메뉴 건너뛰기




Volumn 10, Issue 7, 2014, Pages 2690-2709

An overview of electrostatic free energy computations for solutions and proteins

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84904131114     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct500195p     Document Type: Article
Times cited : (120)

References (108)
  • 2
    • 0023060081 scopus 로고
    • Free energy changes in solvated proteins: Microscopic calculations using a reversible charging process
    • Warshel, A.; Sussman, F.; King, G. Free energy changes in solvated proteins: microscopic calculations using a reversible charging process Biochemistry 1986, 25, 8368-8372
    • (1986) Biochemistry , vol.25 , pp. 8368-8372
    • Warshel, A.1    Sussman, F.2    King, G.3
  • 3
    • 0024445808 scopus 로고
    • Dispersed polaron simulations of electron transfer in photosynthetic reaction centers
    • Warshel, A.; Chu, Z.; Parson, W. Dispersed polaron simulations of electron transfer in photosynthetic reaction centers Science 1989, 246, 112-116
    • (1989) Science , vol.246 , pp. 112-116
    • Warshel, A.1    Chu, Z.2    Parson, W.3
  • 4
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • Kollman, P. Free energy calculations: applications to chemical and biochemical phenomena Chem. Rev. 1993, 93, 2395
    • (1993) Chem. Rev. , vol.93 , pp. 2395
    • Kollman, P.1
  • 6
    • 0007836334 scopus 로고
    • Dynamics of reactions in polar solvents. Semiclassical trajectory studies of electron transfer and proton transfer studies
    • Warshel, A. Dynamics of reactions in polar solvents. Semiclassical trajectory studies of electron transfer and proton transfer studies J. Phys. Chem. 1982, 86, 2218-2224
    • (1982) J. Phys. Chem. , vol.86 , pp. 2218-2224
    • Warshel, A.1
  • 8
    • 84864176671 scopus 로고    scopus 로고
    • Electron transfer reactions in chemistry: Theory and experiment
    • Malmström, B. G. World Scientific Publishing Co. Singapore.
    • Marcus, R. Electron transfer reactions in chemistry: theory and experiment. Nobel Lectures, Chemistry 1991-1995; Malmström, B. G., Ed.; World Scientific Publishing Co.: Singapore, 1997.
    • (1997) Nobel Lectures, Chemistry 1991-1995
    • Marcus, R.1
  • 11
    • 0036286654 scopus 로고    scopus 로고
    • Free energy simulations come of age: The protein-ligand recognition problem
    • Simonson, T.; Archontis, G.; Karplus, M. Free energy simulations come of age: the protein-ligand recognition problem 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
  • 12
    • 0037529067 scopus 로고    scopus 로고
    • Electrostatics and dynamics of proteins
    • Simonson, T. Electrostatics and dynamics of proteins Rep. Prog. Phys. 2003, 66, 737-787
    • (2003) Rep. Prog. Phys. , vol.66 , pp. 737-787
    • Simonson, T.1
  • 14
    • 65249124122 scopus 로고    scopus 로고
    • Computations of Standard Binding Free Energies with Molecular Dynamics Simulations
    • Deng, Y.; Roux, B. Computations of Standard Binding Free Energies with Molecular Dynamics Simulations J. Phys. Chem. B 2009, 113, 2234-2246
    • (2009) J. Phys. Chem. B , vol.113 , pp. 2234-2246
    • Deng, Y.1    Roux, B.2
  • 15
    • 0030134110 scopus 로고    scopus 로고
    • On the Validity of Electrostatic Linear Response in Polar Solvents
    • Aqvist, J.; Hansson, T. On the Validity of Electrostatic Linear Response in Polar Solvents J. Phys. Chem. 1996, 100, 9512-9521
    • (1996) J. Phys. Chem. , vol.100 , pp. 9512-9521
    • Aqvist, J.1    Hansson, T.2
  • 16
    • 33751143432 scopus 로고    scopus 로고
    • Free energy of ionic hydration
    • Hummer, G.; Pratt, L.; Garcia, A. 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.3
  • 17
    • 0000269031 scopus 로고    scopus 로고
    • Electrostatic potentials and free energies of solvation of polar and charged molecules
    • Hummer, G.; Pratt, L.; Garcia, A.; Berne, B. J.; Rick, S. W. Electrostatic potentials and free energies of solvation of polar and charged molecules J. Phys. Chem. B 1997, 101, 3017-3020
    • (1997) J. Phys. Chem. B , vol.101 , pp. 3017-3020
    • Hummer, G.1    Pratt, L.2    Garcia, A.3    Berne, B.J.4    Rick, S.W.5
  • 18
    • 0000078301 scopus 로고    scopus 로고
    • Effects of long-range electrostatic potential truncation on the free energy of ionic hydration
    • Ashbaugh, H. S.; Wood, R. H. Effects of long-range electrostatic potential truncation on the free energy of ionic hydration J. Chem. Phys. 1997, 106, 8135-8139
    • (1997) J. Chem. Phys. , vol.106 , pp. 8135-8139
    • Ashbaugh, H.S.1    Wood, R.H.2
  • 19
    • 0001570192 scopus 로고    scopus 로고
    • Analysis of Electrostatic potential truncation schemes in Polar Solvents
    • Aqvist, J.; Hansson, T. Analysis of Electrostatic potential truncation schemes in Polar Solvents J. Phys. Chem. B 1998, 102, 3837-3840
    • (1998) J. Phys. Chem. B , vol.102 , pp. 3837-3840
    • Aqvist, J.1    Hansson, T.2
  • 20
    • 0001286784 scopus 로고    scopus 로고
    • Reply to comment on "electrostatic potentials and free energies of solvation of polar and charged molecules"
    • Hummer, G.; Pratt, L.; Garcia, A.; Garde, S.; Berne, B. J.; Rick, S. W. Reply to comment on "Electrostatic potentials and free energies of solvation of polar and charged molecules" J. Phys. Chem. B 1998, 102, 3841-3843
    • (1998) J. Phys. Chem. B , vol.102 , pp. 3841-3843
    • Hummer, G.1    Pratt, L.2    Garcia, A.3    Garde, S.4    Berne, B.J.5    Rick, S.W.6
  • 21
    • 0001286785 scopus 로고    scopus 로고
    • Reply to comment on "electrostatic potentials and free energies of solvation of polar and charged molecules"
    • Ashbaugh, H. S.; Sakane, S.; Wood, R. H. Reply to comment on "Electrostatic potentials and free energies of solvation of polar and charged molecules" J. Phys. Chem. B 1998, 102, 3844-3845
    • (1998) J. Phys. Chem. B , vol.102 , pp. 3844-3845
    • Ashbaugh, H.S.1    Sakane, S.2    Wood, R.H.3
  • 22
    • 0000642138 scopus 로고    scopus 로고
    • Ionic charging free energies: Spherical versus periodic boundary conditions
    • Darden, T.; Pearlman, D.; Pedersen, L. Ionic charging free energies: spherical versus periodic boundary conditions J. Chem. Phys. 1998, 109, 10921-10935
    • (1998) J. Chem. Phys. , vol.109 , pp. 10921-10935
    • Darden, T.1    Pearlman, D.2    Pedersen, L.3
  • 23
    • 0032968133 scopus 로고    scopus 로고
    • Implicit solvent models
    • Roux, B.; Simonson, T. Implicit solvent models Biophys. Chem. 1999, 78, 1-20
    • (1999) Biophys. Chem. , vol.78 , pp. 1-20
    • Roux, B.1    Simonson, T.2
  • 24
    • 36849138378 scopus 로고
    • The electrostatic influence of substituents on the dissociation constant of organic acids
    • Kirkwood, J.; Westheimer, F. The electrostatic influence of substituents on the dissociation constant of organic acids J. Chem. Phys. 1938, 6, 506-512
    • (1938) J. Chem. Phys. , vol.6 , pp. 506-512
    • Kirkwood, J.1    Westheimer, F.2
  • 25
    • 84946893847 scopus 로고
    • Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio molecular potentials for the prevision of solvent effects
    • Miertus, S.; Scrocco, E.; Tomasi, J. Electrostatic interaction of a solute with a continuum. A direct utilization of ab initio molecular potentials for the prevision of solvent effects Chem. Phys. 1981, 55, 117-129
    • (1981) Chem. Phys. , vol.55 , pp. 117-129
    • Miertus, S.1    Scrocco, E.2    Tomasi, J.3
  • 26
    • 36549094414 scopus 로고
    • A surface constrained all-atom solvent model for effective simulations of polar solutions
    • King, G.; Warshel, A. A surface constrained all-atom solvent model for effective simulations of polar solutions J. Chem. Phys. 1989, 91, 3647-3661
    • (1989) J. Chem. Phys. , vol.91 , pp. 3647-3661
    • King, G.1    Warshel, A.2
  • 27
    • 0001655657 scopus 로고
    • Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations
    • Beglov, D.; Roux, B. Finite representation of an infinite bulk system: solvent boundary potential for computer simulations J. Chem. Phys. 1994, 100, 9050-9063
    • (1994) J. Chem. Phys. , vol.100 , pp. 9050-9063
    • Beglov, D.1    Roux, B.2
  • 28
    • 84961981091 scopus 로고    scopus 로고
    • Implicit solvent models: Equilibria, structure, spectra, and dynamics
    • Cramer, C.; Truhlar, D. Implicit solvent models: equilibria, structure, spectra, and dynamics Chem. Rev. 1999, 99, 2161-2200
    • (1999) Chem. Rev. , vol.99 , pp. 2161-2200
    • Cramer, C.1    Truhlar, D.2
  • 31
    • 0001786236 scopus 로고
    • Simulation of electric systems in periodic boundary conditions. I. Lattice sums and dielectric constants
    • De Leeuw, S.; Perram, J.; Smith, E. Simulation of electric systems in periodic boundary conditions. I. Lattice sums and dielectric constants Proc. R. Soc. London 1980, A373, 27-56
    • (1980) Proc. R. Soc. London , vol.373 , pp. 27-56
    • De Leeuw, S.1    Perram, J.2    Smith, E.3
  • 32
    • 0001084325 scopus 로고
    • On the energy per particle in three- and two-dimensional Wigner lattices
    • Nijboer, B. R. A.; Ruijgrok, T. W. On the energy per particle in three- and two-dimensional Wigner lattices J. Stat. Phys. 1988, 53, 361-382
    • (1988) J. Stat. Phys. , vol.53 , pp. 361-382
    • Nijboer, B.R.A.1    Ruijgrok, T.W.2
  • 33
    • 0001029719 scopus 로고
    • On finite-size effects in computer simulations using the Ewald potential
    • Figueirido, F. E.; Levy, R. On finite-size effects in computer simulations using the Ewald potential J. Chem. Phys. 1995, 103, 6133-6142
    • (1995) J. Chem. Phys. , vol.103 , pp. 6133-6142
    • Figueirido, F.E.1    Levy, R.2
  • 34
    • 0003871536 scopus 로고    scopus 로고
    • Becker, O. Mackerell, A. Jr. Roux, B. Watanabe, M. Marcel Dekker, New York, Chapter 4.
    • Darden, T. In Computational Biochemistry & Biophysics; Becker, O.; Mackerell, A., Jr.; Roux, B.; Watanabe, M., Eds.; Marcel Dekker, New York, 2001; Chapter 4.
    • (2001) Computational Biochemistry & Biophysics
    • Darden, T.1
  • 35
    • 0001158363 scopus 로고
    • Monte Carlo studies of the dielectric proterties of water-like models
    • Barker, J.; Watts, R. Monte Carlo studies of the dielectric proterties of water-like models Mol. Phys. 1973, 26, 789-792
    • (1973) Mol. Phys. , vol.26 , pp. 789-792
    • Barker, J.1    Watts, R.2
  • 36
    • 0002686742 scopus 로고
    • Inclusion of reaction fields in molecular dynamics: Application to liquid water
    • van Gunsteren, W.; Berendsen, H.; Rullmann, J. Inclusion of reaction fields in molecular dynamics: application to liquid water Faraday Discuss. Chem. Soc. 1979, 66, 58-70
    • (1979) Faraday Discuss. Chem. Soc. , vol.66 , pp. 58-70
    • Van Gunsteren, W.1    Berendsen, H.2    Rullmann, J.3
  • 37
    • 0024673546 scopus 로고
    • Comment on "study on the liquid-vapor interface of water. I. Simulation results of thermodynamic properties and orientational structure
    • Wilson, M. A.; Pohorille, A.; Pratt, L. R. Comment on "Study on the liquid-vapor interface of water. I. Simulation results of thermodynamic properties and orientational structure J. Chem. Phys. 1989, 90, 5211-5213
    • (1989) J. Chem. Phys. , vol.90 , pp. 5211-5213
    • Wilson, M.A.1    Pohorille, A.2    Pratt, L.R.3
  • 38
    • 33644879448 scopus 로고    scopus 로고
    • Absolute Hydration Free Energy Scale for Alkali and Halide Ions Established from Simulations with a Polarizable Force Field
    • Lamoureux, G.; Roux, B. Absolute Hydration Free Energy Scale for Alkali and Halide Ions Established from Simulations with a Polarizable Force Field J. Phys. Chem. B 2006, 110, 3308-3322
    • (2006) J. Phys. Chem. B , vol.110 , pp. 3308-3322
    • Lamoureux, G.1    Roux, B.2
  • 39
    • 0000951252 scopus 로고    scopus 로고
    • Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water
    • Feller, S.; Pastor, R.; Rojnuckarin, A.; Bogusz, S.; Brooks, B. Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water J. Phys. Chem. 1996, 100, 17011-17020
    • (1996) J. Phys. Chem. , vol.100 , pp. 17011-17020
    • Feller, S.1    Pastor, R.2    Rojnuckarin, A.3    Bogusz, S.4    Brooks, B.5
  • 40
    • 57849157822 scopus 로고    scopus 로고
    • On the origin of the electrostatic potential difference at a liquid-vacuum interface
    • Harder, E.; Roux, B. On the origin of the electrostatic potential difference at a liquid-vacuum interface J. Chem. Phys. 2008, 129, 234706
    • (2008) J. Chem. Phys. , vol.129 , pp. 234706
    • Harder, E.1    Roux, B.2
  • 44
    • 33745155379 scopus 로고    scopus 로고
    • Computation of methodology-independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids
    • Kastenholz, M. A.; Hünenberger, P. H. Computation of methodology-independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids J. Chem. Phys. 2006, 124, 224501
    • (2006) J. Chem. Phys. , vol.124 , pp. 224501
    • Kastenholz, M.A.1    Hünenberger, P.H.2
  • 45
    • 33745155379 scopus 로고    scopus 로고
    • Computation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation
    • Kastenholz, M. A.; Hünenberger, P. H. Computation of methodology-independent ionic solvation free energies from molecular simulations. II. The hydration free energy of the sodium cation J. Chem. Phys. 2006, 124, 224501
    • (2006) J. Chem. Phys. , vol.124 , pp. 224501
    • Kastenholz, M.A.1    Hünenberger, P.H.2
  • 46
    • 66749185225 scopus 로고    scopus 로고
    • Ab initio molecular dynamics calculations of ion hydration free energies
    • Leung, K.; Rempe, S. B.; von Lilienfeld, O. A. Ab initio molecular dynamics calculations of ion hydration free energies J. Chem. Phys. 2009, 130, 204507
    • (2009) J. Chem. Phys. , vol.130 , pp. 204507
    • Leung, K.1    Rempe, S.B.2    Von Lilienfeld, O.A.3
  • 48
    • 0034249487 scopus 로고    scopus 로고
    • Convergence of molecular and macroscopic continuum descriptions of ion hydration
    • Ashbaugh, H. S. Convergence of molecular and macroscopic continuum descriptions of ion hydration J. Phys. Chem. B 2000, 104, 7235-7238
    • (2000) J. Phys. Chem. B , vol.104 , pp. 7235-7238
    • Ashbaugh, H.S.1
  • 49
    • 0043014528 scopus 로고    scopus 로고
    • Absolute hydration free energies of ions, ion-water clusters, and quasichemical theory
    • Asthagiri, D.; Pratt, L.; Ashbaugh, H. S. Absolute hydration free energies of ions, ion-water clusters, and quasichemical theory J. Chem. Phys. 2003, 119, 2702-2708
    • (2003) J. Chem. Phys. , vol.119 , pp. 2702-2708
    • Asthagiri, D.1    Pratt, L.2    Ashbaugh, H.S.3
  • 50
    • 0031561292 scopus 로고    scopus 로고
    • Continuum treatment of long-range interactions in free energy calculations. Application to protein-ligand binding
    • Simonson, T.; Archontis, G.; Karplus, M. Continuum treatment of long-range interactions in free energy calculations. Application to protein-ligand binding J. Phys. Chem. B 1997, 101, 8349-8362
    • (1997) J. Phys. Chem. B , vol.101 , pp. 8349-8362
    • Simonson, T.1    Archontis, G.2    Karplus, M.3
  • 51
    • 0037061982 scopus 로고    scopus 로고
    • Ala acceptor stem: Comparison between continuum reaction field and particle-mesh Ewald electrostatic treatments
    • Ala acceptor stem: comparison between continuum reaction field and particle-mesh Ewald electrostatic treatments J. Phys. Chem. B 2002, 106, 3696-3705
    • (2002) J. Phys. Chem. B , vol.106 , pp. 3696-3705
    • Nina, M.1    Simonson, T.2
  • 52
    • 7044249333 scopus 로고    scopus 로고
    • Grand canonical Monte Carlo simulation of water in protein environments
    • Woo, H. J.; Dinner, A.; Roux, B. Grand canonical Monte Carlo simulation of water in protein environments J. Chem. Phys. 2004, 121, 6392-6400
    • (2004) J. Chem. Phys. , vol.121 , pp. 6392-6400
    • Woo, H.J.1    Dinner, A.2    Roux, B.3
  • 53
    • 34250928962 scopus 로고
    • Volumen und hydrationswärme der ionen
    • Born, M. Volumen und hydrationswärme der ionen Zeit. Phys. 1920, 1, 45-48
    • (1920) Zeit. Phys. , vol.1 , pp. 45-48
    • Born, M.1
  • 56
    • 0031185669 scopus 로고    scopus 로고
    • On finite-size corrections to the free energy of hydration
    • Figueirido, F. E.; Del Buono, G. S.; Levy, R. On finite-size corrections to the free energy of hydration J. Phys. Chem. B 1997, 101, 5622-5623
    • (1997) J. Phys. Chem. B , vol.101 , pp. 5622-5623
    • Figueirido, F.E.1    Del Buono, G.S.2    Levy, R.3
  • 57
    • 0001457283 scopus 로고    scopus 로고
    • Continuum electrostatics to the polarization and thermodynamic properties of Ewald sum simulations for ions and ion pairs at infinite dilution
    • Sakane, S.; Ashbaugh, H. S.; Wood, R. H. Continuum electrostatics to the polarization and thermodynamic properties of Ewald sum simulations for ions and ion pairs at infinite dilution J. Phys. Chem. B 1998, 102, 5673-5682
    • (1998) J. Phys. Chem. B , vol.102 , pp. 5673-5682
    • Sakane, S.1    Ashbaugh, H.S.2    Wood, R.H.3
  • 58
    • 0037627173 scopus 로고    scopus 로고
    • Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: A continuum electrostatics study
    • Hunenberger, P.; McCammon, J. Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: A continuum electrostatics study Biophys. Chem. 1999, 78, 69-88
    • (1999) Biophys. Chem. , vol.78 , pp. 69-88
    • Hunenberger, P.1    McCammon, J.2
  • 59
    • 0000123071 scopus 로고    scopus 로고
    • Removal of pressure and free energy artefacts in charged periodic systems via net charge corrections to the Ewald potential
    • Bogusz, S.; Cheatham, T. E.; Brooks, B. R. Removal of pressure and free energy artefacts in charged periodic systems via net charge corrections to the Ewald potential J. Chem. Phys. 1998, 108, 7070-7084
    • (1998) J. Chem. Phys. , vol.108 , pp. 7070-7084
    • Bogusz, S.1    Cheatham, T.E.2    Brooks, B.R.3
  • 61
    • 0347089020 scopus 로고    scopus 로고
    • Energetics of ion conduction through the gramicidin channel
    • Allen, T.; Andersen, O.; Roux, B. Energetics of ion conduction through the gramicidin channel Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 117-122
    • (2004) Proc. Natl. Acad. Sci. U.S.A. , vol.101 , pp. 117-122
    • Allen, T.1    Andersen, O.2    Roux, B.3
  • 62
    • 33750606030 scopus 로고    scopus 로고
    • Molecular dynamics - Potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels
    • Allen, T.; Andersen, O.; Roux, B. Molecular dynamics-potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels Biophys. Chem. 2006, 124, 251-267
    • (2006) Biophys. Chem. , vol.124 , pp. 251-267
    • Allen, T.1    Andersen, O.2    Roux, B.3
  • 63
    • 33646192258 scopus 로고    scopus 로고
    • Ion permeation through a narrow channel: Using gramicidin to ascertain all-atom molecular dynamics potential of mean force methodology and biomolecular force fields
    • Allen, T.; Andersen, O.; Roux, B. Ion permeation through a narrow channel: using gramicidin to ascertain all-atom molecular dynamics potential of mean force methodology and biomolecular force fields Biophys. J. 2006, 90, 3447-3468
    • (2006) Biophys. J. , vol.90 , pp. 3447-3468
    • Allen, T.1    Andersen, O.2    Roux, B.3
  • 64
    • 0030774472 scopus 로고    scopus 로고
    • Multistate gaussian model for electrostatic solvation free energies
    • Hummer, G.; Pratt, L.; Garcia, A. 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.3
  • 65
    • 84903362843 scopus 로고    scopus 로고
    • Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects
    • Rocklin, G. J.; Mobley, D. L.; Dill, K. A.; Hünenberger, P. H. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects J. Chem. Phys. 2013, 139, 184103
    • (2013) J. Chem. Phys. , vol.139 , pp. 184103
    • Rocklin, G.J.1    Mobley, D.L.2    Dill, K.A.3    Hünenberger, P.H.4
  • 66
    • 84867344848 scopus 로고    scopus 로고
    • New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field
    • Reif, M. M.; Hünenberger, P. H.; Oostenbrink, C. New Interaction Parameters for Charged Amino Acid Side Chains in the GROMOS Force Field J. Chem. Theory Comput. 2012, 8, 3705-3723
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 3705-3723
    • Reif, M.M.1    Hünenberger, P.H.2    Oostenbrink, C.3
  • 67
    • 84904098437 scopus 로고    scopus 로고
    • Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation
    • in press.
    • Reif, M. M.; Oostenbrink, C. Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation. J. Chem. Theory Comput. 2013, in press.
    • (2013) J. Chem. Theory Comput.
    • Reif, M.M.1    Oostenbrink, C.2
  • 68
    • 36549092795 scopus 로고
    • Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water
    • Jorgensen, W.; Buckner, K.; Boudon, S.; Tirado-Rives, J. Efficient computation of absolute free energies of binding by computer simulations. Application to the methane dimer in water J. Chem. Phys. 1988, 89, 3742-3746
    • (1988) J. Chem. Phys. , vol.89 , pp. 3742-3746
    • Jorgensen, W.1    Buckner, K.2    Boudon, S.3    Tirado-Rives, J.4
  • 69
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N log(N) method for Ewald sums in large systems
    • Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald: an N log(N) method for Ewald sums in large systems J. Chem. Phys. 1993, 98, 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 70
    • 0041824707 scopus 로고    scopus 로고
    • Ion sizes and finite-size corrections for ionic-solvation free energies
    • Hummer, G.; Pratt, L.; Garcia, A. Ion sizes and finite-size corrections for ionic-solvation free energies J. Phys. Chem. B 1997, 101, 9275-9277
    • (1997) J. Phys. Chem. B , vol.101 , pp. 9275-9277
    • Hummer, G.1    Pratt, L.2    Garcia, A.3
  • 72
    • 84884528689 scopus 로고    scopus 로고
    • The vapor-liquid interface potential of (multi)polar fluids and its influence on ion solvation
    • Horvath, L.; Beu, T.; Manghi, M.; Palmeri, J. The vapor-liquid interface potential of (multi)polar fluids and its influence on ion solvation J. Chem. Phys. 2013, 138, 154702
    • (2013) J. Chem. Phys. , vol.138 , pp. 154702
    • Horvath, L.1    Beu, T.2    Manghi, M.3    Palmeri, J.4
  • 73
    • 84874647898 scopus 로고    scopus 로고
    • The influence of water interfacial potentials on ion hydration in bulk water and near interfaces
    • Beck, T. The influence of water interfacial potentials on ion hydration in bulk water and near interfaces Chem. Phys. Lett. 2013, 561, 1-13
    • (2013) Chem. Phys. Lett. , vol.561 , pp. 1-13
    • Beck, T.1
  • 74
    • 0346850017 scopus 로고    scopus 로고
    • Ion solvation thermodynamics from simulation with a polarizable force field
    • Grossfield, A.; Ren, P.; Ponder, J. W. Ion solvation thermodynamics from simulation with a polarizable force field J. Am. Chem. Soc. 2003, 125, 15671-15682
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 15671-15682
    • Grossfield, A.1    Ren, P.2    Ponder, J.W.3
  • 76
    • 0000875502 scopus 로고    scopus 로고
    • A Poisson-Boltzmann study of charge insertion in an enzyme active site: The effect of dielectric relaxation
    • Simonson, T.; Archontis, G.; Karplus, M. A Poisson-Boltzmann study of charge insertion in an enzyme active site: the effect of dielectric relaxation J. Phys. Chem. B 1999, 103, 6142-6156
    • (1999) J. Phys. Chem. B , vol.103 , pp. 6142-6156
    • Simonson, T.1    Archontis, G.2    Karplus, M.3
  • 77
    • 84874167691 scopus 로고    scopus 로고
    • Charging free energy calculations using the Generalized Solvent Boundary Potential (GSBP) and periodic boundary condition: A comparative analysis using ion solvation and oxidation free energy in proteins
    • Lu, X.; Cui, Q. Charging free energy calculations using the Generalized Solvent Boundary Potential (GSBP) and periodic boundary condition: a comparative analysis using ion solvation and oxidation free energy in proteins J. Phys. Chem. B 2012, 117, 2005-2018
    • (2012) J. Phys. Chem. B , vol.117 , pp. 2005-2018
    • Lu, X.1    Cui, Q.2
  • 78
    • 0035249196 scopus 로고    scopus 로고
    • Generalized solvent boundary potential for computer simulations
    • Im, W.; Bernèche, S.; Roux, B. Generalized solvent boundary potential for computer simulations J. Chem. Phys. 2001, 114, 2924-2937
    • (2001) J. Chem. Phys. , vol.114 , pp. 2924-2937
    • Im, W.1    Bernèche, S.2    Roux, B.3
  • 79
    • 0001155967 scopus 로고    scopus 로고
    • Influence of the treatment of electrostatic interactions on the results of free energy calculations of dipolar systems
    • Brunsteiner, M.; Boresch, S. Influence of the treatment of electrostatic interactions on the results of free energy calculations of dipolar systems J. Chem. Phys. 2000, 112, 6953-6955
    • (2000) J. Chem. Phys. , vol.112 , pp. 6953-6955
    • Brunsteiner, M.1    Boresch, S.2
  • 81
  • 82
    • 84873135773 scopus 로고    scopus 로고
    • Explaining why Gleevec is a specific and potent inhibitor of Abl kinase
    • Lin, Y. L.; Meng, Y.; Jiang, W.; Roux, B. Explaining why Gleevec is a specific and potent inhibitor of Abl kinase Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 1664-1669
    • (2013) Proc. Natl. Acad. Sci. U.S.A. , vol.110 , pp. 1664-1669
    • Lin, Y.L.1    Meng, Y.2    Jiang, W.3    Roux, B.4
  • 83
    • 84885131303 scopus 로고    scopus 로고
    • Computational analysis of the binding specificity of Gleevec to Abl, c-Kit, Lck, and c-Src tyrosine kinases
    • Lin, Y. L.; Roux, B. Computational analysis of the binding specificity of Gleevec to Abl, c-Kit, Lck, and c-Src tyrosine kinases J. Am. Chem. Soc. 2013, 135, 14741-14753
    • (2013) J. Am. Chem. Soc. , vol.135 , pp. 14741-14753
    • Lin, Y.L.1    Roux, B.2
  • 84
    • 33749238080 scopus 로고    scopus 로고
    • Calculation of standard binding free energies: Aromatic molecules in the T4 lysozyme L99A mutant
    • Deng, Y.; Roux, B. Calculation of standard binding free energies: Aromatic molecules in the T4 lysozyme L99A mutant J. Chem. Theory Comput. 2006, 2, 1255-1273
    • (2006) J. Chem. Theory Comput. , vol.2 , pp. 1255-1273
    • Deng, Y.1    Roux, B.2
  • 85
    • 77950894291 scopus 로고    scopus 로고
    • A molecular mechanics model for imatinib and imatinib:kinase binding
    • Aleksandrov, A.; Simonson, T. A molecular mechanics model for imatinib and imatinib:kinase binding J. Comput. Chem. 2010, 31, 1550-1560
    • (2010) J. Comput. Chem. , vol.31 , pp. 1550-1560
    • Aleksandrov, A.1    Simonson, T.2
  • 86
    • 22244445788 scopus 로고    scopus 로고
    • Imaging alpha-hemolysin with molecular dynamics: Ionic conductance, osmotic permeability, and the electrostatic potential map
    • Aksimentiev, A.; Schulten, K. Imaging alpha-hemolysin with molecular dynamics: ionic conductance, osmotic permeability, and the electrostatic potential map Biophys. J. 2005, 88, 3745-3761
    • (2005) Biophys. J. , vol.88 , pp. 3745-3761
    • Aksimentiev, A.1    Schulten, K.2
  • 88
    • 0034091669 scopus 로고    scopus 로고
    • Backbone dipoles generate positive potentials in all proteins: Origins and implications of the effect
    • Gunner, M. R.; Saleh, M.; Cross, E.; ud-Doula, A.; Wise, M. Backbone dipoles generate positive potentials in all proteins: origins and implications of the effect Biophys. J. 2000, 78, 1126-1144
    • (2000) Biophys. J. , vol.78 , pp. 1126-1144
    • Gunner, M.R.1    Saleh, M.2    Cross, E.3    Ud-Doula, A.4    Wise, M.5
  • 89
    • 0032096837 scopus 로고    scopus 로고
    • Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
    • Im, W.; Beglov, D.; Roux, B. Continuum solvation model: computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation Comput. Phys. Commun. 1998, 111, 59-75
    • (1998) Comput. Phys. Commun. , vol.111 , pp. 59-75
    • Im, W.1    Beglov, D.2    Roux, B.3
  • 90
    • 84986512474 scopus 로고
    • CHARMM: A program for macromolecular energy, minimization, and molecular dynamics calculations
    • Brooks, B.; Bruccoleri, R.; Olafson, B.; States, D.; Swaminathan, S.; Karplus, M. CHARMM: a program for macromolecular energy, minimization, and molecular dynamics calculations J. Comput. Chem. 1983, 4, 187-217
    • (1983) J. Comput. Chem. , vol.4 , pp. 187-217
    • Brooks, B.1    Bruccoleri, R.2    Olafson, B.3    States, D.4    Swaminathan, S.5    Karplus, M.6
  • 91
    • 67650500988 scopus 로고    scopus 로고
    • CHARMM: The biomolecular simulation program
    • Brooks, B. CHARMM: The biomolecular simulation program J. Comput. Chem. 2009, 30, 1545-1614
    • (2009) J. Comput. Chem. , vol.30 , pp. 1545-1614
    • Brooks, B.1
  • 92
    • 84872165531 scopus 로고    scopus 로고
    • Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?
    • Gumbart, J. C.; Roux, B.; Chipot, C. Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy? J. Chem. Theory Comput. 2013, 9, 794-802
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 794-802
    • Gumbart, J.C.1    Roux, B.2    Chipot, C.3
  • 93
    • 0037076338 scopus 로고    scopus 로고
    • Gaussian fluctuations and linear response in an electron transfer protein
    • Simonson, T. Gaussian fluctuations and linear response in an electron transfer protein Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 6544-6549
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 6544-6549
    • Simonson, T.1
  • 96
    • 76649086691 scopus 로고    scopus 로고
    • Alchemical free energy simulations for biological complexes: Powerful but temperamental
    • Aleksandrov, A.; Thompson, D.; Simonson, T. Alchemical free energy simulations for biological complexes: powerful but temperamental J. Mol. Recognit. 2010, 23, 117-127
    • (2010) J. Mol. Recognit. , vol.23 , pp. 117-127
    • Aleksandrov, A.1    Thompson, D.2    Simonson, T.3
  • 97
    • 44049091290 scopus 로고    scopus 로고
    • Calculation of protein-ligand binding free energy by using a polarizable potential
    • Jiao, D.; Golubkov, P. A.; Darden, T. A.; Ren, P. Calculation of protein-ligand binding free energy by using a polarizable potential Proc. Natl. Acad. Sci. U.S.A. 2008, 105, 6290-6295
    • (2008) Proc. Natl. Acad. Sci. U.S.A. , vol.105 , pp. 6290-6295
    • Jiao, D.1    Golubkov, P.A.2    Darden, T.A.3    Ren, P.4
  • 98
    • 34547809547 scopus 로고
    • A unified formulation of the constant temperature molecular dynamics method
    • Nose, S. A unified formulation of the constant temperature molecular dynamics method J. Chem. Phys. 1984, 81, 511-519
    • (1984) J. Chem. Phys. , vol.81 , pp. 511-519
    • Nose, S.1
  • 99
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • Hoover, W. G. Canonical dynamics: equilibrium phase-space distributions Phys. Rev. A 1985, 31, 1695-1697
    • (1985) Phys. Rev. A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 100
  • 101
    • 0032558365 scopus 로고    scopus 로고
    • Rationalization of the dielectric properties of common three-site water models in terms of their force field parameters
    • Höchtl, P.; Boresch, S.; Bitomsky, W.; Steinhauser, O. Rationalization of the dielectric properties of common three-site water models in terms of their force field parameters J. Chem. Phys. 1998, 109, 4927-4937
    • (1998) J. Chem. Phys. , vol.109 , pp. 4927-4937
    • Höchtl, P.1    Boresch, S.2    Bitomsky, W.3    Steinhauser, O.4
  • 102
    • 0041784950 scopus 로고    scopus 로고
    • An all-atom empirical potential for molecular modelling and dynamics study of proteins
    • Mackerell, A. D. An all-atom empirical potential for molecular modelling and dynamics study of proteins J. Phys. Chem. B 1998, 102, 3586-3616
    • (1998) J. Phys. Chem. B , vol.102 , pp. 3586-3616
    • MacKerell, A.D.1
  • 103
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free energy calculations on biomolecules. I. The method
    • Kumar, S.; Bouzida, D.; Swendsen, R.; Kollman, P.; Rosenberg, J. The weighted histogram analysis method for free energy calculations on biomolecules. I. The method J. Comput. Chem. 1992, 13, 1011-1021
    • (1992) J. Comput. Chem. , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.3    Kollman, P.4    Rosenberg, J.5
  • 104
    • 0035277126 scopus 로고    scopus 로고
    • Extension to the Weighted Histogram Analysis Method: Combining Umbrella Sampling with Free Energy Calculations
    • Souaille, M.; Roux, B. Extension to the Weighted Histogram Analysis Method: Combining Umbrella Sampling with Free Energy Calculations Comput. Phys. Commun. 2001, 135, 40-57
    • (2001) Comput. Phys. Commun. , vol.135 , pp. 40-57
    • Souaille, M.1    Roux, B.2
  • 106
    • 0003871536 scopus 로고    scopus 로고
    • Becker, O. Mackerell, A. Jr. Roux, B. Watanabe, M. Marcel Dekker: New York, Chapter 9
    • Simonson, T. In Computational Biochemistry & Biophysics; Becker, O.; Mackerell, A., Jr.; Roux, B.; Watanabe, M., Eds.; Marcel Dekker: New York, 2001; Chapter 9.
    • (2001) Computational Biochemistry & Biophysics
    • Simonson, T.1
  • 107
    • 79953020995 scopus 로고    scopus 로고
    • Efficiency of Alchemical Free Energy Simulations II: Improvements for Thermodynamic Integration
    • Bruckner, S.; Boresch, S. Efficiency of Alchemical Free Energy Simulations II: Improvements for Thermodynamic Integration J. Comput. Chem. 2011, 32, 1320-1333
    • (2011) J. Comput. Chem. , vol.32 , pp. 1320-1333
    • Bruckner, S.1    Boresch, S.2
  • 108
    • 0031167555 scopus 로고    scopus 로고
    • Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations
    • Nina, M.; Beglov, D.; Roux, B. Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations J. Phys. Chem. B 1997, 101, 5239-5248
    • (1997) J. Phys. Chem. B , vol.101 , pp. 5239
    • Nina, M.1    Beglov, D.2    Roux, B.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.