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Volumn 54, Issue 1, 2014, Pages 209-217

On the application of good-turing statistics to quantify convergence of biomolecular simulations

Author keywords

[No Author keywords available]

Indexed keywords

FREQUENCY ESTIMATION; PROBABILITY;

EID: 84893430393     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci4005817     Document Type: Article
Times cited : (28)

References (21)
  • 1
    • 69349101503 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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
  • 11
    • 77749344672 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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 scopus 로고    scopus 로고
    • 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


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.