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Volumn 9, Issue 8, 2014, Pages

Simulating metabolism with statistical thermodynamics

Author keywords

[No Author keywords available]

Indexed keywords

NICOTINAMIDE ADENINE DINUCLEOTIDE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE; TRICARBOXYLIC ACID;

EID: 84905457086     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0103582     Document Type: Article
Times cited : (15)

References (34)
  • 1
    • 84876522835 scopus 로고    scopus 로고
    • BRENDA in 2013: Integrated reactions, kinetic data, enzyme function data, improved disease classification: New options and contents in BRENDA
    • Schomburg I, Chang A, Placzek S, Sohngen C, Rother M, et al. (2013) BRENDA in 2013: integrated reactions, kinetic data, enzyme function data, improved disease classification: new options and contents in BRENDA. Nucleic Acids Res 41: D764-772.
    • (2013) Nucleic Acids Res , vol.41
    • Schomburg, I.1    Chang, A.2    Placzek, S.3    Sohngen, C.4    Rother, M.5
  • 2
    • 33745433792 scopus 로고    scopus 로고
    • Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data
    • Kummel A, Panke S, Heinemann M (2006) Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Molecular Systems Biology 2.
    • (2006) Molecular Systems Biology , vol.2
    • Kummel, A.1    Panke, S.2    Heinemann, M.3
  • 3
    • 33847797256 scopus 로고    scopus 로고
    • Thermodynamics-based metabolic flux analysis
    • DOI 10.1529/biophysj.106.093138
    • Henry CS, Broadbelt LJ, Hatzimanikatis V (2007) Thermodynamics-based metabolic flux analysis. Biophysical Journal 92: 1792-1805. (Pubitemid 46393490)
    • (2007) Biophysical Journal , vol.92 , Issue.5 , pp. 1792-1805
    • Henry, C.S.1    Broadbelt, L.J.2    Hatzimanikatis, V.3
  • 4
    • 36248990302 scopus 로고    scopus 로고
    • Including metabolite concentrations into flux balance analysis: Thermodynamic realizability as a constraint on flux distributions in metabolic networks
    • Hoppe A, Hoffmann S, Holzhutter HG (2007) Including metabolite concentrations into flux balance analysis: Thermodynamic realizability as a constraint on flux distributions in metabolic networks. Bmc Systems Biology 1.
    • (2007) Bmc Systems Biology , vol.1
    • Hoppe, A.1    Hoffmann, S.2    Holzhutter, H.G.3
  • 5
    • 46649103793 scopus 로고    scopus 로고
    • Relationship between thermodynamic driving force and one-way fluxes in reversible processes
    • Beard DA, Qian H (2007) Relationship between thermodynamic driving force and one-way fluxes in reversible processes. PloS one 2: e144.
    • (2007) PloS One , vol.2
    • Beard, D.A.1    Qian, H.2
  • 6
    • 0037315604 scopus 로고    scopus 로고
    • Stoichiometric network theory for nonequilibrium biochemical systems
    • DOI 10.1046/j.1432-1033.2003.03357.x
    • Qian H, Beard DA, Liang SD (2003) Stoichiometric network theory for nonequilibrium biochemical systems. Eur J Biochem 270: 415-421. (Pubitemid 36177308)
    • (2003) European Journal of Biochemistry , vol.270 , Issue.3 , pp. 415-421
    • Qian, H.1    Beard, D.A.2    Liang, S.-D.3
  • 7
    • 84859920505 scopus 로고    scopus 로고
    • Quantitative Assignment of Reaction Directionality in a Multicompartmental Human Metabolic Reconstruction
    • Haraldsdóttir HS, Thiele I, Fleming RMT (2012) Quantitative Assignment of Reaction Directionality in a Multicompartmental Human Metabolic Reconstruction. Biophysical Journal 102: 1703-1711.
    • (2012) Biophysical Journal , vol.102 , pp. 1703-1711
    • Haraldsdóttir, H.S.1    Thiele, I.2    Fleming, R.M.T.3
  • 13
    • 0033948752 scopus 로고    scopus 로고
    • Monte Carlo calculations on HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor 8-Cl TIBO: Contribution of the L100I and Y181C variants to protein stability and biological activity
    • Smith MBK, Lamb ML, Tirado-Rives J, Jorgensen WL, Michejda CJ, et al. (2000) Monte Carlo calculations on HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor 8-Cl TIBO: contribution of the L100I and Y181C variants to protein stability and biological activity. Protein Engineering 13: 413-421. (Pubitemid 30450101)
    • (2000) Protein Engineering , vol.13 , Issue.6 , pp. 413-421
    • Kroeger, S.M.B.1    Lamb, M.L.2    Tirado-Rives, J.3    Jorgensen, W.L.4    Michejda, C.J.5    Ruby, S.K.6    Smith Jr., R.H.7
  • 14
    • 0000377939 scopus 로고    scopus 로고
    • Analysis of binding affinities for celecoxib analogues with COX-1 and COX-2 from combined docking and Monte Carlo simulations and insight into the COX-2/COX-1 selectivity
    • Price MLP, Jorgensen WL (2000) Analysis of binding affinities for celecoxib analogues with COX-1 and COX-2 from combined docking and Monte Carlo simulations and insight into the COX-2/COX-1 selectivity. Journal of the American Chemical Society 122: 9455-9466.
    • (2000) Journal of the American Chemical Society , vol.122 , pp. 9455-9466
    • Price, M.L.P.1    Jorgensen, W.L.2
  • 18
    • 77950279914 scopus 로고    scopus 로고
    • Physicochemical/Thermodynamic Framework for the Interpretation of Peptide Tandem Mass Spectra
    • Cannon WR, Rawlins MM (2010) Physicochemical/Thermodynamic Framework for the Interpretation of Peptide Tandem Mass Spectra. Journal of Physical Chemistry C 114: 5360-5366.
    • (2010) Journal of Physical Chemistry C , vol.114 , pp. 5360-5366
    • Cannon, W.R.1    Rawlins, M.M.2
  • 20
    • 0037462837 scopus 로고    scopus 로고
    • Information theory explanation of the fluctuation theorem, maximum entropy production and self-organized criticality in non-equilibrium stationary states
    • Dewar R (2003) Information theory explanation of the fluctuation theorem, maximum entropy production and self-organized criticality in non-equilibrium stationary states. Journal of Physics a-Mathematical and General 36: 631-641.
    • (2003) Journal of Physics A-Mathematical and General , vol.36 , pp. 631-641
    • Dewar, R.1
  • 21
    • 77953351106 scopus 로고    scopus 로고
    • Physical origins of entropy production, free energy dissipation, and their mathematical representations
    • Ge H, Qian H (2010) Physical origins of entropy production, free energy dissipation, and their mathematical representations. Physical Review E 81.
    • (2010) Physical Review e , vol.81
    • Ge, H.1    Qian, H.2
  • 23
    • 8844259501 scopus 로고    scopus 로고
    • Thermodynamics of enzyme-catalyzed reactions - A database for quantitative biochemistry
    • DOI 10.1093/bioinformatics/bth314
    • Goldberg RN, Tewari YB, Bhat TN (2004) Thermodynamics of enzyme-catalyzed reactions - a database for quantitative biochemistry. Bioinformatics 20: 2874-2877. (Pubitemid 39530187)
    • (2004) Bioinformatics , vol.20 , Issue.16 , pp. 2874-2877
    • Goldberg, R.N.1    Tewari, Y.B.2    Bhat, T.N.3
  • 26
    • 68049100110 scopus 로고    scopus 로고
    • Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli
    • Bennett BD, Kimball EH, Gao M, Osterhout R, Van Dien SJ, et al. (2009) Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nature chemical biology 5: 593-599.
    • (2009) Nature Chemical Biology , vol.5 , pp. 593-599
    • Bennett, B.D.1    Kimball, E.H.2    Gao, M.3    Osterhout, R.4    Van Dien, S.J.5
  • 27
    • 77951095380 scopus 로고    scopus 로고
    • Free Energies of Solvation with Surface, Volume, and Local Electrostatic Effects and Atomic Surface Tensions to Represent the First Solvation Shell
    • Liu JJ, Kelly CP, Goren AC, Marenich AV, Cramer CJ, et al. (2010) Free Energies of Solvation with Surface, Volume, and Local Electrostatic Effects and Atomic Surface Tensions to Represent the First Solvation Shell. Journal of Chemical Theory and Computation 6: 1109-1117.
    • (2010) Journal of Chemical Theory and Computation , vol.6 , pp. 1109-1117
    • Liu, J.J.1    Kelly, C.P.2    Goren, A.C.3    Marenich, A.V.4    Cramer, C.J.5
  • 28
    • 84962360267 scopus 로고    scopus 로고
    • Estimating the thermodynamics and kinetics of chlorinated hydrocarbon degradation
    • Bylaska EJ (2006) Estimating the thermodynamics and kinetics of chlorinated hydrocarbon degradation. Theoretical Chemistry Accounts 116: 281-296.
    • (2006) Theoretical Chemistry Accounts , vol.116 , pp. 281-296
    • Bylaska, E.J.1
  • 29
    • 80052319918 scopus 로고    scopus 로고
    • A database of thermodynamic properties of the reactions of glycolysis, the tricarboxylic acid cycle, and the pentose phosphate pathway
    • Li X, Wu F, Qi F, Beard DA (2011) A database of thermodynamic properties of the reactions of glycolysis, the tricarboxylic acid cycle, and the pentose phosphate pathway. Database (Oxford) 2011: bar005.
    • (2011) Database (Oxford) , vol.2011
    • Li, X.1    Wu, F.2    Qi, F.3    Beard, D.A.4
  • 30
    • 84896957611 scopus 로고    scopus 로고
    • Genes without prominence: A reappraisal of the foundations of biology
    • Annila A, Baverstock K (2014) Genes without prominence: a reappraisal of the foundations of biology. J R Soc Interface 11: 20131017.
    • (2014) J R Soc Interface , vol.11 , pp. 20131017
    • Annila, A.1    Baverstock, K.2


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