-
1
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic network model
-
Atilgan, A.R. et al. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J., 80, 505-515.
-
(2001)
Biophys. J.
, vol.80
, pp. 505-515
-
-
Atilgan, A.R.1
-
2
-
-
77952938726
-
Global dynamics of proteins: Bridging between structure and function
-
Bahar, I. et al. (2010) Global dynamics of proteins: bridging between structure and function. Annu. Rev. Biophys., 39, 23-42.
-
(2010)
Annu. Rev. Biophys.
, vol.39
, pp. 23-42
-
-
Bahar, I.1
-
3
-
-
70149090164
-
The intrinsic dynamics of proteins plays a dominant role in determining the structural changes induced upon inhibitor binding
-
Bakan, A. and Bahar, I. (2009) The intrinsic dynamics of proteins plays a dominant role in determining the structural changes induced upon inhibitor binding. Proc. Natl Acad. Sci. USA, 106, 14349-14354.
-
(2009)
Proc. Natl Acad. Sci. USA
, vol.106
, pp. 14349-14354
-
-
Bakan, A.1
Bahar, I.2
-
4
-
-
3242891875
-
MoViES: Molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids
-
Cao, Z.W. et al. (2004) MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids. Nucleic Acids Res, 32, W679-W685.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. W679-W685
-
-
Cao, Z.W.1
-
5
-
-
84901376917
-
Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model
-
Das, A. et al. (2014) Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model. PLoS Comput. Biol., 10, e1003521.
-
(2014)
PLoS Comput. Biol.
, vol.10
, pp. e1003521
-
-
Das, A.1
-
6
-
-
0034663710
-
Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to a-amylase inhibitor
-
Doruker, P. et al. (2000) Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: Application to a-amylase inhibitor. Proteins, 40, 512-524.
-
(2000)
Proteins
, vol.40
, pp. 512-524
-
-
Doruker, P.1
-
7
-
-
33750407288
-
Anisotropic Network Model: Systematic evaluation and a new web interface
-
Eyal, E. et al. (2006) Anisotropic Network Model: systematic evaluation and a new web interface. Bioinformatics, 22, 2619-2627.
-
(2006)
Bioinformatics
, vol.22
, pp. 2619-2627
-
-
Eyal, E.1
-
8
-
-
34249950182
-
Anisotropic fluctuations of amino acids in protein structures: Insights from X-ray crystallography and elastic network models
-
Eyal, E. et al. (2007) Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models. Bioinformatics, 23, i175-i184.
-
(2007)
Bioinformatics
, vol.23
, pp. i175-i184
-
-
Eyal, E.1
-
9
-
-
84869065683
-
Cooperative dynamics of proteins unraveled by network models
-
Eyal, E. et al. (2011) Cooperative dynamics of proteins unraveled by network models. Comp. Mol. Sci., 1, 426-439.
-
(2011)
Comp. Mol. Sci.
, vol.1
, pp. 426-439
-
-
Eyal, E.1
-
10
-
-
0032533790
-
Analysis of domain motions by approximate normal mode calculations
-
Hinsen, K. (1998) Analysis of domain motions by approximate normal mode calculations. Proteins, 33, 417-429.
-
(1998)
Proteins
, vol.33
, pp. 417-429
-
-
Hinsen, K.1
-
11
-
-
25444528449
-
WEBnm: A web application for normal mode analysis of proteins
-
Hollup, S.M. et al. (2005) WEBnm: A web application for normal mode analysis of proteins. BMC Bioinf., 11, 52.
-
(2005)
BMC Bioinf.
, vol.11
, pp. 52
-
-
Hollup, S.M.1
-
12
-
-
84872851728
-
Substrate recognition and motion mode analyses of PVF in complex with viral DNA via coarse-grained models
-
Hu, J. et al. (2013) Substrate recognition and motion mode analyses of PVF in complex with viral DNA via coarse-grained models, PLoS One 8, e54929.
-
(2013)
PLoS One
, vol.8
, pp. e54929
-
-
Hu, J.1
-
13
-
-
84864476417
-
NMSim Web Server: Integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins
-
Jmol: An open-source Java viewer for chemical structures in 3D
-
Jmol: An open-source Java viewer for chemical structures in 3D. Krüger, D.M. et al. (2012) NMSim Web Server: integrated approach for normal mode-based geometric simulations of biologically relevant conformational transitions in proteins. Nucleic Acids Res. 40, W310-W316.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. W310-W316
-
-
Krüger, D.M.1
-
14
-
-
0003851780
-
ARPACK Users' Guide: Solution of Large Scale Eigenvalue Problems with Implicitly Restarted Arrnoldi Methods
-
Lehoucq, R.B. et al. (1998) ARPACK Users' Guide: Solution of Large Scale Eigenvalue Problems with Implicitly Restarted Arrnoldi Methods. SIAM, Philadelphia.
-
(1998)
SIAM, Philadelphia
-
-
Lehoucq, R.B.1
-
15
-
-
80054707836
-
Efficient inclusion of receptor flexibility in grid-based protein-ligand docking
-
Leis, S. and Zacharias, M. (2011) Efficient inclusion of receptor flexibility in grid-based protein-ligand docking. J. Comput. Chem., 32, 3433-3439.
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 3433-3439
-
-
Leis, S.1
Zacharias, M.2
-
16
-
-
33747858757
-
NOMAD-Ref: Visualization, deformation, and refinement of macromolecular structures based on all-atom normal mode analysis
-
Lindahl, E. et al. (2006) NOMAD-Ref: visualization, deformation, and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res, 34, W52-W56.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. W52-W56
-
-
Lindahl, E.1
-
18
-
-
80053142382
-
Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins
-
Meireles, L. et al. (2011) Pre-existing soft modes of motion uniquely defined by native contact topology facilitate ligand binding to proteins. Prot. Sci., 20, 1645-1658.
-
(2011)
Prot. Sci.
, vol.20
, pp. 1645-1658
-
-
Meireles, L.1
-
19
-
-
0030815133
-
Raster3D: Photorealistic molecular graphics
-
Merritt, E.A. and Bacon, D.J. (1997) Raster3D: Photorealistic molecular graphics. Methods Enzymol., 277, 505-524.
-
(1997)
Methods Enzymol.
, vol.277
, pp. 505-524
-
-
Merritt, E.A.1
Bacon, D.J.2
-
20
-
-
84928317559
-
Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations
-
Ostermeir, K. and Zacharias, M. (2014) Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations. Proteins, 82, 3409-3410.
-
(2014)
Proteins
, vol.82
, pp. 3409-3410
-
-
Ostermeir, K.1
Zacharias, M.2
-
21
-
-
77956645008
-
Instantaneous normal modes as an unforced reaction coordinate for protein conformational transitions
-
Peng, C. et al. (2010) Instantaneous normal modes as an unforced reaction coordinate for protein conformational transitions. Biophys. J. 98, 2356-2364.
-
(2010)
Biophys. J.
, vol.98
, pp. 2356-2364
-
-
Peng, C.1
-
22
-
-
65249120827
-
Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes
-
Rueda, M. et al. (2009) Consistent improvement of cross-docking results using binding site ensembles generated with elastic network normal modes. J. Chem. Inf. Model, 49, 716-725.
-
(2009)
J. Chem. Inf. Model
, vol.49
, pp. 716-725
-
-
Rueda, M.1
-
23
-
-
36749078686
-
Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolutions
-
Schrö der, G.F. et al. (2007) Combining efficient conformational sampling with a deformable elastic network model facilitates structure refinement at low resolutions. Structure, 15, 1630-1641.
-
(2007)
Structure
, vol.15
, pp. 1630-1641
-
-
Schrö Der, G.F.1
-
24
-
-
3242875210
-
ElNemo: A normal mode web server for protein movement analysis and the generation of templates for molecular replacement
-
Suhre, K. and Sanejouand, Y.-H. (2004) ElNemo: A normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res. 32, W610-W614.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. W610-W614
-
-
Suhre, K.1
Sanejouand, Y.-H.2
-
25
-
-
0035044995
-
Conformational change of proteins arising from normal modes calculations
-
Tama, F. and Sanejouand, Y.H. (2001) Conformational change of proteins arising from normal modes calculations. Protein Eng. 14, 1-6.
-
(2001)
Protein Eng.
, vol.14
, pp. 1-6
-
-
Tama, F.1
Sanejouand, Y.H.2
-
26
-
-
80053348799
-
Ligand-induced conformational change of a protein reproduced by a linear combination of displacement vectors obtained from normal mode analysis
-
Wako, H. and Endo, S. (2011) Ligand-induced conformational change of a protein reproduced by a linear combination of displacement vectors obtained from normal mode analysis. Biophys. Chem. 159, 257-266.
-
(2011)
Biophys. Chem.
, vol.159
, pp. 257-266
-
-
Wako, H.1
Endo, S.2
-
27
-
-
4344685227
-
Global ribosome motions revealed by elastic network models
-
Wang, Y. et al. (2004) Global ribosome motions revealed by elastic network models. J. Struct. Biol., 147, 302-314.
-
(2004)
J. Struct. Biol.
, vol.147
, pp. 302-314
-
-
Wang, Y.1
-
28
-
-
20444429274
-
IGNM: A database of protein functional motions based on Gaussian Network Model
-
Yang, LW. et al. (2005) iGNM: A database of protein functional motions based on Gaussian Network Model. Bioinformatics, 21, 2978-2987.
-
(2005)
Bioinformatics
, vol.21
, pp. 2978-2987
-
-
Yang, L.W.1
-
29
-
-
33747829284
-
OGNM: Online computation of structural dynamics using the Gaussian Network Model
-
Yang, LW. et al. (2006) oGNM: Online computation of structural dynamics using the Gaussian Network Model. Nucleic Acids Res. 34, W24-W31.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. W24-W31
-
-
Yang, L.W.1
|