-
1
-
-
0000577041
-
Large-amplitude nonlinear motions in proteins
-
Garcia AE. Large-amplitude nonlinear motions in proteins. Phys Rev Lett 1992;68:2696-2699.
-
(1992)
Phys Rev Lett
, vol.68
, pp. 2696-2699
-
-
Garcia, A.E.1
-
3
-
-
0021449809
-
Quasiharmonic method for studying very low frequency modes in proteins
-
Levy RM, Srinivasan AR, Olson WK, McCammon JA. Quasiharmonic method for studying very low frequency modes in proteins. Biopolymers 1984;23:1099-1112.
-
(1984)
Biopolymers
, vol.23
, pp. 1099-1112
-
-
Levy, R.M.1
Srinivasan, A.R.2
Olson, W.K.3
McCammon, J.A.4
-
4
-
-
0000998079
-
The effects of solvent on the conformation and the collective motions of protein: Normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum
-
Kitao A, Hirata F, Gō N. The effects of solvent on the conformation and the collective motions of protein: normal mode analysis and molecular dynamics simulations of melittin in water and in vacuum. J Chem Phys 1991;158:447-472.
-
(1991)
J Chem Phys
, vol.158
, pp. 447-472
-
-
Kitao, A.1
Hirata, F.2
Go, N.3
-
5
-
-
0027732618
-
Effect of solvent on collective motions in globular proteins
-
Hayward S, Kitao A, Hirata F, Gō N. Effect of solvent on collective motions in globular proteins. J Mol Biol 1993;234:1207-1217.
-
(1993)
J Mol Biol
, vol.234
, pp. 1207-1217
-
-
Hayward, S.1
Kitao, A.2
Hirata, F.3
Go, N.4
-
6
-
-
0000081668
-
Collective variable description of native protein dynamics
-
Hayward S, Gō N. Collective variable description of native protein dynamics. Annu Rev Phys Chem 1995;46:223-250.
-
(1995)
Annu Rev Phys Chem
, vol.46
, pp. 223-250
-
-
Hayward, S.1
Go, N.2
-
7
-
-
0029075795
-
The essential dynamics of thermolysin - Confirmation of hinge-bending motion and comparison of simulations in vacuum and water
-
Van Aalten DMF, Amadei A, Vriend G, Linssen ABM, Venema G, Berendsen HJC, Eijsink VGH. The essential dynamics of thermolysin - confirmation of hinge-bending motion and comparison of simulations in vacuum and water. Proteins 1995;22:45-54.
-
(1995)
Proteins
, vol.22
, pp. 45-54
-
-
Van Aalten, D.M.F.1
Amadei, A.2
Vriend, G.3
Linssen, A.B.M.4
Venema, G.5
Berendsen, H.J.C.6
Eijsink, V.G.H.7
-
8
-
-
0029586726
-
Essential dynamics of the cellular retinol binding protein - Evidence for ligand induced conformational changes
-
Van Aalten DMF, Findlay JBC, Amadei A, Berendsen HJC. Essential dynamics of the cellular retinol binding protein -evidence for ligand induced conformational changes. Protein Eng 1995;8:1129-1136.
-
(1995)
Protein Eng
, vol.8
, pp. 1129-1136
-
-
Van Aalten, D.M.F.1
Findlay, J.B.C.2
Amadei, A.3
Berendsen, H.J.C.4
-
9
-
-
0031019423
-
Engineering protein mechanics: Inhibition of concerted motions of the cellular retinol binding protein by site-directed mutagenesis
-
Van Aalten DMF, Jones PC, De Sousa M, Findlay JBC. Engineering protein mechanics: inhibition of concerted motions of the cellular retinol binding protein by site-directed mutagenesis. Protein Eng 1997;10:31-38.
-
(1997)
Protein Eng
, vol.10
, pp. 31-38
-
-
Van Aalten, D.M.F.1
Jones, P.C.2
De Sousa, M.3
Findlay, J.B.C.4
-
10
-
-
0029985860
-
An efficient method for sampling the essential subspace of proteins
-
Amadei A, Linssen ABM, De Groot BL, Van Aalten DMF, Berendsen HJC. An efficient method for sampling the essential subspace of proteins. J Biomol Struct Dyn 1996;13:615-626.
-
(1996)
J Biomol Struct Dyn
, vol.13
, pp. 615-626
-
-
Amadei, A.1
Linssen, A.B.M.2
De Groot, B.L.3
Van Aalten, D.M.F.4
Berendsen, H.J.C.5
-
11
-
-
0029967692
-
Towards an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin
-
De Groot BL, Amadei A, Van Aalten DMF, Berendsen HJC. Towards an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin. J Biomol Struct Dyn 1996;13:741-751.
-
(1996)
J Biomol Struct Dyn
, vol.13
, pp. 741-751
-
-
De Groot, B.L.1
Amadei, A.2
Van Aalten, D.M.F.3
Berendsen, H.J.C.4
-
12
-
-
0029811307
-
An extended sampling of the configurational space of HPr from E. coli
-
De Groot BL, Amadei A, Scheek RM, Van Nuland NAJ, Berendsen HJC. An extended sampling of the configurational space of HPr from E. coli. Proteins 1996;26:314-322.
-
(1996)
Proteins
, vol.26
, pp. 314-322
-
-
De Groot, B.L.1
Amadei, A.2
Scheek, R.M.3
Van Nuland, N.A.J.4
Berendsen, H.J.C.5
-
13
-
-
0031002350
-
The structure of the translational initiation factor IF1 from E. coli contains an oligomer-binding motif
-
Sette M, Van Tilborg P, Spurio RR, Kaptein MP, Gualerzi CO, Boelens R. The structure of the translational initiation factor IF1 from E. coli contains an oligomer-binding motif. EMBO J 1997;16: 1436-1443.
-
(1997)
EMBO J
, vol.16
, pp. 1436-1443
-
-
Sette, M.1
Van Tilborg, P.2
Spurio, R.R.3
Kaptein, M.P.4
Gualerzi, C.O.5
Boelens, R.6
-
14
-
-
0028354429
-
Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR
-
Gallagher T, Alexander P, Bryan P, Gilliland GL. Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR. Biochemistry 1994;33: 4721-4729.
-
(1994)
Biochemistry
, vol.33
, pp. 4721-4729
-
-
Gallagher, T.1
Alexander, P.2
Bryan, P.3
Gilliland, G.L.4
-
15
-
-
4243264015
-
Dynamics of structural transitions in liquids
-
Stillinger FH, Weber TA. Dynamics of structural transitions in liquids. Phys Rev A 1983;28:2408-2416.
-
(1983)
Phys Rev A
, vol.28
, pp. 2408-2416
-
-
Stillinger, F.H.1
Weber, T.A.2
-
16
-
-
0022419152
-
Protein normal-mode dynamics - Trypsin-inhibitor, crambin, ribonuclease, and lysozyme
-
Levitt M, Sander C, Stern PS. Protein normal-mode dynamics -trypsin-inhibitor, crambin, ribonuclease, and lysozyme. J Mol Biol 1985;181:423-447.
-
(1985)
J Mol Biol
, vol.181
, pp. 423-447
-
-
Levitt, M.1
Sander, C.2
Stern, P.S.3
-
17
-
-
0020771265
-
Dynamics of a small globular protein in terms of low-frequency vibrational modes
-
Gō N, Noguti T, Nishikawa T. Dynamics of a small globular protein in terms of low-frequency vibrational modes. Proc Natl Acad Sci USA 1983;80:3696-3700.
-
(1983)
Proc Natl Acad Sci USA
, vol.80
, pp. 3696-3700
-
-
Go, N.1
Noguti, T.2
Nishikawa, T.3
-
18
-
-
0000991642
-
Harmonic dynamics of proteins: Normal modes and fluctuations in bovine pancreatic trypsin inhibitor
-
Brooks BR, Karplus M. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc Natl Acad Sci USA 1983;80:6571-6575.
-
(1983)
Proc Natl Acad Sci USA
, vol.80
, pp. 6571-6575
-
-
Brooks, B.R.1
Karplus, M.2
-
19
-
-
84986469420
-
Harmonic analysis of large systems. II. Comparison of different protein models
-
Janezic D, Brooks BR. Harmonic analysis of large systems. II. Comparison of different protein models. J Comp Chem 1995;16: 1543-1553.
-
(1995)
J Comp Chem
, vol.16
, pp. 1543-1553
-
-
Janezic, D.1
Brooks, B.R.2
-
20
-
-
84986473952
-
Harmonic analysis of large systems. III. Comparison with molecular dynamics
-
Janezic D, Venable M, Brooks BR. Harmonic analysis of large systems. III. Comparison with molecular dynamics. J Comp Chem 1995;16:1707-1713.
-
(1995)
J Comp Chem
, vol.16
, pp. 1707-1713
-
-
Janezic, D.1
Venable, M.2
Brooks, B.R.3
-
21
-
-
0032374086
-
Energy landscape of a native protein: Jumping-among-minima model
-
Kitao A, Hayward S, Gō N. Energy landscape of a native protein: jumping-among-minima model. Proteins 1998;33:496-517.
-
(1998)
Proteins
, vol.33
, pp. 496-517
-
-
Kitao, A.1
Hayward, S.2
Go, N.3
-
22
-
-
0003772631
-
-
Nijenborgh 4, 9747 AG Groningen, The Netherlands. Internet
-
Van der Spoel D, Berendsen HJC, Van Buuren AR, Apol E, Meulenhoff PJ, Sijbers ALTM, Van Drunen R. Gromacs User Manual. Nijenborgh 4, 9747 AG Groningen, The Netherlands. Internet: http://rugmdO.chem.rug.nl/∼gmx 1995.
-
(1995)
Gromacs User Manual
-
-
Van Der Spoel, D.1
Berendsen, H.J.C.2
Van Buuren, A.R.3
Apol, E.4
Meulenhoff, P.J.5
Sijbers, A.L.T.M.6
Van Drunen, R.7
-
24
-
-
0004146515
-
-
BIOMOS, Biomolecular Software, Laboratory of Biophysical Chemistry, The Netherlands: University of Groningen
-
Van Gunsteren WF, Berendsen HJC. Gromos manual. BIOMOS, Biomolecular Software, Laboratory of Biophysical Chemistry, The Netherlands: University of Groningen; 1987.
-
(1987)
Gromos Manual
-
-
Van Gunsteren, W.F.1
Berendsen, H.J.C.2
-
25
-
-
0003544049
-
-
Biomos b.v., Hochschulverlag ETH, Zürich; 903 p
-
Van Gunsteren W, Billeter S, Eising A, Hünenberger P, Krüger P, Mark A, Scott W, Tironi I. Biomolecular simulation: the GROMOS96 manual and user guide. Biomos b.v., Hochschulverlag ETH, Zürich; 1996. 903 p.
-
(1996)
Biomolecular Simulation: the GROMOS96 Manual and User Guide
-
-
Van Gunsteren, W.1
Billeter, S.2
Eising, A.3
Hünenberger, P.4
Krüger, P.5
Mark, A.6
Scott, W.7
Tironi, I.8
-
26
-
-
33646940952
-
Numerical integration of the cartesian equations of motion of a system with constraints; molecular dynamics of n-alkanes
-
Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of the cartesian equations of motion of a system with constraints; molecular dynamics of n-alkanes. J Comp Phys 1977;23:327-341.
-
(1977)
J Comp Phys
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
27
-
-
0002775934
-
Interaction models for water in relation to protein hydration
-
Pullman B, editor Dordrecht: D. Reidel Publishing Company
-
Berendsen HJC, Postma JPM, Van Gunsteren WF, Hermans J. Interaction models for water in relation to protein hydration. In: Pullman B, editor. Intermolecular forces. Dordrecht: D. Reidel Publishing Company; 1981. p 331-342.
-
(1981)
Intermolecular Forces
, pp. 331-342
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Hermans, J.4
-
29
-
-
0029818017
-
The consistency of large concerted motions in proteins in molecular dynamics simulations
-
De Groot BL, Van Aalten DMF, Amadei A, Berendsen HJC. The consistency of large concerted motions in proteins in molecular dynamics simulations. Biophys J 1996;71:1554-1566.
-
(1996)
Biophys J
, vol.71
, pp. 1554-1566
-
-
De Groot, B.L.1
Van Aalten, D.M.F.2
Amadei, A.3
Berendsen, H.J.C.4
-
30
-
-
0000629793
-
Decay of time correlations in two dimensions
-
Wainwright T, Alder BJ, Gass DM. Decay of time correlations in two dimensions. Phys Rev A 1971;4:233-237.
-
(1971)
Phys Rev A
, vol.4
, pp. 233-237
-
-
Wainwright, T.1
Alder, B.J.2
Gass, D.M.3
-
31
-
-
0001314429
-
Shear viscosities away from the melting line: A comparison between equilibrium and non-equilibrium molecular dynamics
-
Holian B, Evans D. Shear viscosities away from the melting line: a comparison between equilibrium and non-equilibrium molecular dynamics. J Chem Phys 1983;78:5147-5150.
-
(1983)
J Chem Phys
, vol.78
, pp. 5147-5150
-
-
Holian, B.1
Evans, D.2
-
32
-
-
0001183646
-
Shear viscosity of the hard-sphere fluid via non-equilibrium molecular dynamics
-
Erpenbeck J. Shear viscosity of the hard-sphere fluid via non-equilibrium molecular dynamics. Phys Rev Lett 1984;52:1333-1335.
-
(1984)
Phys Rev Lett
, vol.52
, pp. 1333-1335
-
-
Erpenbeck, J.1
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