-
1
-
-
69349101503
-
Quantifying Uncertainty and Sampling Quality in Biomolecular Simulations
-
Grossfield, A.; Zuckerman, D. M. Quantifying Uncertainty and Sampling Quality in Biomolecular Simulations Annu. Rep. Comput. Chem. 2009, 5, 23-48
-
(2009)
Annu. Rep. Comput. Chem.
, vol.5
, pp. 23-48
-
-
Grossfield, A.1
Zuckerman, D.M.2
-
2
-
-
36649006642
-
Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms
-
Shao, J.; Tanner, S. W.; Thompson, N.; Cheatham, T. E., III Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms J. Chem. Theory Comput. 2007, 3, 2312-2334
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 2312-2334
-
-
Shao, J.1
Tanner, S.W.2
Thompson, N.3
-
3
-
-
0000803388
-
The population frequencies of species and the estimation of population parameters
-
Good, I. J. The population frequencies of species and the estimation of population parameters Biometrika 1953, 40, 237-264
-
(1953)
Biometrika
, vol.40
, pp. 237-264
-
-
Good, I.J.1
-
4
-
-
84953486351
-
Good-Turing Frequency Estimation Without Tears
-
Gale, W. A.; Sampson, G. Good-Turing Frequency Estimation Without Tears J. Quantitative Linguistics 1995, 2, 217-237
-
(1995)
J. Quantitative Linguistics
, vol.2
, pp. 217-237
-
-
Gale, W.A.1
Sampson, G.2
-
5
-
-
36549102647
-
Error estimates on averages of correlated data
-
Flyvbjerg, H.; Petersen, H. G. Error estimates on averages of correlated data J. Chem. Phys. 1989, 91, 461-467
-
(1989)
J. Chem. Phys.
, vol.91
, pp. 461-467
-
-
Flyvbjerg, H.1
Petersen, H.G.2
-
6
-
-
36248954429
-
On the Structural Convergence of Biomolecular Simulations by Determination of the Effective Sample Size
-
Lyman, E.; Zuckerman, D. M. On the Structural Convergence of Biomolecular Simulations by Determination of the Effective Sample Size J. Phys. Chem. B 2007, 111, 12876-12882
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 12876-12882
-
-
Lyman, E.1
Zuckerman, D.M.2
-
8
-
-
84893426305
-
-
R Foundation for Statistical Computing: Vienna, Austria.
-
Elzhov, T. V.; Mullen, K. M.; Spiess, A. N.; Bolker, B. minpack.lm: R interface to the Levenberg-Marquardt nonlinear least-squares algorithm found in MINPACK, plus support for bounds, 1.1-7; R Foundation for Statistical Computing: Vienna, Austria, 2013.
-
(2013)
Minpack.lm: R Interface to the Levenberg-Marquardt Nonlinear Least-squares Algorithm Found in MINPACK, Plus Support for Bounds, 1.1-7
-
-
Elzhov, T.V.1
Mullen, K.M.2
Spiess, A.N.3
Bolker, B.4
-
10
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. Scalable molecular dynamics with NAMD J. Comput. Chem. 2005, 26, 1781-1802
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
11
-
-
77749344672
-
Molecular dynamics analysis of the conformations of a β-hairpin miniprotein
-
Hatfield, M. P. D.; Murphy, R. F.; Lovas, S. Molecular dynamics analysis of the conformations of a β-hairpin miniprotein J. Phys. Chem. B 2010, 114, 3028-3037
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 3028-3037
-
-
Hatfield, M.P.D.1
Murphy, R.F.2
Lovas, S.3
-
12
-
-
84874930595
-
As good as it gets? Folding molecular dynamics simulations of the LytA choline-binding peptide result to an exceptionally accurate model of the peptide structure
-
Patmanidis, I.; Glykos, N. M. As good as it gets? Folding molecular dynamics simulations of the LytA choline-binding peptide result to an exceptionally accurate model of the peptide structure J. Mol. Graph. Model. 2013, 41, 68-71
-
(2013)
J. Mol. Graph. Model.
, vol.41
, pp. 68-71
-
-
Patmanidis, I.1
Glykos, N.M.2
-
13
-
-
78650880629
-
Order through Disorder: Hyper-Mobile C-Terminal Residues Stabilize the Folded State of a Helical Peptide. A Molecular Dynamics Study
-
Patapati, K. K.; Glykos, N. M. Order through Disorder: Hyper-Mobile C-Terminal Residues Stabilize the Folded State of a Helical Peptide. A Molecular Dynamics Study PLoS One 2010, 5, e15290
-
(2010)
PLoS One
, vol.5
, pp. 15290
-
-
Patapati, K.K.1
Glykos, N.M.2
-
14
-
-
80053373102
-
Three Force Fields' Views of the 310 Helix
-
Patapati, K. K.; Glykos, N. M. Three Force Fields' Views of the 310 Helix Biophys. J. 2011, 101, 1766-1771
-
(2011)
Biophys. J.
, vol.101
, pp. 1766-1771
-
-
Patapati, K.K.1
Glykos, N.M.2
-
15
-
-
33748491706
-
Loopless Rop: Structure and Dynamics of an Engineered Homotetrameric Variant of the Repressor of Primer Protein
-
Glykos, N. M.; Papanikolau, Y.; Vlassi, M.; Kotsifaki, D.; Cesareni, G.; Kokkinidis, M. Loopless Rop: Structure and Dynamics of an Engineered Homotetrameric Variant of the Repressor of Primer Protein Biochemistry 2006, 45, 10905-10919
-
(2006)
Biochemistry
, vol.45
, pp. 10905-10919
-
-
Glykos, N.M.1
Papanikolau, Y.2
Vlassi, M.3
Kotsifaki, D.4
Cesareni, G.5
Kokkinidis, M.6
-
16
-
-
73949118375
-
Molecular Dynamics Simulations of BcZBP, A Deacetylase from Bacillus cereus: Active Site Loops Determine Substrate Accessibility and Specificity
-
Fadouloglou, V. E.; Stavrakoudis, S.; Bouriotis, V.; Kokkinidis, M.; Glykos, N. M. Molecular Dynamics Simulations of BcZBP, A Deacetylase from Bacillus cereus: Active Site Loops Determine Substrate Accessibility and Specificity J. Chem. Theory Comput. 2009, 5, 3299-3311
-
(2009)
J. Chem. Theory Comput.
, vol.5
, pp. 3299-3311
-
-
Fadouloglou, V.E.1
Stavrakoudis, S.2
Bouriotis, V.3
Kokkinidis, M.4
Glykos, N.M.5
-
17
-
-
84255191202
-
Using J-coupling constants for force field validation: Application to hepta-alanine
-
Georgoulia, P. S.; Glykos, N. M. Using J-coupling constants for force field validation: Application to hepta-alanine J. Phys. Chem. B 2011, 115, 15221-15227
-
(2011)
J. Phys. Chem. B
, vol.115
, pp. 15221-15227
-
-
Georgoulia, P.S.1
Glykos, N.M.2
-
18
-
-
34249061686
-
On the application of molecular-dynamics simulations to validate thermal parameters and to optimize TLS-group selection for macromolecular refinement
-
Glykos, N. M. On the application of molecular-dynamics simulations to validate thermal parameters and to optimize TLS-group selection for macromolecular refinement Acta Crystallogr. 2007, D63, 705-713
-
(2007)
Acta Crystallogr.
, vol.63
, pp. 705-713
-
-
Glykos, N.M.1
-
19
-
-
84864750900
-
Molecular dynamics simulation exploration of unfolding and refolding of a ten-amino acid miniprotein
-
Zhao, G. J.; Cheng, C. L. Molecular dynamics simulation exploration of unfolding and refolding of a ten-amino acid miniprotein Amino Acids 2012, 43, 557-565
-
(2012)
Amino Acids
, vol.43
, pp. 557-565
-
-
Zhao, G.J.1
Cheng, C.L.2
-
20
-
-
33749172039
-
Carma: A molecular dynamics analysis program
-
Glykos, N. M. Carma: a molecular dynamics analysis program J. Comput. Chem. 2006, 27, 1765-1768
-
(2006)
J. Comput. Chem.
, vol.27
, pp. 1765-1768
-
-
Glykos, N.M.1
-
21
-
-
84883743019
-
Grcarma: A Fully Automated Task-Oriented Interface for the Analysis of Molecular Dynamics Trajectories
-
Koukos, P. I.; Glykos, N. M. grcarma: A Fully Automated Task-Oriented Interface for the Analysis of Molecular Dynamics Trajectories J. Comput. Chem. 2013, 34, 2310-2312
-
(2013)
J. Comput. Chem.
, vol.34
, pp. 2310-2312
-
-
Koukos, P.I.1
Glykos, N.M.2
|