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Volumn 85, Issue , 2011, Pages 281-322

Advances in implicit models of water solvent to compute conformational free energy and molecular dynamics of proteins at constant PH

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EID: 80052811746     PISSN: 18761623     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-386485-7.00008-9     Document Type: Chapter
Times cited : (32)

References (144)
  • 1
    • 78651330129 scopus 로고    scopus 로고
    • Reducing the secondary structure bias in the generalized Born model via R6 effective Radii
    • B. Aguilar, R. Shadrach, and A.V. Onufriev Reducing the secondary structure bias in the generalized Born model via R6 effective Radii J. Chem. Theory Comput. 6 2010 3613 3630
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 3613-3630
    • Aguilar, B.1    Shadrach, R.2    Onufriev, A.V.3
  • 2
    • 0030134110 scopus 로고    scopus 로고
    • On the validity of electrostatic linear response in polar solvents
    • J. Aqvist, and T. Hansson On the validity of electrostatic linear response in polar solvent J. Phys. Chem. 100 1996 9512 9521 (Pubitemid 126834549)
    • (1996) Journal of Physical Chemistry , vol.100 , Issue.22 , pp. 9512-9521
    • Aqvist, J.1    Hansson, T.2
  • 3
    • 33645511814 scopus 로고    scopus 로고
    • A new force field ECEPP05 for peptides, proteins and organic molecules
    • E.Y. Arnautova, A. Jagielska, and H.A. Scheraga A new force field ECEPP05 for peptides, proteins and organic molecules J Phys. Chem. B 110 2006 5025 5044
    • (2006) J Phys. Chem. B , vol.110 , pp. 5025-5044
    • Arnautova, E.Y.1    Jagielska, A.2    Scheraga, H.A.3
  • 4
    • 70349307198 scopus 로고    scopus 로고
    • Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation
    • E.Y. Arnautova, Y.N. Vorobjev, J.A. Vila, and H.A. Scheraga Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation Proteins 77 2009 38 51
    • (2009) Proteins , vol.77 , pp. 38-51
    • Arnautova, E.Y.1    Vorobjev, Y.N.2    Vila, J.A.3    Scheraga, H.A.4
  • 5
    • 0030970305 scopus 로고    scopus 로고
    • Simulation of protein conformational freedom as a function of pH: Constant-pH molecular dynamics using implicit titration
    • DOI 10.1002/(SICI)1097-0134(199704)27:4<523::AID-PROT6>3.0.CO;2-B
    • M. Baptista, P.J. Martel, and S.B. Petersen Simulation of protein conformation freedom as a function of pH: constant-pH molecular dynamics using implicit titration Proteins 27 1997 523 544 (Pubitemid 27212352)
    • (1997) Proteins: Structure, Function and Genetics , vol.27 , Issue.4 , pp. 523-544
    • Baptista, A.M.1    Martel, P.J.2    Petersen, S.B.3
  • 6
    • 0033001692 scopus 로고    scopus 로고
    • 3 using continuum electrostatics
    • M. Baptista, P.J. Martel, and C.M. Soares Simulation of electron-proton coupling with a Monte Carlo method: application to cytochrome c(3) using continuum electrostatics Biophys. J. 76 1999 2978 2998 (Pubitemid 29269447)
    • (1999) Biophysical Journal , vol.76 , Issue.6 , pp. 2978-2998
    • Baptista, A.M.1    Martel, P.J.2    Soares, C.M.3
  • 7
    • 0033654297 scopus 로고    scopus 로고
    • Generalized born models of macromolecular solvation effects
    • D. Bashford, and A.D. Case Generalized born models of macromolecular solvation effects Annu. Rev. Phys. Chem. 51 2000 129 152
    • (2000) Annu. Rev. Phys. Chem. , vol.51 , pp. 129-152
    • Bashford, D.1    Case, A.D.2
  • 8
    • 0000105585 scopus 로고    scopus 로고
    • Solvation of complex molecules in a polar liquid: An integral equation theory
    • D. Beglov, and B. Roux An integral equation to describe the solvation of polar molecules in liquid water J. Chem. Phys. 104 1996 8678 8689 (Pubitemid 126733028)
    • (1996) Journal of Chemical Physics , vol.104 , Issue.21 , pp. 8678-8689
    • Beglov, D.1    Roux, B.2
  • 9
    • 0031234042 scopus 로고    scopus 로고
    • An integral equation to describe the solvation of polar molecules in liquid water
    • D. Beglov, and B. Roux Solvation of complex molecules in a polar liquid: an integral equation theory J. Phys. Chem. 101 1997 7821 7826 (Pubitemid 127591348)
    • (1997) Journal of Physical Chemistry B , vol.101 , Issue.39 , pp. 7821-7826
    • Beglov, D.1    Roux, B.2
  • 10
    • 0025261918 scopus 로고
    • Solvent effects on protein association and protein folding
    • A. Ben-Naim Solvent effects on protein association and protein folding Biopolymers 29 1990 567 596 (Pubitemid 20085492)
    • (1990) Biopolymers , vol.29 , Issue.3 , pp. 567-596
    • Ben-Naim, A.1
  • 11
    • 33645903407 scopus 로고
    • Solvation thermodynamics of nonionic solutes
    • A. Ben-Naim, and Y. Marcus Solvation thermodynamics of nonionic solutes J. Chem. Phys. 81 1984 2016 2027
    • (1984) J. Chem. Phys. , vol.81 , pp. 2016-2027
    • Ben-Naim, A.1    Marcus, Y.2
  • 12
    • 84986452939 scopus 로고
    • The fast multipole boundary element method for molecular electrostatics: An optimal approach for large systems
    • R. Bharadwaj, A. Windemuth, S. Sridharan, B. Honig, and A. Nicholls The fast multipole boundary element method for molecular electrostatics: an optimal approach for large systems J. Comput. Chem. 16 1995 898 913
    • (1995) J. Comput. Chem. , vol.16 , pp. 898-913
    • Bharadwaj, R.1    Windemuth, A.2    Sridharan, S.3    Honig, B.4    Nicholls, A.5
  • 13
    • 0000123071 scopus 로고    scopus 로고
    • Removal of pressure and free energy artifacts in charged periodic systems via net charge corrections to the Ewald potential
    • S. Bogusz, T.E. Cheatham III, and R.R. Brooks Removal of pressure and free energy artifacts in charged periodic system via net charge corrections to the Ewald potential J. Chem. Phys. 108 1998 7070 7084 (Pubitemid 128594474)
    • (1998) Journal of Chemical Physics , vol.108 , Issue.17 , pp. 7070-7084
    • Bogusz, S.1    Cheatham III, T.E.2    Brooks, B.R.3
  • 14
    • 24944493938 scopus 로고    scopus 로고
    • Biochemistry: Toward high-resolution de novo structure prediction for small proteins
    • DOI 10.1126/science.1113801
    • P. Bradley, K.M. Misura, and D. Baker Towards high-resolution de nove structure prediction for small proteins Science 309 2005 1868 1871 (Pubitemid 41325099)
    • (2005) Science , vol.309 , Issue.5742 , pp. 1868-1871
    • Bradley, P.1    Misura, K.M.S.2    Baker, D.3
  • 15
    • 0001031179 scopus 로고
    • Proteins a theoretical perspectives of dynamics, structure and thermodynamics
    • I. Prigogine, S.A. Rice, John Wiley and Sons New York
    • C.L. Brooks III, M. Karplus, and B.M. Pettitt Proteins a theoretical perspectives of dynamics, structure and thermodynamics I. Prigogine, S.A. Rice, Advance in Chemical Physics, vol. LXXI 1988 John Wiley and Sons New York
    • (1988) Advance in Chemical Physics, Vol. LXXI
    • Brooks Iii, C.L.1    Karplus, M.2    Pettitt, B.M.3
  • 16
    • 77956576423 scopus 로고    scopus 로고
    • Effective approximation of molecular volume using atom-centered dielectric functions in generalized Born models
    • J. Chen Effective approximation of molecular volume using atom-centered dielectric functions in generalized Born models J. Chem. Theory Comput. 6 2010 2790 2803
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 2790-2803
    • Chen, J.1
  • 17
    • 33847676374 scopus 로고    scopus 로고
    • Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions
    • DOI 10.1021/ja068383+
    • J. Chen, and C. Brooks Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions J. Am. Chem. Soc. 129 2007 2444 2445 (Pubitemid 46364044)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.9 , pp. 2444-2445
    • Chen, J.1    Brooks III, C.L.2
  • 18
    • 42049087036 scopus 로고    scopus 로고
    • Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions
    • J. Chen, and C. Brooks Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions Phys. Chem. Chem. Phys. 10 2008 471 481
    • (2008) Phys. Chem. Chem. Phys. , vol.10 , pp. 471-481
    • Chen, J.1    Brooks, C.2
  • 19
    • 0016352763 scopus 로고
    • Hydrophobic bonding and accessible area in proteins
    • C.H. Chothia Hydrophobic bonding and accessible area in proteins Nature 248 1974 338 339
    • (1974) Nature , vol.248 , pp. 338-339
    • Chothia, C.H.1
  • 20
    • 0000538815 scopus 로고
    • Analytical molecular surface calculation
    • M.L. Connolly Analytical molecular surface calculation J. Appl. Crystallogr. 16 1983 548 558
    • (1983) J. Appl. Crystallogr. , vol.16 , pp. 548-558
    • Connolly, M.L.1
  • 21
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • M.L. Connolly Solvent-accessible surfaces of proteins and nucleic acids Science 221 1983 709 713
    • (1983) Science , vol.221 , pp. 709-713
    • Connolly, M.L.1
  • 22
    • 33845377446 scopus 로고
    • Computation of molecular volume
    • M.L. Connolly Computation of molecular volume J. Am. Chem. Soc. 107 1985 1118 1124 http://www.netsci.org/Science/Compchem/feature14e.html
    • (1985) J. Am. Chem. Soc. , vol.107 , pp. 1118-1124
    • Connolly, M.L.1
  • 24
    • 0030392612 scopus 로고    scopus 로고
    • Multigrid methods in science and engineering
    • C.C. Douglas Multigrid methods in science and engineering Comput. Sci. Eng. 3 1996 55 68
    • (1996) Comput. Sci. Eng. , vol.3 , pp. 55-68
    • Douglas, C.C.1
  • 25
    • 0037079585 scopus 로고    scopus 로고
    • Identifying native-like protein structures using physics-based potentials
    • DOI 10.1002/jcc.10018
    • B.N. Dominy, and C.L. Brooks Identifying native-like protein structures using physics-based potentials J. Comput. Chem. 23 2002 147 160 (Pubitemid 34063139)
    • (2002) Journal of Computational Chemistry , vol.23 , Issue.1 , pp. 147-160
    • Dominy, B.N.1    Brooks III, C.L.2
  • 26
    • 0346971105 scopus 로고    scopus 로고
    • Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
    • M. Feig, A. Onufriev, M. Lee, and W. Im Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures J. Comput. Chem. 25 2004 265 284
    • (2004) J. Comput. Chem. , vol.25 , pp. 265-284
    • Feig, M.1    Onufriev, A.2    Lee, M.3    Im, W.4
  • 27
    • 0036681394 scopus 로고    scopus 로고
    • Distinguishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the surface generalized born solvent model
    • DOI 10.1002/prot.10171
    • A.K. Felts, E. Gallicchio, A. Wallqvist, and R.M. Levy Distinquishing native conformations of proteins from decoys with an effective free energy estimator based on the OPLS all-atom force field and the surface generalized Born solvent model Proteins 48 2002 404 422 (Pubitemid 34743427)
    • (2002) Proteins: Structure, Function and Genetics , vol.48 , Issue.2 , pp. 404-422
    • Felts, A.K.1    Gallicchio, E.2    Wallqvist, A.3    Levy, R.M.4
  • 28
    • 0037624841 scopus 로고    scopus 로고
    • 3D-SHORTGUN: A novel, cooperative, fold-recognition meta-predictor
    • D. Fisher 3D-SHORTGUN: a novel, cooperative, fold-recognition meta-predictor Proteins 51 2003 434 444
    • (2003) Proteins , vol.51 , pp. 434-444
    • Fisher, D.1
  • 29
    • 0035976385 scopus 로고    scopus 로고
    • Molecular mechanics and dynamics of biomolecules using a solvent continuum model
    • DOI 10.1002/jcc.1134
    • F. Fogolary, G. Esposito, P. Viglino, and H. Molinari Molecular mechanics and dynamics of biomolecules using a solvent continuum model J. Comput. Chem. 22 2001 1830 1842 (Pubitemid 33044782)
    • (2001) Journal of Computational Chemistry , vol.22 , Issue.15 , pp. 1830-1842
    • Fogolari, F.1    Esposito, G.2    Viglino, P.3    Molinari, H.4
  • 30
    • 1442330396 scopus 로고    scopus 로고
    • AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling
    • E. Gallicchio, and R. Levy AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling J. Comput. Chem. 25 2004 479 499
    • (2004) J. Comput. Chem. , vol.25 , pp. 479-499
    • Gallicchio, E.1    Levy, R.2
  • 31
    • 0034227795 scopus 로고    scopus 로고
    • Enthalpy-entropy and cavity decomposition of alkane hydration free energies: Numerical results and implications for theories of hydrophobic solvation
    • E. Gallicchio, M.M. Kubo, and R.M. Levy Enthalpy-entropy and cavity decomposition of alkane hydration free energies: Numerical results and implications for theories of hydrophobic solvation J. Phys. Chem. B 104 2000 6271 6285
    • (2000) J. Phys. Chem. B , vol.104 , pp. 6271-6285
    • Gallicchio, E.1    Kubo, M.M.2    Levy, R.M.3
  • 32
    • 0037089017 scopus 로고    scopus 로고
    • The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators
    • DOI 10.1002/jcc.10045
    • E. Gallicchio, L.Y. Zhang, and R.M. Levy The SGB/NP hydration free energy model based on the surface genaralized Born solvent reaction field and novel nonpolar hydration free energy estimators J. Comput. Chem. 23 2002 517 529 (Pubitemid 34409032)
    • (2002) Journal of Computational Chemistry , vol.23 , Issue.5 , pp. 517-529
    • Gallicchio, E.1    Zhang, L.Y.2    Levy, R.M.3
  • 34
    • 0011423024 scopus 로고
    • Electrostatic field in inhomogeneous dielectric media. Indirect boundary element method
    • N.S. Goel, F. Gang, and Z. Ko Electrostatic field in inhomogeneous dielectric media. Indirect boundary element method J. Comput. Phys. 118 1995 172 179
    • (1995) J. Comput. Phys. , vol.118 , pp. 172-179
    • Goel, N.S.1    Gang, F.2    Ko, Z.3
  • 35
    • 0035971738 scopus 로고    scopus 로고
    • A smooth permittivity function for Poisson-Boltzmann solvation methods
    • A. Grant, B. Pickup, and A. Nicholls A smooth permittivity function for Poisson-Boltzmann solvation methods J. Comput. Chem. 22 2001 608 640
    • (2001) J. Comput. Chem. , vol.22 , pp. 608-640
    • Grant, A.1    Pickup, B.2    Nicholls, A.3
  • 36
    • 0141453063 scopus 로고    scopus 로고
    • Deficiency of the Coulomb-field approximation in the Generalized Born model: An improvedformula for Born radii evaluation
    • T. Grycuk Deficiency of the Coulomb-field approximation in the Generalized Born model: An improvedformula for Born radii evaluation J. Chem. Phys. 119 2003 4817 4826
    • (2003) J. Chem. Phys. , vol.119 , pp. 4817-4826
    • Grycuk, T.1
  • 37
    • 33748390341 scopus 로고    scopus 로고
    • Parametrized models of aqueous free energies of solvaton based pairwise solute descreening of solute atomic charges from a dielectric medium
    • G.D. Hawkins, C.J. Cramer, and D.G. Truhlar Parametrized models of aqueous free energies of solvaton based pairwise solute descreening of solute atomic charges from a dielectric medium J. Phys. Chem. 100 1996 19824 19836
    • (1996) J. Phys. Chem. , vol.100 , pp. 19824-19836
    • Hawkins, G.D.1    Cramer, C.J.2    Truhlar, D.G.3
  • 38
    • 0011930746 scopus 로고
    • Theory of hydrophobic bonding. II. the correlation of hydrocarbon solubility in water with solvent cavity surface area
    • R.B. Hermann Theory of hydrophobic bonding. II. The correlation of hydrocarbon solubility in water with solvent cavity surface area J. Phys. Chem. 76 1972 2754 2759
    • (1972) J. Phys. Chem. , vol.76 , pp. 2754-2759
    • Hermann, R.B.1
  • 40
    • 84986437211 scopus 로고
    • Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods
    • M. Holst, and F. Saied Numerical solution of the nonlinear Poisson-Boltzmann equation: developing more robust and efficient methods J. Comput. Chem. 16 1995 337 364
    • (1995) J. Comput. Chem. , vol.16 , pp. 337-364
    • Holst, M.1    Saied, F.2
  • 41
    • 0028222670 scopus 로고
    • Treatment of electrostatic effects in proteins: Multigrid-based Newton iterative method for solution of the full nonlinear Poisson-Boltzmann equation
    • M. Holst, R.E. Kozack, F. Saied, and S. Subramaniam Treatment of electrostatic effects in proteins: multigrid-based Newton iterative method for solution of the full nonlinear Poisson-Boltzmann equation Proteins 18 1994 231 245 (Pubitemid 24096734)
    • (1994) Proteins: Structure, Function and Genetics , vol.18 , Issue.3 , pp. 231-245
    • Holst, M.1    Kozack, R.E.2    Saied, F.3    Subramaniam, S.4
  • 42
    • 0000486193 scopus 로고    scopus 로고
    • Adaptive multilevel finite element solution of the Poisson-Boltzmann equation. I. Algorithms and examples
    • M. Holst, N. Baker, and M. Wang Adaptive multilevel finite element solution of the Poisson-Boltzmann equation. I. Algorithms and examples J. Comput. Chem. 21 2000 1319 1342
    • (2000) J. Comput. Chem. , vol.21 , pp. 1319-1342
    • Holst, M.1    Baker, N.2    Wang, M.3
  • 43
    • 33751385054 scopus 로고
    • Macroscopic models of aqueous solutions: Biological and chemical applications
    • B. Honig, K. Sharp, and A.S. Yang Macroscopic models of aqueous solutions: biological and chemical applications J. Phys. Chem. 97 1993 1101 1109
    • (1993) J. Phys. Chem. , vol.97 , pp. 1101-1109
    • Honig, B.1    Sharp, K.2    Yang, A.S.3
  • 44
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • W.G. Hoover Canonical dynamics: equilibrium phase-space distributions Phys. Rev. A 31 1985 1695 1697
    • (1985) Phys. Rev. A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 45
    • 77955584390 scopus 로고    scopus 로고
    • An implicit solvent model for SCC-DFTB with charge-dependent radii
    • G. Hou, X. Zhu, and Q. Cui An implicit solvent model for SCC-DFTB with charge-dependent radii J. Chem. Theory Comput. 6 2010 2303 2314
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 2303-2314
    • Hou, G.1    Zhu, X.2    Cui, Q.3
  • 48
    • 0037627173 scopus 로고    scopus 로고
    • Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: A continuum electrostatics study
    • DOI 10.1016/S0301-4622(99)00007-1, PII S0301462299000071
    • P.H. Hnnenberg, and J.A. McCammon Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatic study Biophys. Chem. 78 1999 69 88 (Pubitemid 29206658)
    • (1999) Biophysical Chemistry , vol.78 , Issue.1-2 , pp. 69-88
    • Hunenberger, P.H.1    McCammon, J.A.2
  • 49
    • 0141956090 scopus 로고    scopus 로고
    • Generalized Born model with a simple smoothing function
    • W. Im, M.S. Lee, and C.L. Brooks III Generalized Born model with a simple smoothing function J. Comput. Chem. 24 2003 1691 1702
    • (2003) J. Comput. Chem. , vol.24 , pp. 1691-1702
    • Im, W.1    Lee, M.S.2    Brooks Iii, C.L.3
  • 51
    • 0028180523 scopus 로고
    • Application of scaled particle theory to model the hydrophobic effect: Implications for molecular association and protein stability
    • R.M. Jackson, and J.E. Sternberg Application of scaled particle theory to model the hydrophobic effect: implications for molecular association and protein stability Protein Eng. 7 1994 371 383 (Pubitemid 24063136)
    • (1994) Protein Engineering , vol.7 , Issue.3 , pp. 371-383
    • Jackson, R.M.1    Sternberg, M.J.E.2
  • 52
    • 0029019869 scopus 로고
    • A continuum model for protein-protein interactions: Applications to the docking problem
    • R.M. Jackson, and J.E. Sternberg A continuum model for protein-protein interactions: applications to the docking problem J. Mol. Biol. 250 1995 258 275
    • (1995) J. Mol. Biol. , vol.250 , pp. 258-275
    • Jackson, R.M.1    Sternberg, J.E.2
  • 53
    • 33749637456 scopus 로고
    • Free energy calculations of ion hydration: An analysis of the Born model in terms of microscopic simulations
    • B. Jayaram, R. Fine, K. Sharp, and B. Honig Free energy calculations of ion hydration: an analysis of the Born model in terms of microscopic simulations J. Phys. Chem. 93 1989 4320 4327
    • (1989) J. Phys. Chem. , vol.93 , pp. 4320-4327
    • Jayaram, B.1    Fine, R.2    Sharp, K.3    Honig, B.4
  • 54
    • 84906391926 scopus 로고
    • Temperature and size dependence for Monte Carlo simulations of TIP4P water
    • W.L. Jorgensen, and J.D. Madura Temperature and size dependence for Monte Carlo simulations of TIP4P water Mol. Phys. 56 1985 1381 1392
    • (1985) Mol. Phys. , vol.56 , pp. 1381-1392
    • Jorgensen, W.L.1    Madura, J.D.2
  • 55
    • 7044260905 scopus 로고    scopus 로고
    • Free energies of hydration from a generalized born model and an all-atom force field
    • W. Jorgensen, and J. Tirado-Rives Free energies of hydration from a generalized born model and an all-atom force field J. Phys. Chem. B. 108 2004 16264 16270
    • (2004) J. Phys. Chem. B. , vol.108 , pp. 16264-16270
    • Jorgensen, W.1    Tirado-Rives, J.2
  • 56
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • DOI 10.1021/ja9621760, PII S0002786396021762
    • W.L. Jorgensen, D.S. Maxwell, and J.J. Tirado-Rives Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids J. Am. Chem. Soc. 118 1996 11225 11236 (Pubitemid 26399746)
    • (1996) Journal of the American Chemical Society , vol.118 , Issue.45 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 58
    • 0028818570 scopus 로고
    • Comparison of atomic solvation parametric sets: Applicability and limitations in protein folding and binding
    • A.H. Juffer, S.J. Eisenbaher, S.J. Hubbard, D. Walter, and P. Argos Comparison of atomic solvation parametric sets: applicability and limitations in protein folding and binding Protein Sci. 4 1995 2499 2509
    • (1995) Protein Sci. , vol.4 , pp. 2499-2509
    • Juffer, A.H.1    Eisenbaher, S.J.2    Hubbard, S.J.3    Walter, D.4    Argos, P.5
  • 59
    • 35948937280 scopus 로고    scopus 로고
    • Systematic study of the boundary composition in poisson boltzmann calculations
    • DOI 10.1002/jcc.20698
    • P. Kar, Y. Wei, U.E. Hansmann, and S. Höfinger Systematic study of the boundary composition in Poisson Boltzmann calculations J. Comput. Chem. 28 2007 2538 2544 (Pubitemid 350074128)
    • (2007) Journal of Computational Chemistry , vol.28 , Issue.16 , pp. 2538-2544
    • Kar, P.1    Wei, Y.2    Hansmann, U.H.E.3    Hofinger, S.4
  • 60
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • DOI 10.1038/nsb0902-646
    • M. Karplus, and A. McCammon Molecular dynamics simulations of biomolecules Nat. Struct. Biol. 9 2002 646 652 (Pubitemid 34977295)
    • (2002) Nature Structural Biology , vol.9 , Issue.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 61
    • 23244440384 scopus 로고    scopus 로고
    • Constant pH molecular dynamics with proton tautomerism
    • DOI 10.1529/biophysj.105.061341
    • J. Khandogin, and C.L. Brooks III Constant pH Molecular Dynamics with Proton Tautomerism Biophys. J. 89 2005 141 157 (Pubitemid 41098271)
    • (2005) Biophysical Journal , vol.89 , Issue.1 , pp. 141-157
    • Khandogin, J.1    Brooks III, C.L.2
  • 62
    • 33747131772 scopus 로고    scopus 로고
    • Toward the accurate first-principles prediction of ionization equilibria in proteins
    • J. Khandogin, and C.L. Brooks III Toward the accurate first-principles prediction of ionization equilibria in proteins Biochemistry 2006 45 2006 9363
    • (2006) Biochemistry , vol.2006 , Issue.45 , pp. 9363
    • Khandogin, J.1    Brooks Iii, C.L.2
  • 64
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • P. Kollman Free energy calculations: applications to chemical and biochemical phenomena Chem. Rev. 93 1993 2395 2417
    • (1993) Chem. Rev. , vol.93 , pp. 2395-2417
    • Kollman, P.1
  • 66
    • 0001692244 scopus 로고    scopus 로고
    • λ-dynamics: A new approach to free energy calculations
    • X. Kong, and C.L. Brooks III λ-dynamics: a new approach to free energy calculations J. Chem. Phys. 105 1996 2414 2423 (Pubitemid 126612871)
    • (1996) Journal of Chemical Physics , vol.105 , Issue.6 , pp. 2414-2423
    • Kong, X.1    Brooks III, C.L.2
  • 68
    • 0000501772 scopus 로고
    • Improvements of the continuum model. Application to the calculation of the vaporization thermodynamic quantities of non-associated liquids
    • J. Langlet, P. Claverie, J. Caillet, and A. Pullman Improvements of the continuum model. Application to the calculation of the vaporization thermodynamic quantities of non-associated liquids J. Phys. Chem. 92 1988 1617 1631
    • (1988) J. Phys. Chem. , vol.92 , pp. 1617-1631
    • Langlet, J.1    Claverie, P.2    Caillet, J.3    Pullman, A.4
  • 69
    • 0033531959 scopus 로고    scopus 로고
    • Discrimination of the native from misfolded protein models with an energy function including implicit solvation
    • DOI 10.1006/jmbi.1999.2685
    • T. Lazaridis, and M. Karplus Discrimination of the native from misfolded protein models with an energy function including implicit solvation J. Mol. Biol. 288 1998 477 487 (Pubitemid 29221815)
    • (1999) Journal of Molecular Biology , vol.288 , Issue.3 , pp. 477-487
    • Lazaridis, T.1    Karplus, M.2
  • 70
    • 0034212858 scopus 로고    scopus 로고
    • Use of MM-PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece
    • M.R. Lee, Y. Duan, and P.A. Kollman Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece Proteins 39 2000 309 316 (Pubitemid 30414169)
    • (2000) Proteins: Structure, Function and Genetics , vol.39 , Issue.4 , pp. 309-316
    • Lee, M.R.1    Duan, Y.2    Kollman, P.A.3
  • 71
    • 0038792211 scopus 로고    scopus 로고
    • New analytic approximation to the standart molecular volume definition and its application to generalizaed Born calculations
    • M.S. Lee, M. Feig, F.R. Salsbury Jr., and C.L. Brooks III New analytic approximation to the standart molecular volume definition and its application to generalizaed Born calculations J. Comput. Chem. 24 2003 1348 1356
    • (2003) J. Comput. Chem. , vol.24 , pp. 1348-1356
    • Lee, M.S.1    Feig, M.2    Salsbury Jr., F.R.3    Brooks Iii, C.L.4
  • 73
    • 77955574013 scopus 로고    scopus 로고
    • Protein Folding Simulations Combining Self-Guided Langevin Dynamics and Temperature-Based Replica Exchange
    • M.S. Lee, and M.A. Olson Protein Folding Simulations Combining Self-Guided Langevin Dynamics and Temperature-Based Replica Exchange J. Chem. Theory Comput. 2010 2010 2477 2487
    • (2010) J. Chem. Theory Comput. , vol.2010 , pp. 2477-2487
    • Lee, M.S.1    Olson, M.A.2
  • 74
    • 5544264558 scopus 로고
    • Gaussian fluctuation formula for electrostatic free energy changes in solution
    • R.M. Levy, M. Belhadj, and D.B. Kitchen Gaussian fluctuation formula for electrostatic free energy changes in solution J. Chem. Phys. 95 1991 3627 3633
    • (1991) J. Chem. Phys. , vol.95 , pp. 3627-3633
    • Levy, R.M.1    Belhadj, M.2    Kitchen, D.B.3
  • 75
    • 0042208326 scopus 로고    scopus 로고
    • On the nonpolar hydration free energy of proteins: Surface area and continuum solvent models for the solute-solvent interaction energy
    • DOI 10.1021/ja029833a
    • R.M. Levy, L.Y. Zhanh, E. Gallicchio, and A. Felts On the non polar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy J. Am. Chem. Soc. 25 2003 9523 9530 (Pubitemid 36936069)
    • (2003) Journal of the American Chemical Society , vol.125 , Issue.31 , pp. 9523-9530
    • Levy, R.M.1    Zhang, L.Y.2    Gallicchio, E.3    Felts, A.K.4
  • 77
    • 34548772137 scopus 로고    scopus 로고
    • Improved boundary element method for Poisson-Boltzman electrostatic potential and force calculatins
    • B. Lu, and A. McCammon Improved boundary element method for Poisson-Boltzman electrostatic potential and force calculatins J. Chem. Theory Comput. 3 2007 1134 1142
    • (2007) J. Chem. Theory Comput. , vol.3 , pp. 1134-1142
    • Lu, B.1    McCammon, A.2
  • 79
    • 33644745556 scopus 로고    scopus 로고
    • Constant-pH molecular dynamics with ionic strength effects: Protonation-conformation coupling in decalysine
    • DOI 10.1021/jp056456q
    • M. Machuqueiro, and A.M. Baptista Constant-pH molecular dynamics with ionic strength effects: protonation-conformation coupling in decalysine J. Phys. Chem. 110 2006 2927 2933 (Pubitemid 43342889)
    • (2006) Journal of Physical Chemistry B , vol.110 , Issue.6 , pp. 2927-2933
    • Machuqueiro, M.1    Baptista, A.M.2
  • 81
    • 33847318371 scopus 로고    scopus 로고
    • Molecular dynamics simulations of RNA: An in silico single molecule approach
    • S.C. McDowell, N. Špackova, J. Šponer, and N.G. Walter Molecular dynamics simulations of RNA: an in silico single molecule approach Biopolymers 85 2007 169 184
    • (2007) Biopolymers , vol.85 , pp. 169-184
    • McDowell, S.C.1    Špackova, N.2    Šponer, J.3    Walter, N.G.4
  • 82
    • 0000339157 scopus 로고
    • A fast Poisson solver for complex geometries
    • A. McKenney, and L. Greengard A fast Poisson solver for complex geometries J. Comput. Phys. 118 1995 348 355
    • (1995) J. Comput. Phys. , vol.118 , pp. 348-355
    • McKenney, A.1    Greengard, L.2
  • 83
    • 9244223045 scopus 로고    scopus 로고
    • Constant pH molecular dynamics in generalized Born implicit solvent
    • J. Mongan, D.A. Case, and J.A. McCammon Constant pH molecular dynamics in generalized Born implicit solvent J. Comput. Chem. 25 2004 2038 2064
    • (2004) J. Comput. Chem. , vol.25 , pp. 2038-2064
    • Mongan, J.1    Case, D.A.2    McCammon, J.A.3
  • 85
    • 36148936033 scopus 로고    scopus 로고
    • Analisys of integral expressions for effective Born radii
    • J. Mongan, W.A. Svrcek-Seiler, and A. Onufriev Analisys of integral expressions for effective Born radii J. Chem. Phys. 127 2007 18510 18521
    • (2007) J. Chem. Phys. , vol.127 , pp. 18510-18521
    • Mongan, J.1    Svrcek-Seiler, W.A.2    Onufriev, A.3
  • 86
    • 0031167555 scopus 로고    scopus 로고
    • Atomic radii for continuum electrostatics calculations based on molecular dynamics free energy simulations
    • M. Nina, D. Beglov, and B. Roux Atomic radii for continuum electrostatic calculations based on molecular dynamics free energy simulations J. Phys. Chem. 101 1997 5239 5248 (Pubitemid 127609289)
    • (1997) Journal of Physical Chemistry B , vol.101 , Issue.26 , pp. 5239-5248
    • Nina, M.1    Beglov, D.2    Roux, B.3
  • 87
    • 0032968444 scopus 로고    scopus 로고
    • Optimized atomic radii for protein continuum electrostatics solvation forces
    • DOI 10.1016/S0301-4622(98)00236-1, PII S0301462298002361
    • M. Nina, W. Im, and B. Roux Optimized atomic radii for protein contiuum electrostatic solvation forces Biophys. Chem. 78 1999 89 96 (Pubitemid 29206659)
    • (1999) Biophysical Chemistry , vol.78 , Issue.1-2 , pp. 89-96
    • Nina, M.1    Im, W.2    Roux, B.3
  • 88
    • 34547809547 scopus 로고
    • A unified formulation of the constant temperature molecular dynamics methods
    • S.J. Nose A unified formulation of the constant temperature molecular dynamics methods J. Chem. Phys. 81 1984 511 519
    • (1984) J. Chem. Phys. , vol.81 , pp. 511-519
    • Nose, S.J.1
  • 89
    • 0031547977 scopus 로고    scopus 로고
    • Empirical free energy calculations: A blind test and further improvements to the method
    • DOI 10.1006/jmbi.1997.0961
    • J. Novotny, R.E. Brucooleri, M. Davis, and K.A. Sharp Empirical free energy calculations: a blind test and further improvements of the method J. Mol. Biol. 268 1997 401 411 (Pubitemid 27208063)
    • (1997) Journal of Molecular Biology , vol.268 , Issue.2 , pp. 401-411
    • Novotny, J.1    Bruccoleri, R.E.2    Davis, M.3    Sharp, K.A.4
  • 90
    • 54849427905 scopus 로고    scopus 로고
    • Implicit solvent models in molecular dynamics simulations: A brief overview
    • A. Onufriev Implicit solvent models in molecular dynamics simulations: a brief overview Annu. Rep. Comput. Chem. 4 2008 125 137
    • (2008) Annu. Rep. Comput. Chem. , vol.4 , pp. 125-137
    • Onufriev, A.1
  • 91
    • 0037110472 scopus 로고    scopus 로고
    • Effective Born radii in the generalized Born approximation: The importance of being perfect
    • DOI 10.1002/jcc.10126
    • A. Onufriev, D. Case, and D. Bashford Effective Born radii the generalized Born approximation: the importance of being perfect J. Comput. Chem. 23 2002 1297 1304 (Pubitemid 35186231)
    • (2002) Journal of Computational Chemistry , vol.23 , Issue.14 , pp. 1297-1304
    • Onufriev, A.1    Case, D.A.2    Bashford, D.3
  • 92
    • 1842479952 scopus 로고    scopus 로고
    • Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model
    • DOI 10.1002/prot.20033
    • A. Onufriev, D. Bashford, and D. Case Eploring protein native states and large scale conformational changes with modified generalized Born model Proteins 55 2004 383 394 (Pubitemid 38437495)
    • (2004) Proteins: Structure, Function and Genetics , vol.55 , Issue.2 , pp. 383-394
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 93
    • 0023338543 scopus 로고
    • Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides
    • T. Ooi, M. Oobatake, G. Nemethy, and H.A. Scheraga Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides Proc. Natl. Acad. Sci. USA 84 1987 3086 3090
    • (1987) Proc. Natl. Acad. Sci. USA , vol.84 , pp. 3086-3090
    • Ooi, T.1    Oobatake, M.2    Nemethy, G.3    Scheraga, H.A.4
  • 94
    • 0037149093 scopus 로고    scopus 로고
    • A generalized-born solvation model for macromolecular hybrid-potential calculations
    • DOI 10.1021/jp0135050
    • E. Pellegrini, and M.J. Field A generalized-born solvation model for macromolecular hybrid-potential calculations J. Phys. Chem. A 106 2002 1316 1326 (Pubitemid 35264278)
    • (2002) Journal of Physical Chemistry A , vol.106 , Issue.7 , pp. 1316-1326
    • Pellegrini, E.1    Field, M.J.2
  • 95
    • 84986462300 scopus 로고
    • MSEED: A program for rapid analytical determination of accessible surface areas and their derivatives
    • G.B. Perrot, B. Cheng, K.D. Gibson, J. Vila, K.A. Palmer, and A. Nayeem MSEED: a program for rapid analytical determination of accessible surface areas and their derivatives J. Comput. Chem. 13 1992 1 11
    • (1992) J. Comput. Chem. , vol.13 , pp. 1-11
    • Perrot, G.B.1    Cheng, B.2    Gibson, K.D.3    Vila, J.4    Palmer, K.A.5    Nayeem, A.6
  • 96
    • 33747754400 scopus 로고
    • A scaled particle theory of aqueous and non-aqueous solutions
    • R.A. Pierotti A scaled particle theory of aqueous and non-aqueous solutions Chem. Rev. 76 1976 717 726
    • (1976) Chem. Rev. , vol.76 , pp. 717-726
    • Pierotti, R.A.1
  • 99
    • 0000003059 scopus 로고    scopus 로고
    • Free energy calculation methods: A theoretical and empirical comparison of numerical errors and a new method for qualitative estimates of free energy changes
    • R.J. Radmer, and P.A. Kollman Free energy calculation methods: a theoretical and empirical comparison of numerical errors and a new method for qualitative estimates of free energy changes J. Comput. Chem. 18 1997 902 919 (Pubitemid 127598577)
    • (1997) Journal of Computational Chemistry , vol.18 , Issue.7 , pp. 902-919
    • Radmer, R.J.1    Kollman, P.A.2
  • 100
    • 26844574873 scopus 로고
    • Hydration phenomena, classical electrostatics, and the boundary element method
    • A.A. Rashin Hydration phenomena, classical electrostatics, and the boundary element method J. Phys. Chem. 94 1990 1725 17358
    • (1990) J. Phys. Chem. , vol.94 , pp. 1725-17358
    • Rashin, A.A.1
  • 101
    • 0028144858 scopus 로고
    • Quantitative evaluation of hydration thermodynamics with a continuum model
    • DOI 10.1016/0301-4622(94)00058-1
    • A.A. Rashin, L. Young, and I.A. Topol Quantitative evaluation of hydration thermodynamics with continuum model Biophys. Chem. 51 1994 359 374 (Pubitemid 24244012)
    • (1994) Biophysical Chemistry , vol.51 , Issue.2-3 , pp. 359-374
    • Rashin, A.A.1    Young, L.2    Topol, I.A.3
  • 102
  • 103
    • 80052806033 scopus 로고
    • Areas, volume, packing and protein structures
    • F.M. Richards Areas, volume, packing and protein structures Annu. Rev. Biophys. Biophys. Chem. 19 1977 301 332
    • (1977) Annu. Rev. Biophys. Biophys. Chem. , vol.19 , pp. 301-332
    • Richards, F.M.1
  • 104
    • 0001458825 scopus 로고
    • The aqueous solvation of water: A comparison of continuum methods with molecular dynamics
    • S.W. Rick, and B.J. Berne The aqueous solvation of water: a comparison of continuum methods with molecular dynamics J. Am. Chem. Soc. 116 1994 3949 3954 (Pubitemid 24980982)
    • (1994) Journal of the American Chemical Society , vol.116 , Issue.9 , pp. 3949-3954
    • Rick, S.W.1    Berne, B.J.2
  • 105
    • 0030582736 scopus 로고    scopus 로고
    • Coupling between folding and ionization equilibria: Effects of pH on the conformational preferences of polypeptides
    • DOI 10.1006/jmbi.1996.0676
    • D.R. Ripoll, Y.N. Vorobjev, A. Liwo, J.A. Vila, and H.A. Scheraga Coupling between folding and ionization equilibria: effect of pH on the conformational preferences of polypeptides J. Mol. Biol. 264 1996 770 783 (Pubitemid 27013560)
    • (1996) Journal of Molecular Biology , vol.264 , Issue.4 , pp. 770-783
    • Ripoll, D.R.1    Vorobjev, Y.N.2    Liwo, A.3    Vila, J.A.4    Scheraga, H.A.5
  • 106
    • 0037080244 scopus 로고    scopus 로고
    • Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: Applications to the molecular systems and geometric objects
    • DOI 10.1002/jcc.1161
    • W. Rocchia, S. Sridharan, A. Nicholls, E. Alexov, A. Chiabrera, and B. Honig Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects J. Comput. Chem. 23 2002 128 137 (Pubitemid 34063137)
    • (2002) Journal of Computational Chemistry , vol.23 , Issue.1 , pp. 128-137
    • Rocchia, W.1    Sridharan, S.2    Nicholls, A.3    Alexov, E.4    Chiabrera, A.5    Honig, B.6
  • 107
    • 0032968133 scopus 로고    scopus 로고
    • Implicit solvent models
    • DOI 10.1016/S0301-4622(98)00226-9, PII S0301462298002269
    • B. Roux, and T. Simonson Implicit solvent models Biopys. Chem. 78 1999 1 20 (Pubitemid 29206654)
    • (1999) Biophysical Chemistry , vol.78 , Issue.1-2 , pp. 1-20
    • Roux, B.1    Simonson, T.2
  • 108
    • 0000763912 scopus 로고
    • Molecular basis for the Born model of ion solvation
    • B. Roux, H.A. Yu, and M. Karplus Molecular basis for the Born model of ion solvation J. Phys. Chem. 94 1990 4683 4688
    • (1990) J. Phys. Chem. , vol.94 , pp. 4683-4688
    • Roux, B.1    Yu, H.A.2    Karplus, M.3
  • 109
    • 0030040323 scopus 로고    scopus 로고
    • Reduced surface: An efficient way to compute molecular surfaces
    • M.F. Sanner, A.J. Olson, and J.C. Spehner Reduced surface: an efficient way to compute molecular surfaces Biopolymers 38 1996 305 320
    • (1996) Biopolymers , vol.38 , pp. 305-320
    • Sanner, M.F.1    Olson, A.J.2    Spehner, J.C.3
  • 110
    • 0025661993 scopus 로고
    • A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution
    • M. Schaefer, and C. Froemmel A precise analytical method for calculating the electrostatic energy of macromolecules in aqueous solution J. Mol. Biol. 216 1990 1045 1066
    • (1990) J. Mol. Biol. , vol.216 , pp. 1045-1066
    • Schaefer, M.1    Froemmel, C.2
  • 111
    • 0016699207 scopus 로고
    • Macromolecular binding
    • J.A. Schellman Macromolecular binding Biopolymers 14 1975 999 1018
    • (1975) Biopolymers , vol.14 , pp. 999-1018
    • Schellman, J.A.1
  • 114
    • 0000831520 scopus 로고
    • Solvation free energies estimated from macroscopic continuum theory: An accuracy assessment
    • T. Simonson, and A. Brünger Solvation free energies estimated from macroscopic continuum theory: an accuracy assessment J. Phys. Chem. 98 1994 4683 4694
    • (1994) J. Phys. Chem. , vol.98 , pp. 4683-4694
    • Simonson, T.1    Brünger, A.2
  • 115
    • 32844457567 scopus 로고
    • Accurate calculation of hydration free energies using macroscopic solvent models
    • D. Sitkoff, K.A. Sharp, and B. Honig Accurate calculation of hydration free energies using macroscopic solvent models J. Phys. Chem. 98 1994 1978 1988
    • (1994) J. Phys. Chem. , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 116
    • 0037174385 scopus 로고    scopus 로고
    • All-atom structure prediction and folding simulations of a stable protein
    • C. Simmerling, B. Strockbine, and A.E. Roitberg All-atom structure prediction and folding simulations of a stable protein J. Am. Chem. Soc. 124 2002 11258 11259
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 11258-11259
    • Simmerling, C.1    Strockbine, B.2    Roitberg, A.E.3
  • 119
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechanics and dynamics
    • W.C. Still, A. Tempezyk, R.C. Hawley, and T. Hendricson Semianalytical treatment of solvation for molecular mechanics and dynamics J. Am. Chem. Soc. 112 1990 6127 6129
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 6127-6129
    • Still, W.C.1    Tempezyk, A.2    Hawley, R.C.3    Hendricson, T.4
  • 120
    • 0014718113 scopus 로고
    • Protein denaturation: Part C. Theoretical models for denaturation
    • C. Tanford Protein denaturation: part C. Theoretical models for denaturation Adv. Protein Chem. 24 1970 1 95
    • (1970) Adv. Protein Chem. , vol.24 , pp. 1-95
    • Tanford, C.1
  • 121
    • 0015520587 scopus 로고
    • The interpretation of protein titration curves. Application to lysozyme
    • C. Tanford, and R. Roxby The interpretation of protein titration curves. Application to lysozyme Biochemistry 1972 11 1972 2192 2198
    • (1972) Biochemistry , vol.1972 , Issue.11 , pp. 2192-2198
    • Tanford, C.1    Roxby, R.2
  • 122
    • 11744256643 scopus 로고
    • Molecular interactions in solution: An overview of methods based on continuous distributions of the solvent
    • J. Tomasi, and M. Persico Molecular interactions in solution: overview of methods based on continuum distribution of the solvent Chem. Rev. 94 1994 2027 2094 (Pubitemid 124000195)
    • (1994) Chemical Reviews , vol.94 , Issue.7 , pp. 2027-2094
    • Tomasi, J.1    Persico, M.2
  • 125
    • 0001547345 scopus 로고
    • A Combined Iterative and Boundary Element Approach for Solution of the Nonlinear Poisson-Boltzmann Equation
    • Y.N. Vorobjev, J.A. Grant, and H.A. Scheraga A Combined Iterative and Boundary Element Approach for Solution of the Nonlinear Poisson-Boltzmann Equation J. Am. Chem. Soc. 114 1992 3189 3196
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 3189-3196
    • Vorobjev, Y.N.1    Grant, J.A.2    Scheraga, H.A.3
  • 126
    • 0030793507 scopus 로고    scopus 로고
    • SIMS: Computation of a smooth invariant molecular surface
    • Y.N. Vorobjev, and J. Hermans SIMS, computation of a smooth invariant molecular surface Biophys. J. 73 1997 722 732 (Pubitemid 27337607)
    • (1997) Biophysical Journal , vol.73 , Issue.2 , pp. 722-732
    • Vorobjev, Y.N.1    Hermans, J.2
  • 127
    • 0033003955 scopus 로고    scopus 로고
    • ES/IS: Estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model
    • DOI 10.1016/S0301-4622(98)00230-0, PII S0301462298002300
    • Y.N. Vorobjev, and J. Hermans ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model Biopys. Chem. 78 1999 195 205 (Pubitemid 29206666)
    • (1999) Biophysical Chemistry , vol.78 , Issue.1-2 , pp. 195-205
    • Vorobjev, Y.N.1    Hermans, J.2
  • 128
    • 0035186285 scopus 로고    scopus 로고
    • Free energies of protein decoys provide insight into determinants of protein stability
    • DOI 10.1110/ps.ps.15501
    • Y.N. Vorobjev, and J. Hermans Free energies of protein decoys provide insight into determinant of protein stability Protein Sci. 10 2001 2498 2506 (Pubitemid 33091573)
    • (2001) Protein Science , vol.10 , Issue.12 , pp. 2498-2506
    • Vorobjev, Y.N.1    Hermans, J.2
  • 129
    • 0001445346 scopus 로고    scopus 로고
    • A fast adaptive multigrid boundary element method for macromolecular electrostatic computations in a solvent
    • Y.N. Vorobjev, and H.A. Scheraga A fast adaptive multigrid boundary element method for macromolecular electrostatics in a solvent J. Comput. Chem. 18 1997 569 583 (Pubitemid 127780803)
    • (1997) Journal of Computational Chemistry , vol.18 , Issue.4 , pp. 569-583
    • Vorobjev, Y.N.1    Scheraga, H.A.2
  • 130
    • 0031872292 scopus 로고    scopus 로고
    • Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model
    • DOI 10.1002/(SICI)1097-0134(19980901)32:4<399::AID-PROT1>3.0.CO;2-C
    • Y.N. Vorobjev, J.C. Almagro, and J. Hermans Discrimination between native and intentionally misfolded conformation of proteins: ES/IS, new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and implicit solvent continuum model Proteins 32 1998 399 413 (Pubitemid 28380782)
    • (1998) Proteins: Structure, Function and Genetics , vol.32 , Issue.4 , pp. 399-413
    • Vorobjev, Y.N.1    Almagro, J.C.2    Hermans, J.3
  • 131
    • 52349088763 scopus 로고    scopus 로고
    • FAMBE-pH: A fast and accurate method to compute the total solvation free energies of proteins
    • Y.N. Vorobjev, J. Vila, and H.A. Scheraga FAMBE-pH: a fast and accurate method to compute the total solvation free energies of proteins J. Phys. Chem. B 112 2008 11122 11136
    • (2008) J. Phys. Chem. B , vol.112 , pp. 11122-11136
    • Vorobjev, Y.N.1    Vila, J.2    Scheraga, H.A.3
  • 133
    • 0001229923 scopus 로고
    • Molecular dynamics study of the dependence of water solvation free energy on solute curvature and surface area
    • W. Wallqvist, and B.J. Berne Molecular dynamics study of the dependence of water solvation free energy on solute curvature and surface area J. Phys. Chem. 99 1995 2885 2892
    • (1995) J. Phys. Chem. , vol.99 , pp. 2885-2892
    • Wallqvist, W.1    Berne, B.J.2
  • 134
    • 33751155475 scopus 로고
    • Computer simulation of hydrophobic hydration forces on stacked plates at short range
    • W. Wallqvist, and B.J. Berne Computer simulation of hydrophobic hydration forces on stacked plates at short range J. Phys. Chem. 99 1995 2893 2899
    • (1995) J. Phys. Chem. , vol.99 , pp. 2893-2899
    • Wallqvist, W.1    Berne, B.J.2
  • 135
    • 77950113751 scopus 로고    scopus 로고
    • Coupling constant pH molecular dynamics with accelerated molecular dynamics
    • S.L. Williams, C.A.F. Oliveira, and J.A. McCammon Coupling constant pH molecular dynamics with accelerated molecular dynamics J. Chem. Theory Comput. 6 2010 560 568
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 560-568
    • Williams, S.L.1    Oliveira, C.A.F.2    McCammon, J.A.3
  • 136
    • 34547298869 scopus 로고    scopus 로고
    • Can a physics-based, all-atom potential find a protein's native structure among misfolded structures? I. Large scale AMBER benchmarking
    • DOI 10.1002/jcc.20720
    • L. Wroblewska, and J. Skolnick Can a physics-based, all-atom potential find a protein's native structure among misfolded structures. I. Largescale AMBER benchmarking J. Comput. Chem 28 2007 2059 2066 (Pubitemid 47153603)
    • (2007) Journal of Computational Chemistry , vol.28 , Issue.12 , pp. 2059-2066
    • Wroblewska, L.1    Skolnick, J.2
  • 137
    • 0027231258 scopus 로고
    • On the pH dependence of protein stability
    • DOI 10.1006/jmbi.1993.1294
    • S.A. Yang, and B. Honig On the pH dependence of protein stability J. Mol. Biol. 231 1993 459 474 (Pubitemid 23188265)
    • (1993) Journal of Molecular Biology , vol.231 , Issue.2 , pp. 459-474
    • Yang, A.-S.1    Honig, B.2
  • 138
    • 84962478456 scopus 로고
    • A boundary element method for molecular electrostatics with electrolyte effects
    • B.J. Yoon, and A.M. Lenhoff A boundary element method for molecular electrostatics with electrolyte effects J. Comput. Chem. 11 1990 1080 1086
    • (1990) J. Comput. Chem. , vol.11 , pp. 1080-1086
    • Yoon, B.J.1    Lenhoff, A.M.2
  • 139
    • 84988110397 scopus 로고
    • The rigorous computation of the molecular electric potential
    • R.J. Zauhar, and R.S. Morgan The rigorous computation of the molecular electric potential J. Comput. Chem. 9 1988 171 187
    • (1988) J. Comput. Chem. , vol.9 , pp. 171-187
    • Zauhar, R.J.1    Morgan, R.S.2
  • 140
    • 0029286072 scopus 로고
    • SMATR: A solvent-accessible triangulated surface generator for molecular graphics and boundary element applications
    • R.J. Zauhar SMATR: a solvent-accessible triangulated surface generator for molecular graphics and boundary element applications J. Comput. Aid. Mol. Des. 9 1995 149 159
    • (1995) J. Comput. Aid. Mol. Des. , vol.9 , pp. 149-159
    • Zauhar, R.J.1
  • 141
    • 84962420696 scopus 로고    scopus 로고
    • A fast and space-efficient boundary element method for computing electrostatic and hydration effects in large molecules
    • R.J. Zauhar, and A.A. Varnek Fast and space-efficient boundary element method for computing electrostatics and hydration effects in large molecules J. Comput. Chem. 17 1996 864 877 (Pubitemid 126579188)
    • (1996) Journal of Computational Chemistry , vol.17 , Issue.7 , pp. 864-877
    • Zauhar, R.J.1    Varnek, A.2
  • 143
    • 85033849708 scopus 로고    scopus 로고
    • Finite-difference solution of the Poisson - Boltzmann equation: Complete elimination of self-energy
    • Z. Zhou, P. Payne, M. Vasquez, N. Kuhn, and M. Levitt Finite-difference solution of the Poisson-Boltzmann equation: complete elimination of self-energy J. Comput. Chem. 17 1996 1344 1351 (Pubitemid 126576751)
    • (1996) Journal of Computational Chemistry , vol.17 , Issue.11 , pp. 1344-1351
    • Zhou, Z.1    Payne, P.2    Vasquez, M.3    Kuhn, N.4    Levitt, M.5
  • 144
    • 37649005586 scopus 로고    scopus 로고
    • Higly accurate biomolecular electrostatics in continuum dielectric environments
    • Y.C. Zhou, M. Feig, and G.W. Wei Higly accurate biomolecular electrostatics in continuum dielectric environments J. Comput. Chem. 29 2008 87 97
    • (2008) J. Comput. Chem. , vol.29 , pp. 87-97
    • Zhou, Y.C.1    Feig, M.2    Wei, G.W.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.