1
-
16
-
-
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. 91, 43-56 (1995)
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 43-56
-
-
Berendsen, H.J.C.1
Van Der Spoel, D.2
Van Drunen, R.3
-
17
-
-
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. Molecular Modeling 7, 306-317 (2001)
-
(2001)
J. Molecular Modeling
, vol.7
, pp. 306-317
-
-
Lindahl, E.1
Hess, B.2
Van Der Spoel, D.3
-
18
-
-
2142813682
-
Computer simulation of molecular dynamics: Methodology, applications, and perspectives in chemistry
-
van Gunsteren, W.F., Berendsen, H.J.C.: Computer simulation of molecular dynamics: methodology, applications, and perspectives in chemistry. Angew. Chem. Int. Ed. Engl. 29, 992-1023 (1990)
-
(1990)
Angew. Chem. Int. Ed. Engl.
, vol.29
, pp. 992-1023
-
-
Van Gunsteren, W.F.1
Berendsen, H.J.C.2
-
19
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L.: Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926-935 (1983)
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
20
-
-
0000454818
-
A force field for liquid dimethyl sulfoxide and liquid properties of liquid dimethyl sulfoxide calculated using molecular dynamics simulation
-
Liu, H., Müller-Plathe, F., van Gunsteren, W.F.: A force field for liquid dimethyl sulfoxide and liquid properties of liquid dimethyl sulfoxide calculated using molecular dynamics simulation. J. Am. Chem. Soc. 117, 4363-4366 (1995)
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 4363-4366
-
-
Liu, H.1
Müller-Plathe, F.2
Van Gunsteren, W.F.3
-
21
-
-
0008025298
-
Convergence properties of free energy calculations: Cyclodextrin complexes as a case study
-
Mark, A.E., van Helden, S.P., Smith, P.E., Janssen, L.H.M., van Gunsteren, W.F.: Convergence properties of free energy calculations: cyclodextrin complexes as a case study. J. Am. Chem. Soc. 116, 6293-6302 (1994)
-
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 6293-6302
-
-
Mark, A.E.1
Van Helden, S.P.2
Smith, P.E.3
Janssen, L.H.M.4
Van Gunsteren, W.F.5
-
22
-
-
0027642798
-
Molecular dynamics simulation of the stability of a 22 residue alpha-helix in water and 30% trifluoroethanol
-
van Buuren, A.R., Berendsen, H.J.C.: Molecular dynamics simulation of the stability of a 22 residue alpha-helix in water and 30% trifluoroethanol. Biopolymers 33, 1159-1166 (1993)
-
(1993)
Biopolymers
, vol.33
, pp. 1159-1166
-
-
Van Buuren, A.R.1
Berendsen, H.J.C.2
-
23
-
-
0011746241
-
A molecular dynamics study of the decane/water interface
-
van Buuren, A.R., Marrink, S.J., Berendsen, H.J.C.: A molecular dynamics study of the decane/water interface. J. Phys. Chem. 97, 9206-9212 (1993)
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 9206-9212
-
-
Van Buuren, A.R.1
Marrink, S.J.2
Berendsen, H.J.C.3
-
24
-
-
0003831852
-
Gromos-87 manual
-
AG Groningen, The Netherlands
-
van Gunsteren, W.F., Berendsen, H.J.C.: Gromos-87 manual. Biomos BV Nijenborgh, vol. 4, p. 9747. AG Groningen, The Netherlands (1987)
-
(1987)
Biomos BV Nijenborgh
, vol.4
, pp. 9747
-
-
Van Gunsteren, W.F.1
Berendsen, H.J.C.2
-
25
-
-
0000388705
-
LINCS: A linear constraint solver for molecular simulations
-
Hess, B., Bekker, H., Berendsen, H.J.C., Fraaije, J.G.E.M.: LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18, 1463-1472 (1997)
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.J.C.3
Fraaije, J.G.E.M.4
-
26
-
-
84986440341
-
SETTLE 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. 13, 952-962 (1992)
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
27
-
-
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. 91, 6269-6271 (1987)
-
(1987)
J. Chem. Phys.
, vol.91
, pp. 6269-6271
-
-
Berendsen, H.J.C.1
Grigera, J.R.2
Straatsma, T.P.3
-
28
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H.J.C., Postma, J.P.M., DiNola, A., Haak, J.R.: Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684-3690 (1984)
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Dinola, A.3
Haak, J.R.4
-
29
-
-
36248975150
-
-
van der Spoel, D., Lindahl, E., Hess, B., van Buuren, A.R., Apol, E., Meulenhoff, P.J., Tieleman, D.P., Sijbers, A.L.T.M., Feenstra, K.A., van Drunen, R., Berendsen, H.J.C.: Gromacs user manual version 3.2, www.gromacs.org (2004)
-
(2004)
Gromacs User Manual Version 3.2
-
-
Van Der Spoel, D.1
Lindahl, E.2
Hess, B.3
Van Buuren, A.R.4
Apol, E.5
Meulenhoff, P.J.6
Tieleman, D.P.7
Sijbers, A.L.T.M.8
Feenstra, K.A.9
Van Drunen, R.10
Berendsen, H.J.C.11
|