메뉴 건너뛰기




Volumn 86, Issue , 2007, Pages 33-75

Calculating free energy differences using perturbation theory

Author keywords

[No Author keywords available]

Indexed keywords


EID: 47949084920     PISSN: 01726218     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-540-38448-9_2     Document Type: Review
Times cited : (49)

References (52)
  • 1
    • 34250928962 scopus 로고
    • Volumen und Hydratationswarme der Ionen
    • Born, M., Volumen und Hydratationswarme der Ionen, Z. Phys. 1920, 1, 45-48
    • (1920) Z. Phys , vol.1 , pp. 45-48
    • Born, M.1
  • 2
    • 33646471468 scopus 로고
    • Statistical mechanics of fluid mixtures
    • Kirkwood, J. G., Statistical mechanics of fluid mixtures, J. Chem. Phys. 1935, 3, 300-313
    • (1935) J. Chem. Phys , vol.3 , pp. 300-313
    • Kirkwood, J.G.1
  • 3
    • 36849122972 scopus 로고
    • High-temperature equation of state by a perturbation method. I. Nonpolar gases
    • Zwanzig, R. W., High-temperature equation of state by a perturbation method. I. Nonpolar gases, J. Chem. Phys. 1954, 22, 1420-1426
    • (1954) J. Chem. Phys , vol.22 , pp. 1420-1426
    • Zwanzig, R.W.1
  • 4
    • 0004504539 scopus 로고
    • Monte Carlo simulation of differences in free energies of hydration
    • Jorgensen, W. L.; Ravimohan, C., Monte Carlo simulation of differences in free energies of hydration, J. Chem. Phys. 1985, 83, 3050-3054
    • (1985) J. Chem. Phys , vol.83 , pp. 3050-3054
    • Jorgensen, W.L.1    Ravimohan, C.2
  • 5
    • 0036286654 scopus 로고    scopus 로고
    • Free energy simulations come of age: Protein-ligand recognition
    • Simonson, T.; Archontis, G.; Karplus, M., Free energy simulations come of age: protein-ligand recognition, Acc. Chem. Res. 2002, 35, 430-437
    • (2002) Acc. Chem. Res , vol.35 , pp. 430-437
    • Simonson, T.1    Archontis, G.2    Karplus, M.3
  • 6
    • 6744231939 scopus 로고
    • The chemical potential in dense fluids and fluid mixtures via computer simulation
    • Shing, K. S.; Gubbins, K. E., The chemical potential in dense fluids and fluid mixtures via computer simulation, Mol. Phys. 1982, 46, 1109-1128
    • (1982) Mol. Phys , vol.46 , pp. 1109-1128
    • Shing, K.S.1    Gubbins, K.E.2
  • 8
    • 33751143432 scopus 로고    scopus 로고
    • Free energy of ionic hydration
    • Hummer, G.; Pratt, L.; Garcia, A. E., Free energy of ionic hydration, J. Phys. Chem. 1996, 100, 1206-1215
    • (1996) J. Phys. Chem , vol.100 , pp. 1206-1215
    • Hummer, G.1    Pratt, L.2    Garcia, A.E.3
  • 9
    • 0038683517 scopus 로고    scopus 로고
    • Ewald artifacts in computer simulations of ionic solvation and ion-ion interactions: A continuum electrostatics study
    • Hünenberger, P. H.; McCammon, J. A., Ewald artifacts in computer simulations of ionic solvation and ion-ion interactions: a continuum electrostatics study, J. Chem. Phys. 1999, 110, 1856-1872
    • (1999) J. Chem. Phys , vol.110 , pp. 1856-1872
    • Hünenberger, P.H.1    McCammon, J.A.2
  • 11
    • 0030309180 scopus 로고    scopus 로고
    • Molecular modeling of protocellular functions
    • Hunter, L, Klein, T. E, Eds. World Scientific: Singapore
    • Pohorille, A.; Chipot, C.; New, M.; Wilson, M. A. Molecular modeling of protocellular functions, in Pacific Symposium on Biocomputing '96, Hunter, L.; Klein, T. E., Eds. World Scientific: Singapore, 1996, pp. 550-569
    • (1996) Pacific Symposium on Biocomputing '96 , pp. 550-569
    • Pohorille, A.1    Chipot, C.2    New, M.3    Wilson, M.A.4
  • 12
    • 0343791148 scopus 로고
    • Electric moments of molecules in liquids
    • Onsager, L., Electric moments of molecules in liquids, J. Am. Chem. Soc. 1936, 58, 1486-1493
    • (1936) J. Am. Chem. Soc , vol.58 , pp. 1486-1493
    • Onsager, L.1
  • 13
    • 0000433021 scopus 로고    scopus 로고
    • Pearlman, D. A.; Kollman, P. A., A new method for carrying out free energy perturbation calculations: dynamically modified windows, J. Chem. Phys. 1989, 90, 2460-2470
    • Pearlman, D. A.; Kollman, P. A., A new method for carrying out free energy perturbation calculations: dynamically modified windows, J. Chem. Phys. 1989, 90, 2460-2470
  • 14
    • 0035334524 scopus 로고    scopus 로고
    • Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling
    • Lu, N.; Kofke, D. A., Accuracy of free-energy perturbation calculations in molecular simulation. I. Modeling, J. Chem. Phys. 2001, 114, 7303-7312
    • (2001) J. Chem. Phys , vol.114 , pp. 7303-7312
    • Lu, N.1    Kofke, D.A.2
  • 15
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • Kollman, P. A., Free energy calculations: Applications to chemical and biochemical phenomena, Chem. Rev. 1993, 93, 2395-2417
    • (1993) Chem. Rev , vol.93 , pp. 2395-2417
    • Kollman, P.A.1
  • 16
    • 0001737514 scopus 로고
    • Free energy via molecular simulation: A primer
    • Van Gunsteren, W. F, Weiner, P. K, Wilkinson, A. J, Eds, ESCOM: Leiden
    • King, P. M. Free energy via molecular simulation: A primer. in Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, Van Gunsteren, W. F.; Weiner, P. K.; Wilkinson, A. J., Eds., vol. 2. ESCOM: Leiden, 1993, pp. 267-314
    • (1993) Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications , vol.2 , pp. 267-314
    • King, P.M.1
  • 17
    • 2542564912 scopus 로고    scopus 로고
    • Advances and continuing challenges in achieving realistic and predictive simulations of the properties of organic and biological molecules
    • Kollman, P. A., Advances and continuing challenges in achieving realistic and predictive simulations of the properties of organic and biological molecules, Acc. Chem. Res. 1996, 29, 461-469
    • (1996) Acc. Chem. Res , vol.29 , pp. 461-469
    • Kollman, P.A.1
  • 20
    • 0027898605 scopus 로고
    • Structure and energetics of model amphiphilic molecules at the water liquid-vapor interface. A molecular dynamic study
    • Pohorille, A.; Benjamin, I., Structure and energetics of model amphiphilic molecules at the water liquid-vapor interface. A molecular dynamic study, J. Phys. Chem. 1993, 97, 2664-2670
    • (1993) J. Phys. Chem , vol.97 , pp. 2664-2670
    • Pohorille, A.1    Benjamin, I.2
  • 21
    • 0031590888 scopus 로고    scopus 로고
    • Interactions of anesthetics with the water-hexane interface. A molecular dynamics study
    • Chipot, C.; Wilson, M. A.; Pohorille, A., Interactions of anesthetics with the water-hexane interface. A molecular dynamics study, J. Phys. Chem. B 1997, 101, 782-791
    • (1997) J. Phys. Chem. B , vol.101 , pp. 782-791
    • Chipot, C.1    Wilson, M.A.2    Pohorille, A.3
  • 22
    • 0031239424 scopus 로고    scopus 로고
    • Biotechnological applications of surface plasmon resonance
    • Silin, V.; Plant, A., Biotechnological applications of surface plasmon resonance, Trends Biotechnol. 1997, 15, 353-359
    • (1997) Trends Biotechnol , vol.15 , pp. 353-359
    • Silin, V.1    Plant, A.2
  • 23
    • 0031058541 scopus 로고    scopus 로고
    • The statistical-thermodynamic basis for computation of binding affinities: A critical review
    • Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A., The statistical-thermodynamic basis for computation of binding affinities: a critical review, Biophys. J. 1997, 72, 1047-1069
    • (1997) Biophys. J , vol.72 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, J.A.4
  • 24
    • 0030887944 scopus 로고    scopus 로고
    • Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme
    • Hermans, J.; Wang, L., Inclusion of loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme, J. Am. Chem. Soc. 1997, 119, 2707-2714
    • (1997) J. Am. Chem. Soc , vol.119 , pp. 2707-2714
    • Hermans, J.1    Wang, L.2
  • 25
    • 0030134642 scopus 로고    scopus 로고
    • Estimating the relative free energy of different molecular states with respect to a single reference state
    • Liu, S. Y.; Mark, A. E.; van Gunsteren, W. F., Estimating the relative free energy of different molecular states with respect to a single reference state, J. Phys. Chem. 1996, 100, 9485-9494
    • (1996) J. Phys. Chem , vol.100 , pp. 9485-9494
    • Liu, S.Y.1    Mark, A.E.2    van Gunsteren, W.F.3
  • 26
    • 18744411546 scopus 로고    scopus 로고
    • Free energies of ligand binding for structurally diverse compounds
    • Oostenbrink, C.; van Gunsteren, W. F., Free energies of ligand binding for structurally diverse compounds, Proc. Natl Acad. Sci. USA 2005, 102, 6750-6754
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 6750-6754
    • Oostenbrink, C.1    van Gunsteren, W.F.2
  • 27
    • 0009235161 scopus 로고    scopus 로고
    • Pearlman, D. A., A comparison of alternative approaches to free energy calculations, J. Phys. Chem. 1994, 98, 1487-1493
    • Pearlman, D. A., A comparison of alternative approaches to free energy calculations, J. Phys. Chem. 1994, 98, 1487-1493
  • 28
    • 0023346161 scopus 로고
    • Free energy calculations by computer simulation
    • Bash, P. A.; Singh, U. C.; Langridge, R.; Kollman, P. A., Free energy calculations by computer simulation, Science 1987, 236, 564-568
    • (1987) Science , vol.236 , pp. 564-568
    • Bash, P.A.1    Singh, U.C.2    Langridge, R.3    Kollman, P.A.4
  • 29
    • 0023106632 scopus 로고
    • Calculation of the relative change in binding free energy of a protein-inhibitor complex
    • Bash, P. A.; Singh, U. C.; Brown, F. K.; Langridge, R.; Kollman, P. A., Calculation of the relative change in binding free energy of a protein-inhibitor complex, Science 1987, 235, 574-576
    • (1987) Science , vol.235 , pp. 574-576
    • Bash, P.A.1    Singh, U.C.2    Brown, F.K.3    Langridge, R.4    Kollman, P.A.5
  • 30
    • 36449005776 scopus 로고
    • The overlooked bond-stretching contribution in free energy perturbation calculations
    • Pearlman, D. A.; Kollman, P. A., The overlooked bond-stretching contribution in free energy perturbation calculations, J. Chem. Phys. 1991, 94, 4532-4545
    • (1991) J. Chem. Phys , vol.94 , pp. 4532-4545
    • Pearlman, D.A.1    Kollman, P.A.2
  • 31
    • 0006379192 scopus 로고
    • Change of bond length in free-energy simulations: Algorithmic improvements, but when is it necessary?
    • Wang, L.; Hermans, J., Change of bond length in free-energy simulations: algorithmic improvements, but when is it necessary?, J. Chem. Phys. 1994, 100, 9129-9139
    • (1994) J. Chem. Phys , vol.100 , pp. 9129-9139
    • Wang, L.1    Hermans, J.2
  • 32
    • 0024365336 scopus 로고
    • Hidden thermodynamics of mutant proteins: A molecular dynamics analysis
    • Gao, J.; Kuczera, K.; Tidor, B.; Karplus, M., Hidden thermodynamics of mutant proteins: a molecular dynamics analysis, Science 1989, 244, 1069-1072
    • (1989) Science , vol.244 , pp. 1069-1072
    • Gao, J.1    Kuczera, K.2    Tidor, B.3    Karplus, M.4
  • 33
    • 0042787283 scopus 로고    scopus 로고
    • The role of bonded terms in free energy simulations: I. Theoretical analysis
    • Boresch, S.; Karplus, M., The role of bonded terms in free energy simulations: I. Theoretical analysis, J. Phys. Chem. A 1999, 103, 103-118
    • (1999) J. Phys. Chem. A , vol.103 , pp. 103-118
    • Boresch, S.1    Karplus, M.2
  • 34
    • 16444377080 scopus 로고    scopus 로고
    • The role of bonded terms in free energy simulations: II. Calculation of their influence on free energy differences of solvation
    • Boresch, S.; Karplus, M., The role of bonded terms in free energy simulations: II. Calculation of their influence on free energy differences of solvation, J. Phys. Chem. A 1999, 103, 119-136
    • (1999) J. Phys. Chem. A , vol.103 , pp. 119-136
    • Boresch, S.1    Karplus, M.2
  • 35
    • 0000249851 scopus 로고
    • Avoiding singularities and neumerical instabilities in free energy calculations based on molecular simulations
    • Beutler, T. C.; Mark, A. E.; van Schaik, R. C.; Gerber, P. R.; van Gunsteren, W. F., Avoiding singularities and neumerical instabilities in free energy calculations based on molecular simulations, Chem. Phys. Lett. 1994, 222, 529-539
    • (1994) Chem. Phys. Lett , vol.222 , pp. 529-539
    • Beutler, T.C.1    Mark, A.E.2    van Schaik, R.C.3    Gerber, P.R.4    van Gunsteren, W.F.5
  • 36
    • 36749109235 scopus 로고
    • The surface tension of water: A Monte Carlo calculation using an umbrella sampling algorithm
    • Lee, C. Y.; Scott, H. L., The surface tension of water: A Monte Carlo calculation using an umbrella sampling algorithm, J. Chem. Phys. 1980, 73, 4591-4596
    • (1980) J. Chem. Phys , vol.73 , pp. 4591-4596
    • Lee, C.Y.1    Scott, H.L.2
  • 37
    • 5244304444 scopus 로고
    • Efficient estimation of free energy differences from Monte Carlo data
    • Bennett, C. H., Efficient estimation of free energy differences from Monte Carlo data, J. Comp. Phys. 1976, 22, 245-268
    • (1976) J. Comp. Phys , vol.22 , pp. 245-268
    • Bennett, C.H.1
  • 38
    • 0031578972 scopus 로고    scopus 로고
    • Parallel tempering algorithm for conformational studies of biological molecules
    • Hansmann, U. H. E., Parallel tempering algorithm for conformational studies of biological molecules, Chem. Phys. Lett. 1997, 281, 140-150
    • (1997) Chem. Phys. Lett , vol.281 , pp. 140-150
    • Hansmann, U.H.E.1
  • 39
    • 0037157317 scopus 로고    scopus 로고
    • On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
    • Fukunishi, O. Watanabe; Takada, S., On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: application to protein structure prediction, J. Chem. Phys. 2002, 116, 9058-9067
    • (2002) J. Chem. Phys , vol.116 , pp. 9058-9067
    • Fukunishi, O.1    Watanabe2    Takada, S.3
  • 40
    • 0030774472 scopus 로고    scopus 로고
    • Multistate Gaussian model for electrostatic solvation free energies
    • Hummer, G.; Pratt, L.; Garcia, A. E., Multistate Gaussian model for electrostatic solvation free energies, J. Am. Chem. Soc. 1997, 119, 8523-8527
    • (1997) J. Am. Chem. Soc , vol.119 , pp. 8523-8527
    • Hummer, G.1    Pratt, L.2    Garcia, A.E.3
  • 41
    • 0004073954 scopus 로고
    • 4th edition, American Mathematical Society: Providence
    • Szegö, G., Orthogonal Polynomials, [4th edition], American Mathematical Society: Providence, 1975
    • (1975) Orthogonal Polynomials
    • Szegö, G.1
  • 45
    • 0001605134 scopus 로고    scopus 로고
    • The quasi-Gaussian entropy theory: Free energy calculations based on the potential energy distribution function
    • Amadei, A.; Apol, M. E. F.; Berendsen, H. J. C., The quasi-Gaussian entropy theory: free energy calculations based on the potential energy distribution function, J. Chem. Phys. 1996, 104, 1560-1574
    • (1996) J. Chem. Phys , vol.104 , pp. 1560-1574
    • Amadei, A.1    Apol, M.E.F.2    Berendsen, H.J.C.3
  • 47
    • 24144501116 scopus 로고    scopus 로고
    • Nanda, H.; Lu, N.; Kofke, D. A., Using non-Gaussian density functional fits to improve relative free energy calculations, J. Chem. Phys. 2005, 122, 134110:1-8
    • Nanda, H.; Lu, N.; Kofke, D. A., Using non-Gaussian density functional fits to improve relative free energy calculations, J. Chem. Phys. 2005, 122, 134110:1-8
  • 48
    • 0000008625 scopus 로고    scopus 로고
    • Free energy calculations: Methods and applications
    • Allinger, N. L, Clark, T, Gasteiger, J, Kollman, P. A, Schaefer III, H. F, Schreiner, P. R, Eds, 2. Wiley: Chichester
    • Pearlman, D. A.; Rao, B. G. Free energy calculations: Methods and applications. in Encyclopedia of computational chemistry, Schleyer, P. v. R.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer III, H. F.; Schreiner, P. R., Eds., vol. 2. Wiley: Chichester, 1998, pp. 1036-1061
    • (1998) Encyclopedia of computational chemistry, Schleyer, P , vol.R , pp. 1036-1061
    • Pearlman, D.A.1    Rao, B.G.2
  • 49
    • 0001661731 scopus 로고
    • Thermodynamics of aqueous solvation: Solution properties of alchohols and alkanes
    • Fleischman, S. H.; Brooks III, C. L., Thermodynamics of aqueous solvation: solution properties of alchohols and alkanes, J. Chem. Phys. 1987, 87, 3029-3037
    • (1987) J. Chem. Phys , vol.87 , pp. 3029-3037
    • Fleischman, S.H.1    Brooks III, C.L.2
  • 50
    • 0038001529 scopus 로고    scopus 로고
    • Staging is more important than perturbation method for computation of enthalpy and entropy changes in complex systems
    • Lu, N.; Kofke, D. A.; Woolf, T. B., Staging is more important than perturbation method for computation of enthalpy and entropy changes in complex systems, J. Phys. Chem. B 2003, 107, 5598-5611
    • (2003) J. Phys. Chem. B , vol.107 , pp. 5598-5611
    • Lu, N.1    Kofke, D.A.2    Woolf, T.B.3
  • 51
    • 20444499328 scopus 로고    scopus 로고
    • Insights into the recognition and association of transmembrane α-helices. The free energy of α-helix dimerization in glycophorin A
    • Hénin, J.; Pohorille, A.; Chipot, C., Insights into the recognition and association of transmembrane α-helices. The free energy of α-helix dimerization in glycophorin A., J. Am. Chem. Soc. 2005, 127, 8478-8484
    • (2005) J. Am. Chem. Soc , vol.127 , pp. 8478-8484
    • Hénin, J.1    Pohorille, A.2    Chipot, C.3
  • 52
    • 36449009782 scopus 로고
    • Predictions of free energy differences from a single simulation of the initial state
    • Smith, P. E.; van Gunsteren, W. F., Predictions of free energy differences from a single simulation of the initial state, J. Chem. Phys. 1994, 100, 577-585
    • (1994) J. Chem. Phys , vol.100 , pp. 577-585
    • Smith, P.E.1    van Gunsteren, W.F.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.