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Volumn 27, Issue 4, 2001, Pages 215-236

A comparison of seven fast but approximate methods to compute the free energy of deprotonation for amino acids in aqueous solution

Author keywords

Amino acid; Free energy; Molecular dynamics; Protonation

Indexed keywords


EID: 18844481006     PISSN: 08927022     EISSN: None     Source Type: Journal    
DOI: 10.1080/08927020108027948     Document Type: Article
Times cited : (7)

References (30)
  • 1
    • 0001492503 scopus 로고
    • Computation of free energy in practice: Choice of approximations and accuracy limiting factors
    • van Gunsteren, W. F., Weiner, P. K. and Wilkinson, A. J. (Eds.), ESCOM Science Publishers, Leiden, The Netherlands
    • van Gunsteren, W. F., Beutler, T. C., Fraternali, F., King, P. M., Mark, A. E. and Smith, P. E. (1993). "Computation of free energy in practice: choice of approximations and accuracy limiting factors", In: van Gunsteren, W. F., Weiner, P. K. and Wilkinson, A. J. (Eds.), Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications, 2, 315-348. ESCOM Science Publishers, Leiden, The Netherlands.
    • (1993) Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications , vol.2 , pp. 315-348
    • Van Gunsteren, W.F.1    Beutler, T.C.2    Fraternali, F.3    King, P.M.4    Mark, A.E.5    Smith, P.E.6
  • 4
    • 0024578173 scopus 로고
    • Free-energy via molecular simulation -applications to chemical and biomolecular systems
    • Beveridge, D. L. and DiCapua, F. M. (1989). "Free-energy via molecular simulation -applications to chemical and biomolecular systems", Annu. Rev. Biophys. Biophys. Chem., 18, 431.
    • (1989) Annu. Rev. Biophys. Biophys. Chem. , vol.18 , pp. 431
    • Beveridge, D.L.1    DiCapua, F.M.2
  • 6
    • 0001577491 scopus 로고    scopus 로고
    • Free energy perturbation calculations
    • von Ragué Schleyer, P., Allinger, N. L., Clark, T., Gasteiger, J., Kollman, P. A., Schaefer III, H. F. and Schreiner, P. R. (Eds.), Wiley, Chichester
    • Mark, A. E. (1998). "Free energy perturbation calculations", In: von Ragué Schleyer, P., Allinger, N. L., Clark, T., Gasteiger, J., Kollman, P. A., Schaefer III, H. F. and Schreiner, P. R. (Eds.), Encyclopaedia of Computational Chemistry, 2, 1070-1083. Wiley, Chichester.
    • (1998) Encyclopaedia of Computational Chemistry , vol.2 , pp. 1070-1083
    • Mark, A.E.1
  • 7
    • 0001737514 scopus 로고
    • Free energy via molecular simulation: A primer
    • van Gunsteren, W. F., Weiner, P. K. and Wilkinson, A. J. (Eds.), Escom Science Publisher, Leiden
    • King, P. M. (1993). "Free energy via molecular simulation: A primer", In: van Gunsteren, W. F., Weiner, P. K. and Wilkinson, A. J. (Eds.), Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications, 2, 267-314. Escom Science Publisher, Leiden.
    • (1993) Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications , vol.2 , pp. 267-314
    • King, P.M.1
  • 8
    • 0242677212 scopus 로고
    • Calculation of electrostatic free-energy differences with a time-saving approximate method
    • King, G. and Barford, R. A. (1993). "Calculation of electrostatic free-energy differences with a time-saving approximate method", J. Phys. Chem., 97, 8798.
    • (1993) J. Phys. Chem. , vol.97 , pp. 8798
    • King, G.1    Barford, R.A.2
  • 9
    • 5544264558 scopus 로고
    • Gaussian fluctuation formula for electrostatic free-energy changes in solution
    • Levy, R. M., Belhadj, M. and Kitchen, D. B. (1991). "Gaussian fluctuation formula for electrostatic free-energy changes in solution", J. Chem. Phys., 95, 3627.
    • (1991) J. Chem. Phys. , vol.95 , pp. 3627
    • Levy, R.M.1    Belhadj, M.2    Kitchen, D.B.3
  • 10
    • 36449009782 scopus 로고
    • Predictions of free energy differences from a single simulation of the initial state
    • Smith, P. E. and van Gunsteren, W. F. (1994). "Predictions of free energy differences from a single simulation of the initial state", J. Chem. Phys., 100, 577.
    • (1994) J. Chem. Phys. , vol.100 , pp. 577
    • Smith, P.E.1    Van Gunsteren, W.F.2
  • 11
    • 0028155689 scopus 로고
    • A new method for predicting binding affinity in computer-aided drug design
    • Åqvist, J., Medina, C. and Samuelsson, J.-E. (1994). "A new method for predicting binding affinity in computer-aided drug design", Protein Eng., 7, 385.
    • (1994) Protein Eng. , vol.7 , pp. 385
    • Åqvist, J.1    Medina, C.2    Samuelsson, J.-E.3
  • 12
    • 0242364982 scopus 로고    scopus 로고
    • Calculation of free-energy differences from computer simulations of initial and final states
    • Hummer, G. and Szabo, A. (1996). "Calculation of free-energy differences from computer simulations of initial and final states", J. Chem. Phys., 105, 2004.
    • (1996) J. Chem. Phys. , vol.105 , pp. 2004
    • Hummer, G.1    Szabo, A.2
  • 13
    • 0001692244 scopus 로고    scopus 로고
    • A-dynamics: A new approach to free energy calculations
    • Kong, X. J. and Brooks III, C. L. (1996). "A-dynamics: A new approach to free energy calculations", J. Chem. Phys., 105, 2414.
    • (1996) J. Chem. Phys. , vol.105 , pp. 2414
    • Kong, X.J.1    Brooks C.L. III2
  • 14
    • 0030134642 scopus 로고    scopus 로고
    • Estimating the relative free energy of different molecular states with respect to a single reference state
    • Liu, H., Mark, A. E. and van Gunsteren, W. F. (1996). "Estimating the relative free energy of different molecular states with respect to a single reference state", J. Phys. Chem., 100, 9485.
    • (1996) J. Phys. Chem. , vol.100 , pp. 9485
    • Liu, H.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 15
    • 0001272783 scopus 로고    scopus 로고
    • Estimating relative free energies from a single ensemble: Hydration free energies
    • Schäfer, H., van Gunsteren, W. F. and Mark, A. E. (1999). "Estimating relative free energies from a single ensemble: Hydration free energies", J. Comput. Chem., 20, 1604.
    • (1999) J. Comput. Chem. , vol.20 , pp. 1604
    • Schäfer, H.1    Van Gunsteren, W.F.2    Mark, A.E.3
  • 16
    • 0001389474 scopus 로고    scopus 로고
    • An extended linear-response method for determining free-energies of hydration
    • Carlson, H. A. and Jörgensen, W. L. (1999). "An extended linear-response method for determining free-energies of hydration", J. Phys. Chem., 99, 10667.
    • (1999) J. Phys. Chem. , vol.99 , pp. 10667
    • Carlson, H.A.1    Jörgensen, W.L.2
  • 17
    • 0030062224 scopus 로고    scopus 로고
    • Free energies of transfer of Trp analogs from chloroform to water: Comparison of theory and experiment and the importance of adequate treatment of electrostatic and internal interactions
    • Daura, X., Hünenberger, P. H., Mark, A. E., Querol, E., Avilés, F. X. and van Gunsteren, W. F. (1996). "Free energies of transfer of Trp analogs from chloroform to water: Comparison of theory and experiment and the importance of adequate treatment of electrostatic and internal interactions", J. Am. Chem. Soc., 118, 6285.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 6285
    • Daura, X.1    Hünenberger, P.H.2    Mark, A.E.3    Querol, E.4    Avilés, F.X.5    Van Gunsteren, W.F.6
  • 18
    • 0001127721 scopus 로고    scopus 로고
    • Free energies of solvation in chloroform and water from a linear response approach
    • McDonald, N. A., Carlson, H. A. and Jörgensen, W. L. (1997). "Free energies of solvation in chloroform and water from a linear response approach", J. Phys. Org. Chem., 10, 563.
    • (1997) J. Phys. Org. Chem. , vol.10 , pp. 563
    • McDonald, N.A.1    Carlson, H.A.2    Jörgensen, W.L.3
  • 19
    • 0032481614 scopus 로고    scopus 로고
    • Rapid screening of binding affinities: Application of the A-dynamics method to a trypsin-inhibitor system
    • Guo, Z. Y. and Brooks III, C. L. (1998). "Rapid screening of binding affinities: Application of the A-dynamics method to a trypsin-inhibitor system", J. Am. Chem. Soc., 120, 1920.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 1920
    • Guo, Z.Y.1    Brooks C.L. III2
  • 20
    • 0346052295 scopus 로고    scopus 로고
    • Generalized linear response method: Application to hydration free energy calculations
    • Chen, X. and Tropsha, A. (1999). "Generalized linear response method: Application to hydration free energy calculations", J. Comput. Chem., 20, 749.
    • (1999) J. Comput. Chem. , vol.20 , pp. 749
    • Chen, X.1    Tropsha, A.2
  • 21
    • 33646471468 scopus 로고
    • Statistical mechanics of fluid mixtures
    • Kirkwood, J. G. (1935). "Statistical mechanics of fluid mixtures", J. Chem. Phys., 3, 300.
    • (1935) J. Chem. Phys. , vol.3 , pp. 300
    • Kirkwood, J.G.1
  • 22
    • 36849122972 scopus 로고
    • High-temperature equation of state by a perturbation method. I. Nonpolar gases
    • Zwanzig, R. W. (1954). "High-temperature equation of state by a perturbation method. I. Nonpolar gases", J. Chem. Phys., 22, 1420.
    • (1954) J. Chem. Phys. , vol.22 , pp. 1420
    • Zwanzig, R.W.1
  • 23
    • 0344227487 scopus 로고
    • Thermodynamics of cavity formation in water: A molecular dynamics study
    • Postma, J. P. M., Berendsen, H. J. C. and Haak, J. R. (1982). "Thermodynamics of cavity formation in water: A molecular dynamics study", Faraday Symp. Chem. Soc., 17, 55.
    • (1982) Faraday Symp. Chem. Soc. , vol.17 , pp. 55
    • Postma, J.P.M.1    Berendsen, H.J.C.2    Haak, J.R.3
  • 25
    • 0002775934 scopus 로고
    • Interaction models for water in relation to protein hydration
    • Pullman, B. (Ed.), Reidel, Dordrecht
    • Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F. and Hermans, J. (1981). "Interaction models for water in relation to protein hydration", In: Pullman, B. (Ed.), Intermolecular Forces, pp. 331-342. Reidel, Dordrecht.
    • (1981) Intermolecular Forces , pp. 331-342
    • Berendsen, H.J.C.1    Postma, J.P.M.2    Van Gunsteren, W.F.3    Hermans, J.4
  • 27
    • 4544369164 scopus 로고
    • A generalized reaction field method for molecular dynamics simulations
    • Tironi, I. G., Sperb, R., Smith, P. E. and van Gunsteren, W. F. (1995). "A generalized reaction field method for molecular dynamics simulations", J. Chem. Phys., 102, 5451.
    • (1995) J. Chem. Phys. , vol.102 , pp. 5451
    • Tironi, I.G.1    Sperb, R.2    Smith, P.E.3    Van Gunsteren, W.F.4
  • 28
    • 0000925957 scopus 로고
    • Reaction field effects on the simulated properties of liquid water
    • Smith, P. E. and van Gunsteren, W. F. (1995). "Reaction field effects on the simulated properties of liquid water", Mol. Simulation, 15, 233.
    • (1995) Mol. Simulation , vol.15 , pp. 233
    • Smith, P.E.1    Van Gunsteren, W.F.2
  • 30
    • 0000249851 scopus 로고
    • Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations
    • Beutler, T. C., Mark, A. E., van Schaik, R. C., Gerber, P. R. and van Gunsteren, W. F. (1994). "Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations", Chem. Phys. Letters, 22, 529.
    • (1994) Chem. Phys. Letters , vol.22 , pp. 529
    • Beutler, T.C.1    Mark, A.E.2    Van Schaik, R.C.3    Gerber, P.R.4    Van Gunsteren, W.F.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.