-
1
-
-
23244467144
-
Initial conformational changes of human transthyretin under partially denaturing conditions
-
Yang, M.; Lei, M.; Brüschweiler, R.; Huo, S. Initial conformational changes of human transthyretin under partially denaturing conditions Biophys. J. 2005, 89 (1) 433-443
-
(2005)
Biophys. J.
, vol.89
, Issue.1
, pp. 433-443
-
-
Yang, M.1
Lei, M.2
Brüschweiler, R.3
Huo, S.4
-
2
-
-
33749325449
-
The Sequence-Dependent Unfolding Pathway Plays a Critical Role in the Amyloidogenicity of Transthyretin
-
Yang, M.; Yordanov, B.; Levy, Y.; Bruschweiler, R.; Huo, S. The Sequence-Dependent Unfolding Pathway Plays a Critical Role in the Amyloidogenicity of Transthyretin Biochemistry 2006, 45, 11992-12002
-
(2006)
Biochemistry
, vol.45
, pp. 11992-12002
-
-
Yang, M.1
Yordanov, B.2
Levy, Y.3
Bruschweiler, R.4
Huo, S.5
-
3
-
-
0027441950
-
Essential dynamics of proteins
-
Amadei, A.; Linssen, A. B.; Berendsen, H. J. Essential dynamics of proteins Proteins: Struct., Funct., Bioinf. 1993, 17 (4) 412-425
-
(1993)
Proteins: Struct., Funct., Bioinf.
, vol.17
, Issue.4
, pp. 412-425
-
-
Amadei, A.1
Linssen, A.B.2
Berendsen, H.J.3
-
4
-
-
6944235051
-
Hidden complexity of free energy surfaces for peptide (protein) folding
-
Krivov, S. V.; Karplus, M. Hidden complexity of free energy surfaces for peptide (protein) folding Proc. Natl. Acad. Sci. U. S. A. 2004, 101 (41) 14766-70
-
(2004)
Proc. Natl. Acad. Sci. U. S. A.
, vol.101
, Issue.41
, pp. 14766-14770
-
-
Krivov, S.V.1
Karplus, M.2
-
6
-
-
0034704222
-
Nonlinear dimensionality reduction by locally linear embedding
-
Roweis, S. T.; Saul, L. K. Nonlinear dimensionality reduction by locally linear embedding Science 2000, 290 (5500) 2323-2326
-
(2000)
Science
, vol.290
, Issue.5500
, pp. 2323-2326
-
-
Roweis, S.T.1
Saul, L.K.2
-
7
-
-
0034704229
-
A global geometric framework for nonlinear dimensionality reduction
-
Tenenbaum, J. B.; de Silva, V.; Langford, J. C. A global geometric framework for nonlinear dimensionality reduction Science 2000, 290 (5500) 2319-2323
-
(2000)
Science
, vol.290
, Issue.5500
, pp. 2319-2323
-
-
Tenenbaum, J.B.1
De Silva, V.2
Langford, J.C.3
-
8
-
-
19644394100
-
Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps
-
Coifman, R. R.; Lafon, S.; Lee, A. B.; Maggioni, M.; Nadler, B.; Warner, F.; Zucker, S. W. Geometric diffusions as a tool for harmonic analysis and structure definition of data: diffusion maps Proc. Natl. Acad. Sci. U. S. A. 2005, 102 (21) 7426-7431
-
(2005)
Proc. Natl. Acad. Sci. U. S. A.
, vol.102
, Issue.21
, pp. 7426-7431
-
-
Coifman, R.R.1
Lafon, S.2
Lee, A.B.3
Maggioni, M.4
Nadler, B.5
Warner, F.6
Zucker, S.W.7
-
9
-
-
0026076090
-
Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations
-
Ichiye, T.; Karplus, M. Collective motions in proteins: a covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations Proteins: Struct., Funct., Bioinf. 1991, 11 (3) 205-217
-
(1991)
Proteins: Struct., Funct., Bioinf.
, vol.11
, Issue.3
, pp. 205-217
-
-
Ichiye, T.1
Karplus, M.2
-
10
-
-
33745611125
-
Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction
-
Das, P.; Moll, M.; Stamati, H.; Kavraki, L. E.; Clementi, C. Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction Proc. Natl. Acad. Sci. U. S. A. 2006, 103 (26) 9885-9890
-
(2006)
Proc. Natl. Acad. Sci. U. S. A.
, vol.103
, Issue.26
, pp. 9885-9890
-
-
Das, P.1
Moll, M.2
Stamati, H.3
Kavraki, L.E.4
Clementi, C.5
-
11
-
-
77449099723
-
Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides
-
Stamati, H.; Clementi, C.; Kavraki, L. E. Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides Proteins: Struct., Funct., Bioinf. 2010, 78 (2) 223-235
-
(2010)
Proteins: Struct., Funct., Bioinf.
, vol.78
, Issue.2
, pp. 223-235
-
-
Stamati, H.1
Clementi, C.2
Kavraki, L.E.3
-
12
-
-
49749151039
-
Algorithmic dimensionality reduction for molecular structure analysis
-
Brown, W. M.; Martin, S.; Pollock, S. N.; Coutsias, E. A.; Watson, J. P. Algorithmic dimensionality reduction for molecular structure analysis J. Chem. Phys. 2008, 129 (6) 064118
-
(2008)
J. Chem. Phys.
, vol.129
, Issue.6
, pp. 064118
-
-
Brown, W.M.1
Martin, S.2
Pollock, S.N.3
Coutsias, E.A.4
Watson, J.P.5
-
13
-
-
55849087551
-
Calculation of the free energy and cooperativity of protein folding
-
Kentsis, A.; Gindin, T.; Mezei, M.; Osman, R. Calculation of the free energy and cooperativity of protein folding PLoS One 2007, 2 (5) e446
-
(2007)
PLoS One
, vol.2
, Issue.5
, pp. 446
-
-
Kentsis, A.1
Gindin, T.2
Mezei, M.3
Osman, R.4
-
14
-
-
34248590146
-
Fast and reliable analysis of molecular motion using proximity relations and dimensionality reduction
-
Plaku, E.; Stamati, H.; Clementi, C.; Kavraki, L. E. Fast and reliable analysis of molecular motion using proximity relations and dimensionality reduction Proteins: Struct., Funct., Bioinf. 2007, 67 (4) 897-907
-
(2007)
Proteins: Struct., Funct., Bioinf.
, vol.67
, Issue.4
, pp. 897-907
-
-
Plaku, E.1
Stamati, H.2
Clementi, C.3
Kavraki, L.E.4
-
15
-
-
84877761210
-
-
Dimensionality Reduction Techniques for Protein Folding Trajectories. Hansmann, U. H. E. Meinke, J. Mohanty, S. Zimmermann, O. John von Neumann Institute for Computing: Jülich, Germany, NIC Series
-
Eitrich, T.; Mohanty, S.; Xiao, X.; Hansmann, U. H. E. Dimensionality Reduction Techniques for Protein Folding Trajectories. From Computational Biophysics to Systems Biology (CBSB07); Hansmann, U. H. E.; Meinke, J.; Mohanty, S.; Zimmermann, O., Eds.; John von Neumann Institute for Computing: Jülich, Germany, 2007; NIC Series, pp 99-102.
-
(2007)
From Computational Biophysics to Systems Biology (CBSB07)
, pp. 99-102
-
-
Eitrich, T.1
Mohanty, S.2
Xiao, X.3
Hansmann, U.H.E.4
-
16
-
-
77956391259
-
Systematic determination of order parameters for chain dynamics using diffusion maps
-
Ferguson, A. L.; Panagiotopoulos, A. Z.; Debenedetti, P. G.; Kevrekidis, I. G. Systematic determination of order parameters for chain dynamics using diffusion maps Proc. Natl. Acad. Sci. U. S. A. 2010, 107 (31) 13597-13602
-
(2010)
Proc. Natl. Acad. Sci. U. S. A.
, vol.107
, Issue.31
, pp. 13597-13602
-
-
Ferguson, A.L.1
Panagiotopoulos, A.Z.2
Debenedetti, P.G.3
Kevrekidis, I.G.4
-
17
-
-
79957744623
-
Nonlinear dimensionality reduction in molecular simulation: The diffusion map approach
-
Ferguson, A. L.; Panagiotopoulos, A. Z.; Kevrekidis, I. G.; Debenedetti, P. G. Nonlinear dimensionality reduction in molecular simulation: The diffusion map approach Chem. Phys. Lett. 2011, 509, 1-11
-
(2011)
Chem. Phys. Lett.
, vol.509
, pp. 1-11
-
-
Ferguson, A.L.1
Panagiotopoulos, A.Z.2
Kevrekidis, I.G.3
Debenedetti, P.G.4
-
18
-
-
78349259753
-
An experimental and computational investigation of spontaneous lasso formation in microcin J25
-
Ferguson, A. L.; Zhang, S.; Dikiy, I.; Panagiotopoulos, A. Z.; Debenedetti, P. G.; James Link, A. An experimental and computational investigation of spontaneous lasso formation in microcin J25 Biophys. J. 2010, 99 (9) 3056-3065
-
(2010)
Biophys. J.
, vol.99
, Issue.9
, pp. 3056-3065
-
-
Ferguson, A.L.1
Zhang, S.2
Dikiy, I.3
Panagiotopoulos, A.Z.4
Debenedetti, P.G.5
James Link, A.6
-
19
-
-
80455127024
-
Delineation of folding pathways of a beta-sheet miniprotein
-
Zheng, W.; Qi, B.; Rohrdanz, M. A.; Caflisch, A.; Dinner, A. R.; Clementi, C. Delineation of folding pathways of a beta-sheet miniprotein J. Phys. Chem. B 2011, 115 (44) 13065-13074
-
(2011)
J. Phys. Chem. B
, vol.115
, Issue.44
, pp. 13065-13074
-
-
Zheng, W.1
Qi, B.2
Rohrdanz, M.A.3
Caflisch, A.4
Dinner, A.R.5
Clementi, C.6
-
20
-
-
79953320021
-
Determination of reaction coordinates via locally scaled diffusion map
-
Rohrdanz, M. A.; Zheng, W.; Maggioni, M.; Clementi, C. Determination of reaction coordinates via locally scaled diffusion map J. Chem. Phys. 2011, 134 (12) 124116
-
(2011)
J. Chem. Phys.
, vol.134
, Issue.12
, pp. 124116
-
-
Rohrdanz, M.A.1
Zheng, W.2
Maggioni, M.3
Clementi, C.4
-
21
-
-
79954557298
-
Integrating diffusion maps with umbrella sampling: Application to alanine dipeptide
-
Ferguson, A. L.; Panagiotopoulos, A. Z.; Debenedetti, P. G.; Kevrekidis, I. G. Integrating diffusion maps with umbrella sampling: application to alanine dipeptide J. Chem. Phys. 2011, 134 (13) 135103
-
(2011)
J. Chem. Phys.
, vol.134
, Issue.13
, pp. 135103
-
-
Ferguson, A.L.1
Panagiotopoulos, A.Z.2
Debenedetti, P.G.3
Kevrekidis, I.G.4
-
22
-
-
83755206813
-
Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap
-
Spiwok, V. e.; Králová, B. Metadynamics in the conformational space nonlinearly dimensionally reduced by Isomap J. Chem. Phys. 2011, 135, 224504
-
(2011)
J. Chem. Phys.
, vol.135
, pp. 224504
-
-
Spiwok, V.E.1
Králová, B.2
-
23
-
-
84986512474
-
CHARMM: A program for macromolecular energy, minimization and dynamics calculations
-
Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; 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
-
24
-
-
0000036869
-
Simulation of activation free energies in molecular systems
-
Neria, E.; Fischer, S.; Karplus, M. Simulation of activation free energies in molecular systems J. Chem. Phys. 1996, 105, 1902-1921
-
(1996)
J. Chem. Phys.
, vol.105
, pp. 1902-1921
-
-
Neria, E.1
Fischer, S.2
Karplus, M.3
-
25
-
-
0033135638
-
Effective energy function for proteins in solution
-
Lazaridis, T.; Karplus, M. Effective energy function for proteins in solution Proteins: Struct., Funct., Bioinf. 1999, 35 (2) 133-152
-
(1999)
Proteins: Struct., Funct., Bioinf.
, vol.35
, Issue.2
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
27
-
-
38049123863
-
Evaluation of configurational entropy methods from peptide folding-unfolding simulation
-
Li, D. W.; Khanlarzadeh, M.; Wang, J.; Huo, S.; Brüschweiler, R. Evaluation of configurational entropy methods from peptide folding-unfolding simulation J. Phys. Chem. B 2007, 111 (49) 13807-13813
-
(2007)
J. Phys. Chem. B
, vol.111
, Issue.49
, pp. 13807-13813
-
-
Li, D.W.1
Khanlarzadeh, M.2
Wang, J.3
Huo, S.4
Brüschweiler, R.5
-
29
-
-
4444221565
-
UCSF Chimera - A visualization system for exploratory research and analysis
-
Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. UCSF Chimera - a visualization system for exploratory research and analysis J. Comput. Chem. 2004, 25 (13) 1605-1612
-
(2004)
J. Comput. Chem.
, vol.25
, Issue.13
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
|