-
1
-
-
84986512474
-
CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M: CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J Comput Chem 1983, 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
-
2
-
-
0020771265
-
Dynamics of a small globular proteins in terms of low frequency normal modes
-
Go N, Noguti T, Nishikawa T: Dynamics of a small globular proteins in terms of low frequency normal 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
-
3
-
-
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
-
5
-
-
0027576952
-
Diagonalization in a mixed basis: A method to compute normal-modes for large macromolecules
-
Mouawad L, Perahia D: Diagonalization in a mixed basis: a method to compute normal-modes for large macromolecules. Biopolymers 1993, 33:599-611.
-
(1993)
Biopolymers
, vol.33
, pp. 599-611
-
-
Mouawad, L.1
Perahia, D.2
-
6
-
-
0029560322
-
Hinge-bending motion in citrate synthase arising from normal mode calculations
-
Marques O, Sanejouand YH: Hinge-bending motion in citrate synthase arising from normal mode calculations. Proteins 1995, 23:557-560.
-
(1995)
Proteins
, vol.23
, pp. 557-560
-
-
Marques, O.1
Sanejouand, Y.H.2
-
7
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
-
Tirion MM: Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 1996, 77:1905-1908.
-
(1996)
Phys. Rev. Lett.
, vol.77
, pp. 1905-1908
-
-
Tirion, M.M.1
-
8
-
-
0030623823
-
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
-
Bahar I, Atilgan AR, Erman B: Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Folding Des 1997, 2:173-181.
-
(1997)
Folding Des.
, vol.2
, pp. 173-181
-
-
Bahar, I.1
Atilgan, A.R.2
Erman, B.3
-
9
-
-
0038072330
-
Normal Mode Analysis
-
Edited by: P. Schleyer NATCJGPKHSPS. Chichester, UK, John Wiley & Sons
-
Cornell WD, Louise-May S: Normal Mode Analysis. In Encyclopedia of Computational Chemistry Edited by: P. Schleyer NATCJGPKHSPS. Chichester, UK, John Wiley & Sons.; 1998:1904-1913.
-
(1998)
Encyclopedia of Computational Chemistry
, pp. 1904-1913
-
-
Cornell, W.D.1
Louise-May, S.2
-
10
-
-
0032533790
-
Analysis of domain motions by approximate normal mode calculations
-
Hinsen K: Analysis of domain motions by approximate normal mode calculations. Proteins 1998, 33:417-429.
-
(1998)
Proteins
, vol.33
, pp. 417-429
-
-
Hinsen, K.1
-
11
-
-
0033557178
-
Analysis of domain motions in large proteins
-
Hinsen K, Thomas A, Field MJ: Analysis of domain motions in large proteins. Proteins 1999, 34:369-382.
-
(1999)
Proteins
, vol.34
, pp. 369-382
-
-
Hinsen, K.1
Thomas, A.2
Field, M.J.3
-
12
-
-
0034127361
-
Collective protein dynamics in relation to function
-
Berendsen HJ, Hayward S: Collective protein dynamics in relation to function. Curr Opin Struct Biol 2000, 10:165-169.
-
(2000)
Curr. Opin. Struct. Biol.
, vol.10
, pp. 165-169
-
-
Berendsen, H.J.1
Hayward, S.2
-
13
-
-
0034333103
-
Harmonicity in slow protein dynamics
-
Hinsen K, Petrescu AJ, Dellerue S, Bellissent-Funel MC, Kneller GR: Harmonicity in slow protein dynamics. Chem Phys 2000, 261:25-37.
-
(2000)
Chem. Phys.
, vol.261
, pp. 25-37
-
-
Hinsen, K.1
Petrescu, A.J.2
Dellerue, S.3
Bellissent-Funel, M.C.4
Kneller, G.R.5
-
14
-
-
0034308140
-
Building-block approach for determining low-frequency normal modes of macromolecules
-
Tama F, Gadea FX, Marques O, Sanejouand YH: Building-block approach for determining low-frequency normal modes of macromolecules. Proteins 2000, 41:1-7.
-
(2000)
Proteins
, vol.41
, pp. 1-7
-
-
Tama, F.1
Gadea, F.X.2
Marques, O.3
Sanejouand, Y.H.4
-
15
-
-
0038342653
-
Normal mode analysis of biological molecules
-
Edited by: Becker OM, MacKerell AD, Roux B and Watanabe M. New-York, Marcel Dekker, Inc
-
Hayward S: Normal mode analysis of biological molecules. In Computational biochemistry and biophysics Edited by: Becker OM, MacKerell AD, Roux B and Watanabe M. New-York, Marcel Dekker, Inc.; 2001:153-168.
-
(2001)
Computational Biochemistry and Biophysics
, pp. 153-168
-
-
Hayward, S.1
-
16
-
-
0036840202
-
A coarsed-grained normal mode approach for macromolecules: An efficient implementation and application to Ca++-ATPase
-
Li G, Cui Q: A coarsed-grained normal mode approach for macromolecules: an efficient implementation and application to Ca++-ATPase. Biophys J 2002, 83:2457-2474.
-
(2002)
Biophys. J.
, vol.83
, pp. 2457-2474
-
-
Li, G.1
Cui, Q.2
-
17
-
-
2942511344
-
A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase
-
Cui Q, Li G, Ma J, Karplus M: A normal mode analysis of structural plasticity in the biomolecular motor F(1)-ATPase. J Mol Biol 2004, 340:345-372.
-
(2004)
J. Mol. Biol.
, vol.340
, pp. 345-372
-
-
Cui, Q.1
Li, G.2
Ma, J.3
Karplus, M.4
-
18
-
-
8444243746
-
Collective motions of RNA polymerases. Analysis of core enzyme, elongation complex and holoenzyme
-
Yildirim Y, Doruker P: Collective motions of RNA polymerases. Analysis of core enzyme, elongation complex and holoenzyme. J Biomol Struct Dyn 2004, 22:267-280.
-
(2004)
J. Biomol. Struct. Dyn.
, vol.22
, pp. 267-280
-
-
Yildirim, Y.1
Doruker, P.2
-
19
-
-
9644266693
-
Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis
-
Tama F, Brooks CL: Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis. J Mol Biol 2005, 345:299-314.
-
(2005)
J. Mol. Biol.
, vol.345
, pp. 299-314
-
-
Tama, F.1
Brooks, C.L.2
-
20
-
-
3242875210
-
ElNemo: A normal mode web server for protein movement analysis and the generation of templates for molecular replacement
-
Suhre K, Sanejouand YH: ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res 2004, 32:W610-4.
-
(2004)
Nucleic Acids Res.
, vol.32
-
-
Suhre, K.1
Sanejouand, Y.H.2
-
21
-
-
84874661505
-
Normal mode calculation and visualisation using Pymol
-
Delarue M, Lindahl E: Normal mode calculation and visualisation using Pymol. 2004 [http://lorentz.immstr.pasteur.fr/nma/].
-
(2004)
-
-
Delarue, M.1
Lindahl, E.2
-
22
-
-
0037246863
-
MolMovDB: Analysis and visualization of conformational change and structural flexibility
-
Echols N, Milburn D, Gerstein M: MolMovDB: analysis and visualization of conformational change and structural flexibility. Nucleic Acids Res 2003, 31:478-482.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 478-482
-
-
Echols, N.1
Milburn, D.2
Gerstein, M.3
-
23
-
-
3242891875
-
MoViES: Molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids
-
Cao ZW, Xue Y, Han LY, Xie B, Zhou H, Zheng CJ, Lin HH, Chen YZ: MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids. Nucleic Acids Research 2004, 32:W679-W685.
-
(2004)
Nucleic Acids Research
, vol.32
-
-
Cao, Z.W.1
Xue, Y.2
Han, L.Y.3
Xie, B.4
Zhou, H.5
Zheng, C.J.6
Lin, H.H.7
Chen, Y.Z.8
-
24
-
-
0029011701
-
A second generation force field for the simulation of proteins and nucleic acids
-
Cornell W, Cieplak P, Bayly C, Gould I, Merz KM, Ferguson D, Spellmeyer D, Fox T, Caldwell J, Kollman P: A second generation force field for the simulation of proteins and nucleic acids. J Am Chem Soc 1995, 117:5179-5197.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.1
Cieplak, P.2
Bayly, C.3
Gould, I.4
Merz, K.M.5
Ferguson, D.6
Spellmeyer, D.7
Fox, T.8
Caldwell, J.9
Kollman, P.10
-
25
-
-
4544280144
-
ProMode: A database of normal mode analyses on protein molecules with a full-atom model
-
Wako H, Kato M, Endo S: ProMode: a database of normal mode analyses on protein molecules with a full-atom model. Bioinformatics 2004, 20:2035-2043.
-
(2004)
Bioinformatics
, vol.20
, pp. 2035-2043
-
-
Wako, H.1
Kato, M.2
Endo, S.3
-
26
-
-
0032006209
-
Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme
-
Hayward S, Berendsen HJ: Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme. Proteins 1998, 30:144-154.
-
(1998)
Proteins
, vol.30
, pp. 144-154
-
-
Hayward, S.1
Berendsen, H.J.2
-
27
-
-
0001962564
-
The Molecular Modeling Toolkit: A new approach to molecular simulations
-
Hinsen K: The Molecular Modeling Toolkit: a new approach to molecular simulations. J Comput Chem 2000, 21:79-85.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 79-85
-
-
Hinsen, K.1
-
28
-
-
84874660164
-
-
Zope Open Source web application server
-
Zope Open Source web application server. [http://www.zope.org/]
-
-
-
-
29
-
-
84874650807
-
-
R Copyright (C) Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
-
R Copyright (C) 1989, 1991 Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA [http://www.rproject.org/].
-
(1989)
-
-
-
32
-
-
0042415783
-
NAMD2: Greater scalability for parallel molecular dynamics
-
Kalé L, Skeel R, Bhandarkar M, Brunner R, Gursoy A, Krawetz N, Phillips J, Shinozaki A, Varadarajan K, Schulten K: NAMD2: Greater scalability for parallel molecular dynamics. Journal of Computational Physics 1999, 151:283-312.
-
(1999)
Journal of Computational Physics
, vol.151
, pp. 283-312
-
-
Kalé, 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
-
34
-
-
0029119568
-
RasMol: Biomolecular graphics for all
-
Sayle R, Milner-White EJ: RasMol: Biomolecular graphics for all. TIBS 1995, 20:374.
-
(1995)
TIBS
, vol.20
, pp. 374
-
-
Sayle, R.1
Milner-White, E.J.2
-
35
-
-
0034284122
-
Recent changes to RasMol, recombining the variants
-
Bernstein HJ: Recent changes to RasMol, recombining the variants. TIBS 2000, 9:453-455.
-
(2000)
TIBS
, vol.9
, pp. 453-455
-
-
Bernstein, H.J.1
-
37
-
-
84874661528
-
The Biaz application server
-
Saelensminde G: The Biaz application server. 2003 [http://www.bioinfo.no/tools/Biaz].
-
(2003)
-
-
Saelensminde, G.1
-
38
-
-
0141865614
-
Transconformations of the SERCA1 Ca-ATPase: A normal mode study
-
Reuter N, Hinsen K, Lacapere JJ: Transconformations of the SERCA1 Ca-ATPase: a normal mode study. Biophys J 2003, 85:2186-2197.
-
(2003)
Biophys. J.
, vol.85
, pp. 2186-2197
-
-
Reuter, N.1
Hinsen, K.2
Lacapere, J.J.3
-
39
-
-
0032932341
-
Tertiary and quaternary conformational changes in aspartate transcarbamylase: A normal mode study
-
Thomas A, Hinsen K, Field MJ, Perahia D: Tertiary and quaternary conformational changes in aspartate transcarbamylase: a normal mode study. Proteins 1999, 34:96-112.
-
(1999)
Proteins
, vol.34
, pp. 96-112
-
-
Thomas, A.1
Hinsen, K.2
Field, M.J.3
Perahia, D.4
|