메뉴 건너뛰기




Volumn 12, Issue , 1998, Pages 1-74

Calculation of the Free Energy and the Entropy of Macromolecular Systems by Computer Simulation

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; ENTROPY;

EID: 0032342086     PISSN: 10693599     EISSN: None     Source Type: Book Series    
DOI: None     Document Type: Article
Times cited : (42)

References (303)
  • 3
    • 34548717559 scopus 로고
    • Phase Transition of Hard Sphere System
    • B. J. Alder and T. E. Wainwright, J. Chem. Phys., 27, 1208 (1957). Phase Transition of Hard Sphere System.
    • (1957) J. Chem. Phys. , vol.27 , pp. 1208
    • Alder, B.J.1    Wainwright, T.E.2
  • 4
    • 36849126204 scopus 로고
    • Studies of Molecular Dynamics. I. General Method
    • B. J. Alder and T. E. Wainwright, J. Chem. Phys., 31, 459 (1959). Studies of Molecular Dynamics. I. General Method.
    • (1959) J. Chem. Phys. , vol.31 , pp. 459
    • Alder, B.J.1    Wainwright, T.E.2
  • 6
    • 51149216498 scopus 로고
    • Analysis of the Contribution of Internal Vibrations to the Statistical Weights of Equilibrium Conformations of Macromolecules
    • N. Gō and H. A. Scheraga, J. Chem. Phys., 51, 4751 (1969). Analysis of the Contribution of Internal Vibrations to the Statistical Weights of Equilibrium Conformations of Macromolecules.
    • (1969) J. Chem. Phys. , vol.51 , pp. 4751
    • Go, N.1    Scheraga, H.A.2
  • 7
    • 0001182617 scopus 로고
    • Computer Simulation of the Conformational Properties of Oligopeptides. Comparison of Theoretical Methods and Analysis of Experimental Results
    • A. T. Hagler, P. S. Stern, R. Sharon, J. M. Becker, and F. Naider, J. Am. Chem. Soc., 101, 6842 (1979). Computer Simulation of the Conformational Properties of Oligopeptides. Comparison of Theoretical Methods and Analysis of Experimental Results.
    • (1979) J. Am. Chem. Soc. , vol.101 , pp. 6842
    • Hagler, A.T.1    Stern, P.S.2    Sharon, R.3    Becker, J.M.4    Naider, F.5
  • 8
    • 0000127140 scopus 로고
    • Method for Estimating the Configurational Entropy of Macromolecules
    • M. Karplus and J. N. Kushick, Macromolecules, 14, 325 (1981). Method for Estimating the Configurational Entropy of Macromolecules.
    • (1981) Macromolecules , vol.14 , pp. 325
    • Karplus, M.1    Kushick, J.N.2
  • 9
    • 36849116054 scopus 로고
    • Machine Calculation of Thermodynamic Properties of a Simple Fluid
    • I. R. McDonald and K. Singer, J. Chem. Phys., 47, 4766 (1967). Machine Calculation of Thermodynamic Properties of a Simple Fluid.
    • (1967) J. Chem. Phys. , vol.47 , pp. 4766
    • McDonald, I.R.1    Singer, K.2
  • 10
    • 0014665094 scopus 로고
    • Phase Transition of the Lennard-Jones System
    • J.-P. Hansen and L. Verlet, Phys. Rev., 184, 151 (1969). Phase Transition of the Lennard-Jones System.
    • (1969) Phys. Rev. , vol.184 , pp. 151
    • Hansen, J.-P.1    Verlet, L.2
  • 11
    • 36849097857 scopus 로고
    • Use of Computer Experiments to Locate the Melting Transition and Calculate the Entropy in the Solid Phase
    • W. G. Hoover and F. H. Ree, J. Chem. Phys., 47, 4783 (1967). Use of Computer Experiments to Locate the Melting Transition and Calculate the Entropy in the Solid Phase.
    • (1967) J. Chem. Phys. , vol.47 , pp. 4783
    • Hoover, W.G.1    Ree, F.H.2
  • 13
    • 33646471468 scopus 로고
    • Statistical Mechanics of Fluid Mixtures
    • J. G. Kirkwood, J. Chem. Phys., 3, 300 (1935). Statistical Mechanics of Fluid Mixtures.
    • (1935) J. Chem. Phys. , vol.3 , pp. 300
    • Kirkwood, J.G.1
  • 14
    • 36849122972 scopus 로고
    • High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases
    • R. W. Zwanzig, J. Chem. Phys., 22, 1420 (1954). High-Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases.
    • (1954) J. Chem. Phys. , vol.22 , pp. 1420
    • Zwanzig, R.W.1
  • 15
    • 36849102181 scopus 로고
    • Monte Carlo Simulation of Vacancies in Rare-Gas Crystals
    • D. R. Squire and W. G. Hoover, J. Chem. Phys., 50, 701 (1969). Monte Carlo Simulation of Vacancies in Rare-Gas Crystals.
    • (1969) J. Chem. Phys. , vol.50 , pp. 701
    • Squire, D.R.1    Hoover, W.G.2
  • 16
    • 16444385400 scopus 로고
    • Monte Carlo Free Energy Estimates Using Non-Boltzmann Sampling: Application to the Sub-Critical Lennard-Jones Fluid
    • G. M. Torrie and J. P. Valleau, Chem. Phys. Lett., 28, 578 (1974). Monte Carlo Free Energy Estimates Using Non-Boltzmann Sampling: Application to the Sub-Critical Lennard-Jones Fluid.
    • (1974) Chem. Phys. Lett. , vol.28 , pp. 578
    • Torrie, G.M.1    Valleau, J.P.2
  • 17
    • 0342929614 scopus 로고
    • Nonphysical Sampling Distributions in Monte Carlo Free-Energy Estimation: Umbrella Sampling
    • G. M. Torrie and J. P. Valleau, J. Comput. Phys., 23, 187 (1977). Nonphysical Sampling Distributions in Monte Carlo Free-Energy Estimation: Umbrella Sampling.
    • (1977) J. Comput. Phys. , vol.23 , pp. 187
    • Torrie, G.M.1    Valleau, J.P.2
  • 18
    • 0024578173 scopus 로고
    • Free Energy Via Molecular Simulation: Application to Chemical and Biomolecular Systems
    • D. L. Beveridge and F. M. DiCapua, Annu. Rev. Biophys. Chem., 18, 431 (1989). Free Energy Via Molecular Simulation: Application to Chemical and Biomolecular Systems.
    • (1989) Annu. Rev. Biophys. Chem. , vol.18 , pp. 431
    • Beveridge, D.L.1    DiCapua, F.M.2
  • 19
    • 7044239742 scopus 로고
    • Free Energy Calculations: Applications to Chemical and Biochemical Phenomena
    • P. A. Kollman, Chem. Rev., 93, 2395 (1993). Free Energy Calculations: Applications to Chemical and Biochemical Phenomena.
    • (1993) Chem. Rev. , vol.93 , pp. 2395
    • Kollman, P.A.1
  • 21
    • 0030601792 scopus 로고    scopus 로고
    • Contribution to Conformational Entropy Arising from Bond Vector Fluctuations Measured from NMR-Derived Order Parameters: Application to Protein Folding
    • D. Yang and L. E. Kay, J. Mol. Biol. 263, 369 (1996). Contribution to Conformational Entropy Arising from Bond Vector Fluctuations Measured from NMR-Derived Order Parameters: Application to Protein Folding.
    • (1996) J. Mol. Biol. , vol.263 , pp. 369
    • Yang, D.1    Kay, L.E.2
  • 22
    • 0030299991 scopus 로고    scopus 로고
    • 15N NMR Relaxation Studies of Free and Inhibitor-Bound 4-Oxalocrotonate Tautomerase: Backbone Dynamics and Entropy Changes of an Enzyme upon Inhibitor Binding
    • 15N NMR Relaxation Studies of Free and Inhibitor-Bound 4-Oxalocrotonate Tautomerase: Backbone Dynamics and Entropy Changes of an Enzyme upon Inhibitor Binding.
    • (1996) Biochemistry , vol.35 , pp. 16036
    • Stivers, J.T.1    Abeygunawardana, C.2    Mildvan, A.S.3    Whitman, C.P.4
  • 23
    • 0030961098 scopus 로고    scopus 로고
    • The Backbone Entropy of Loops as a Measure of Their Flexibility. Application to a ras Protein Simulated by Molecular Dynamics
    • H. Meirovitch and T. F. Hendrickson, Proteins, 29, 127 (1997). The Backbone Entropy of Loops as a Measure of Their Flexibility. Application to a ras Protein Simulated by Molecular Dynamics.
    • (1997) Proteins , vol.29 , pp. 127
    • Meirovitch, H.1    Hendrickson, T.F.2
  • 24
    • 0001290941 scopus 로고
    • Conformational Energy Calculations on Polypeptides and Proteins
    • M. Vásquez, G. Némethy, and H. A. Scheraga, Chem. Rev., 94, 2183 (1994). Conformational Energy Calculations on Polypeptides and Proteins.
    • (1994) Chem. Rev. , vol.94 , pp. 2183
    • Vásquez, M.1    Némethy, G.2    Scheraga, H.A.3
  • 25
    • 36849135374 scopus 로고
    • Statistical Computation of Mean Dimensions of Macromolecules
    • F. T. Wall, L. A. Hiller, and D. J. Wheeler, J. Chem. Phys., 22, 1036 (1954). Statistical Computation of Mean Dimensions of Macromolecules.
    • (1954) J. Chem. Phys. , vol.22 , pp. 1036
    • Wall, F.T.1    Hiller, L.A.2    Wheeler, D.J.3
  • 26
    • 36849137515 scopus 로고
    • Monte Carlo Calculation of the Average Extension of Molecular Chains
    • M. N. Rosenbluth and A. W. Rosenbluth, J. Chem. Phys., 23, 356 (1955). Monte Carlo Calculation of the Average Extension of Molecular Chains.
    • (1955) J. Chem. Phys. , vol.23 , pp. 356
    • Rosenbluth, M.N.1    Rosenbluth, A.W.2
  • 27
    • 36849136789 scopus 로고
    • New Method for the Statistical Computation of Polymer Dimensions
    • F. T. Wall and J. J. Erpenbeck, J. Chem. Phys., 30, 634 (1959). New Method for the Statistical Computation of Polymer Dimensions.
    • (1959) J. Chem. Phys. , vol.30 , pp. 634
    • Wall, F.T.1    Erpenbeck, J.J.2
  • 28
    • 0002647323 scopus 로고
    • Improved Statistical Method for Computing Mean Dimensions of Polymer Molecules
    • F. T. Wall, R. J. Rubin, and L. M. Isaacson, J. Chem. Phys., 27, 186 (1957). Improved Statistical Method for Computing Mean Dimensions of Polymer Molecules.
    • (1957) J. Chem. Phys. , vol.27 , pp. 186
    • Wall, F.T.1    Rubin, R.J.2    Isaacson, L.M.3
  • 29
    • 0007037570 scopus 로고
    • Monte Carlo Methods Applied to Configurations of Flexible Polymer Molecules
    • F. T. Wall, S. Windwer, P. J. Gans, and L. M. Isaacson, Methods Comput. Phys., 1, 217 (1963). Monte Carlo Methods Applied to Configurations of Flexible Polymer Molecules.
    • (1963) Methods Comput. Phys. , vol.1 , pp. 217
    • Wall, F.T.1    Windwer, S.2    Gans, P.J.3    Isaacson, L.M.4
  • 30
    • 0010928516 scopus 로고
    • Monte Carlo Studies of Self-Interacting Polymer Chains with Excluded Volume. I. Squared Radii of Gyration and Mean-Square End-to-End Distances and Their Moments
    • F. L. MacCrackin, J. Mazur, and C. M. Guttman, Macromolecules, 6, 859 (1973). Monte Carlo Studies of Self-Interacting Polymer Chains with Excluded Volume. I. Squared Radii of Gyration and Mean-Square End-to-End Distances and Their Moments.
    • (1973) Macromolecules , vol.6 , pp. 859
    • MacCrackin, F.L.1    Mazur, J.2    Guttman, C.M.3
  • 31
    • 4043180889 scopus 로고
    • A New Method for Simulation of Real Chains. Scanning Future Steps
    • H. Meirovitch, J. Phys. A, 15, L735 (1982). A New Method for Simulation of Real Chains. Scanning Future Steps.
    • (1982) J. Phys. A , vol.15
    • Meirovitch, H.1
  • 32
    • 0001563695 scopus 로고
    • Statistical Properties of the Scanning Simulation Method for Polymer Chains
    • H. Meirovitch, J. Chem. Phys., 89, 2514 (1988). Statistical Properties of the Scanning Simulation Method for Polymer Chains.
    • (1988) J. Chem. Phys. , vol.89 , pp. 2514
    • Meirovitch, H.1
  • 33
    • 0038890264 scopus 로고
    • The Collapse Transition of Self-Avoiding Walks on a Square Lattice in the Bulk and Near a Linear Wall: The Universality Class of the θ and θ′ points
    • I. Chang and H. Meirovitch, Phys. Rev. E, 48, 3656 (1993). The Collapse Transition of Self-Avoiding Walks on a Square Lattice in the Bulk and Near a Linear Wall: The Universality Class of the θ and θ′ points.
    • (1993) Phys. Rev. E , vol.48 , pp. 3656
    • Chang, I.1    Meirovitch, H.2
  • 34
    • 0027897634 scopus 로고
    • Biasing a Monte Carlo Chain Growth Method with Ramachandran's Plot: Application to Twenty-L-Alanine
    • J. Bascle, T. Garel, H. Orland, and B. Velikson, Biopolymers, 33, 1843 (1993). Biasing a Monte Carlo Chain Growth Method with Ramachandran's Plot: Application to Twenty-L-Alanine.
    • (1993) Biopolymers , vol.33 , pp. 1843
    • Bascle, J.1    Garel, T.2    Orland, H.3    Velikson, B.4
  • 35
    • 21344488309 scopus 로고
    • Chain Polymers Near an Adsorbing Surface
    • P. Grassberger and R. Hegger, J. Phys. A, 27, 4069 (1994). Chain Polymers Near an Adsorbing Surface.
    • (1994) J. Phys. A , vol.27 , pp. 4069
    • Grassberger, P.1    Hegger, R.2
  • 36
    • 0001598816 scopus 로고
    • Calculation of Entropy with Computer Simulation Methods
    • H. Meirovitch, Chem. Phys. Lett., 45, 389 (1977). Calculation of Entropy with Computer Simulation Methods.
    • (1977) Chem. Phys. Lett. , vol.45 , pp. 389
    • Meirovitch, H.1
  • 37
    • 0028166871 scopus 로고
    • Computer Simulation of the Free Energy of Peptides with the Local States Method: Analogues of Gonadotropin Releasing Hormone in the Random Coil and Stable States
    • H. Meirovitch, S. C. Koerber, J. Rivier, and A. T. Hagler, Biopolymers, 34, 815 (1994). Computer Simulation of the Free Energy of Peptides with the Local States Method: Analogues of Gonadotropin Releasing Hormone in the Random Coil and Stable States.
    • (1994) Biopolymers , vol.34 , pp. 815
    • Meirovitch, H.1    Koerber, S.C.2    Rivier, J.3    Hagler, A.T.4
  • 38
    • 0001251117 scopus 로고
    • Computer Simulation of the Free Energy of Polymer Chains with Excluded Volume and with Finite Interactions
    • H. Meirovitch, Phys. Rev. A, 32, 3709 (1985). Computer Simulation of the Free Energy of Polymer Chains with Excluded Volume and with Finite Interactions.
    • (1985) Phys. Rev. A , vol.32 , pp. 3709
    • Meirovitch, H.1
  • 39
    • 58749107488 scopus 로고
    • Stochastic Models for the Statistical Description of Lattice Systems
    • Z. Alexandrowicz, J. Chem. Phys., 55, 2765 (1971). Stochastic Models for the Statistical Description of Lattice Systems.
    • (1971) J. Chem. Phys. , vol.55 , pp. 2765
    • Alexandrowicz, Z.1
  • 40
    • 0346756918 scopus 로고
    • Stochastic Model for a Fluid of Hard Cubes with Attractive Potential
    • Z. Alexandrowicz and M. Mostow, J. Chem. Phys., 56, 1274 (1972). Stochastic Model for a Fluid of Hard Cubes with Attractive Potential.
    • (1972) J. Chem. Phys. , vol.56 , pp. 1274
    • Alexandrowicz, Z.1    Mostow, M.2
  • 41
    • 34250300786 scopus 로고
    • The Stochastic Models Method Applied to the Critical Behavior of Ising Lattices
    • H. Meirovitch and Z. Alexandrowicz, J. Stat. Phys., 15, 121 (1977). The Stochastic Models Method Applied to the Critical Behavior of Ising Lattices.
    • (1977) J. Stat. Phys. , vol.15 , pp. 121
    • Meirovitch, H.1    Alexandrowicz, Z.2
  • 42
    • 0005648839 scopus 로고
    • Methods for Estimating the Entropy with Computer Simulation. The Simple Cubic Ising Lattice
    • H. Meirovitch, J. Phys. A, 16, 839 (1983). Methods for Estimating the Entropy with Computer Simulation. The Simple Cubic Ising Lattice.
    • (1983) J. Phys. A , vol.16 , pp. 839
    • Meirovitch, H.1
  • 43
    • 0042950804 scopus 로고
    • Computer Simulation Study of Hysteresis and Free Energy in the fcc Ising Antiferromagnet
    • H. Meirovitch, Phys. Rev. B, 30, 2866 (1984). Computer Simulation Study of Hysteresis and Free Energy in the fcc Ising Antiferromagnet.
    • (1984) Phys. Rev. B , vol.30 , pp. 2866
    • Meirovitch, H.1
  • 44
    • 0000106469 scopus 로고
    • Multicanonical Algorithms for First Order Phase Transition
    • B. A. Berg and T. Neuhaus, Phys. Lett., B267, 249 (1991). Multicanonical Algorithms for First Order Phase Transition.
    • (1991) Phys. Lett. , vol.B267 , pp. 249
    • Berg, B.A.1    Neuhaus, T.2
  • 45
    • 0000235749 scopus 로고
    • The Multicanonical Ensemble: A New Approach for Computer Simulations
    • B. A. Berg, Int. J. Mod. Phys. C, 3, 1083 (1992). The Multicanonical Ensemble: A New Approach for Computer Simulations.
    • (1992) Int. J. Mod. Phys. C , vol.3 , pp. 1083
    • Berg, B.A.1
  • 46
    • 0002061484 scopus 로고
    • New Monte Carlo Algorithm: Entropic Sampling
    • J. Lee, Phys. Rev. Lett., 71, 211 (1993). New Monte Carlo Algorithm: Entropic Sampling.
    • (1993) Phys. Rev. Lett. , vol.71 , pp. 211
    • Lee, J.1
  • 47
    • 5244260010 scopus 로고
    • Prediction of Peptide Conformation by a Multicanonical Algorithm: New Approach to the Multiple Minima Problem
    • U. H. E. Hansmann and Y. Okamoto, J. Comput. Chem., 14, 1333 (1993). Prediction of Peptide Conformation by a Multicanonical Algorithm: New Approach to the Multiple Minima Problem.
    • (1993) J. Comput. Chem. , vol.14 , pp. 1333
    • Hansmann, U.H.E.1    Okamoto, Y.2
  • 48
    • 0000515198 scopus 로고
    • Monte Carlo Simulation of a First-Order Transition for Protein Folding
    • M.-H. Hao and H. A. Scheraga, J. Phys. Chem., 98, 4940 (1994). Monte Carlo Simulation of a First-Order Transition for Protein Folding.
    • (1994) J. Phys. Chem. , vol.98 , pp. 4940
    • Hao, M.-H.1    Scheraga, H.A.2
  • 49
    • 0029809182 scopus 로고    scopus 로고
    • On the Origin of the Cooperativity of Protein Folding: Implications from Model Simulations
    • A. Kolinski, W. Galazka, and J. Skolnick, Proteins, 26, 271 (1996). On the Origin of the Cooperativity of Protein Folding: Implications from Model Simulations.
    • (1996) Proteins , vol.26 , pp. 271
    • Kolinski, A.1    Galazka, W.2    Skolnick, J.3
  • 52
    • 0001031179 scopus 로고
    • Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics
    • C. L. Brooks III, M. Karplus, and B. M. Pettitt, Adv. Chem. Phys., 71 (1988). Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics.
    • (1988) Adv. Chem. Phys. , vol.71
    • Brooks C.L. III1    Karplus, M.2    Pettitt, B.M.3
  • 55
    • 33746340574 scopus 로고
    • Free Energy Calculations in Drug Design: A Practical Guide
    • Proceedings of the Ninth International Roundtable, April 11-13, Turnbury, Scotland, P. M. Dean, G. Jolles, and C. G. Newton, Eds., Academic Press, San Diego, CA
    • (c) A. E. Mark and W. F. van Gunsteren, in New Perspectives in Drug Design, Proceedings of the Ninth International Roundtable, April 11-13, 1994, Turnbury, Scotland, P. M. Dean, G. Jolles, and C. G. Newton, Eds., Academic Press, San Diego, CA, 1995, pp. 185-200. Free Energy Calculations in Drug Design: A Practical Guide.
    • (1994) New Perspectives in Drug Design , pp. 185-200
    • Mark, A.E.1    Van Gunsteren, W.F.2
  • 56
    • 0009590921 scopus 로고
    • Free Energy Calculations: A Breakthrough for Modeling Organic Chemistry in Solution
    • W. L. Jorgensen, Acc. Chem. Res., 22, 184 (1989). Free Energy Calculations: A Breakthrough for Modeling Organic Chemistry in Solution.
    • (1989) Acc. Chem. Res. , vol.22 , pp. 184
    • Jorgensen, W.L.1
  • 57
    • 0346756932 scopus 로고
    • Microfolding: Use of Simulations to Study Peptide/Protein Conformational Equilibria
    • D. L. Beveridge and R. Lavery Eds., Adenine Press, Guilderland, NY
    • J. Hermans and A. G. Anderson, in Theoretical Biochemistry and Molecular Biophysics, D. L. Beveridge and R. Lavery Eds., Adenine Press, Guilderland, NY, 1990, pp. 45-51. Microfolding: Use of Simulations to Study Peptide/Protein Conformational Equilibria.
    • (1990) Theoretical Biochemistry and Molecular Biophysics , pp. 45-51
    • Hermans, J.1    Anderson, A.G.2
  • 59
    • 0027849737 scopus 로고
    • Calculation of Solvation Free-Energy Differences for Large Solute Change from Computer Simulations with Quadrature-Based Nearly Linear Thermodynamic Integration
    • M. Mezei, Mol. Simulation, 10, 225 (1993). Calculation of Solvation Free-Energy Differences for Large Solute Change from Computer Simulations with Quadrature-Based Nearly Linear Thermodynamic Integration.
    • (1993) Mol. Simulation , vol.10 , pp. 225
    • Mezei, M.1
  • 60
    • 0347927466 scopus 로고
    • Free Energies of Hydration for Organic Molecules from Monte Carlo Simulations
    • W. L. Jorgensen and J. Tirado-Rives, Perspect. Drug Discovery Design, 3, 123 (1995). Free Energies of Hydration for Organic Molecules from Monte Carlo Simulations.
    • (1995) Perspect. Drug Discovery Design , vol.3 , pp. 123
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 61
    • 0043203165 scopus 로고
    • Calculations of Solvation Free Energies in Chemistry and Biology
    • C. J. Cramer and D. G. Truhlar, Eds., ACS Symposium Series No. 568, American Chemical Society, Washington, DC
    • (a) A. Warshel and Z. T. Chu, in Structure and Reactivity in Aqueous Solution. Characterization of Chemical and Biological Systems, C. J. Cramer and D. G. Truhlar, Eds., ACS Symposium Series No. 568, American Chemical Society, Washington, DC, 1994, pp. 71-94. Calculations of Solvation Free Energies in Chemistry and Biology.
    • (1994) Structure and Reactivity in Aqueous Solution. Characterization of Chemical and Biological Systems , pp. 71-94
    • Warshel, A.1    Chu, Z.T.2
  • 63
    • 2542564912 scopus 로고    scopus 로고
    • Advances and Continuing Challenges in Achieving Realistic and Predictive Simulations of the Properties of Organic and Biological Molecules
    • P. A. Kollman, Acc. Chem. Res., 29, 461 (1996). Advances and Continuing Challenges in Achieving Realistic and Predictive Simulations of the Properties of Organic and Biological Molecules.
    • (1996) Acc. Chem. Res. , vol.29 , pp. 461
    • Kollman, P.A.1
  • 64
    • 84862582328 scopus 로고
    • Computer Simulation of Biomolecular Systems Using Molecular Dynamics and Free Energy Perturbation Methods
    • K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York
    • (a) T. P. Lybrand, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1990. Vol. 1, pp. 295-320. Computer Simulation of Biomolecular Systems Using Molecular Dynamics and Free Energy Perturbation Methods.
    • (1990) Reviews in Computational Chemistry , vol.1 , pp. 295-320
    • Lybrand, T.P.1
  • 65
    • 0030503687 scopus 로고    scopus 로고
    • Free Energy by Molecular Simulation
    • K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York
    • (b) T. P. Straatsma, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1996, Vol. 9, pp. 81-127. Free Energy by Molecular Simulation.
    • (1996) Reviews in Computational Chemistry , vol.9 , pp. 81-127
    • Straatsma, T.P.1
  • 67
    • 0031479825 scopus 로고    scopus 로고
    • Visualizing Molecular Phase Space: Nonstatistical Effects in Reaction Dynamics
    • K. B. Lipkowitz and D. B Boyd, Eds., VCH Publishers, New York
    • (a) R. Q. Topper, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B Boyd, Eds., VCH Publishers, New York, 1997, Vol. 10, pp. 101-176. Visualizing Molecular Phase Space: Nonstatistical Effects in Reaction Dynamics.
    • (1997) Reviews in Computational Chemistry , vol.10 , pp. 101-176
    • Topper, R.Q.1
  • 68
    • 0031522220 scopus 로고    scopus 로고
    • Computational Studies in Nonlinear Dynamics
    • K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York
    • (b) R. Larter and K. Showalter, in Reviews in Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New York, 1997, Vol. 10, pp. 177-270. Computational Studies in Nonlinear Dynamics.
    • (1997) Reviews in Computational Chemistry , vol.10 , pp. 177-270
    • Larter, R.1    Showalter, K.2
  • 70
    • 36849131860 scopus 로고
    • Application of the Monte Carlo Method to the Lattice Gas Model. I. Two-Dimensional Triangular Lattice
    • Z. W. Salsburg, J. D. Jacobson, W. Fickett, and W. W. Wood, J. Chem. Phys., 30, 65 (1959). Application of the Monte Carlo Method to the Lattice Gas Model. I. Two-Dimensional Triangular Lattice.
    • (1959) J. Chem. Phys. , vol.30 , pp. 65
    • Salsburg, Z.W.1    Jacobson, J.D.2    Fickett, W.3    Wood, W.W.4
  • 72
    • 0005635371 scopus 로고
    • On the Zero Fluctuation of the Microscopic Free Energy and Its Potential Use
    • H. Meirovitch and Z. Alexandrowicz, J. Stat. Phys., 15, 123 (1976). On the Zero Fluctuation of the Microscopic Free Energy and Its Potential Use.
    • (1976) J. Stat. Phys. , vol.15 , pp. 123
    • Meirovitch, H.1    Alexandrowicz, Z.2
  • 73
    • 5244304444 scopus 로고
    • Efficient Estimation of Free Energy Differences
    • C. H. Bennett, J. Comput. Phys., 22, 245 (1976). Efficient Estimation of Free Energy Differences.
    • (1976) J. Comput. Phys. , vol.22 , pp. 245
    • Bennett, C.H.1
  • 74
    • 0042640726 scopus 로고
    • Some Topics in the Theory of Fluids
    • B. Widom, J. Chem. Phys., 39, 2808 (1963). Some Topics in the Theory of Fluids.
    • (1963) J. Chem. Phys. , vol.39 , pp. 2808
    • Widom, B.1
  • 75
    • 0346126180 scopus 로고
    • Potential Distribution Method in Equilibrium Statistical Mechanics
    • J. L. Jackson and L. S. Klein, The Physics of Fluids, 7, 228 (1964). Potential Distribution Method in Equilibrium Statistical Mechanics.
    • (1964) The Physics of Fluids , vol.7 , pp. 228
    • Jackson, J.L.1    Klein, L.S.2
  • 76
    • 0001343746 scopus 로고
    • The Chemical Potential from Computer Simulation. Test Particle Method with Umbrella Sampling
    • K. S. Shing and K. E. Gubbins, Mol. Phys., 43, 717 (1981). The Chemical Potential from Computer Simulation. Test Particle Method with Umbrella Sampling.
    • (1981) Mol. Phys. , vol.43 , pp. 717
    • Shing, K.S.1    Gubbins, K.E.2
  • 77
    • 6744231939 scopus 로고
    • The Chemical Potential in Dense Fluids and Fluid Mixtures via Computer Simulation
    • K. S. Shing and K. E. Gubbins, Mol. Phys., 46, 1109 (1982). The Chemical Potential in Dense Fluids and Fluid Mixtures via Computer Simulation.
    • (1982) Mol. Phys. , vol.46 , pp. 1109
    • Shing, K.S.1    Gubbins, K.E.2
  • 78
    • 0000955960 scopus 로고    scopus 로고
    • Chemical Potential and Dimensions of Chain Molecules in Athermal Environments
    • F. A. Escobedo and J. J. de Pablo, Mol. Phys., 89, 1733 (1996). Chemical Potential and Dimensions of Chain Molecules in Athermal Environments.
    • (1996) Mol. Phys. , vol.89 , pp. 1733
    • Escobedo, F.A.1    De Pablo, J.J.2
  • 79
    • 0001044103 scopus 로고    scopus 로고
    • Computation of the Chemical Potential in High Density Fluids by a Monte Carlo Method
    • N. G. Parsonage, Mol. Phys., 89, 1133 (1996). Computation of the Chemical Potential in High Density Fluids by a Monte Carlo Method.
    • (1996) Mol. Phys. , vol.89 , pp. 1133
    • Parsonage, N.G.1
  • 80
    • 0348017845 scopus 로고    scopus 로고
    • Simulation of Free Energy Without Particle Insertion in the NPT Ensemble
    • P. Bereolos, J. Talbot, and K.-C. Chao, Mol. Phys., 89, 1621 (1996). Simulation of Free Energy Without Particle Insertion in the NPT Ensemble.
    • (1996) Mol. Phys. , vol.89 , pp. 1621
    • Bereolos, P.1    Talbot, J.2    Chao, K.-C.3
  • 82
    • 0001432119 scopus 로고
    • Methods of Reducing Sample Size in Monte Carlo Computations
    • M. Kahn and A. W. Marshall, Oper. Res. 1, 263 (1953). Methods of Reducing Sample Size in Monte Carlo Computations.
    • (1953) Oper. Res. , vol.1 , pp. 263
    • Kahn, M.1    Marshall, A.W.2
  • 86
    • 5944250450 scopus 로고
    • Energy Parameters in Polypeptides. VII. Geometric Parameters, Partial Atomic Charges, Nonbonded Interactions, Hydrogen Bond Interactions, and Intrinsic Torsional Potentials for the Naturally Occurring Amino Acids
    • F. A. Momany, R. F. McGuire, A. W. Burgess, and H. A. Scheraga, J. Phys. Chem., 79, 2361 (1975). Energy Parameters in Polypeptides. VII. Geometric Parameters, Partial Atomic Charges, Nonbonded Interactions, Hydrogen Bond Interactions, and Intrinsic Torsional Potentials for the Naturally Occurring Amino Acids.
    • (1975) J. Phys. Chem. , vol.79 , pp. 2361
    • Momany, F.A.1    McGuire, R.F.2    Burgess, A.W.3    Scheraga, H.A.4
  • 87
    • 27244454740 scopus 로고
    • Intermolecular Potentials from the Crystal Data. 6. Determination of Empirical Potentials for O -H⋯O=C Hydrogen Bonds from Packing Configurations
    • M. J. Sippl, G. Némethy, and H. A. Scheraga, J. Phys. Chem., 88, 6231 (1984). Intermolecular Potentials from the Crystal Data. 6. Determination of Empirical Potentials for O -H⋯O=C Hydrogen Bonds from Packing Configurations.
    • (1984) J. Phys. Chem. , vol.88 , pp. 6231
    • Sippl, M.J.1    Némethy, G.2    Scheraga, H.A.3
  • 90
    • 0000349059 scopus 로고
    • Configuration Entropy of the Alanine Dipeptide in Vacuum and in Solution: A Molecular Dynamics Study
    • J. Brady and M. Karplus, J. Am. Chem. Soc., 107, 6103 (1985). Configuration Entropy of the Alanine Dipeptide in Vacuum and in Solution: A Molecular Dynamics Study.
    • (1985) J. Am. Chem. Soc. , vol.107 , pp. 6103
    • Brady, J.1    Karplus, M.2
  • 91
    • 0030060129 scopus 로고    scopus 로고
    • New Theoretical Methodology for Elucidating the Solution Structure of Peptides from NMR Data. II. Free Energy of Dominant Microstates of Leu-enkephalin and Population-Weighted Average Nuclear Overhauser Effects Intensities
    • E. Meirovitch and H. Meirovitch, Biopolymers, 38, 69 (1996). New Theoretical Methodology for Elucidating the Solution Structure of Peptides from NMR Data. II. Free Energy of Dominant Microstates of Leu-enkephalin and Population-Weighted Average Nuclear Overhauser Effects Intensities.
    • (1996) Biopolymers , vol.38 , pp. 69
    • Meirovitch, E.1    Meirovitch, H.2
  • 92
    • 0030102542 scopus 로고    scopus 로고
    • New Theoretical Methodology for Elucidating the Solution Structure of Peptides from NMR Data. III. Solvation Effects
    • H. Meirovitch and E. Meirovitch, J. Phys. Chem., 100, 5123 (1996). New Theoretical Methodology for Elucidating the Solution Structure of Peptides from NMR Data. III. Solvation Effects.
    • (1996) J. Phys. Chem. , vol.100 , pp. 5123
    • Meirovitch, H.1    Meirovitch, E.2
  • 93
    • 0042091834 scopus 로고
    • Packing Structures and Transitions in Liquids and Solids
    • F. H. Stillinger and T. A. Weber, Science, 225, 983 (1984). Packing Structures and Transitions in Liquids and Solids.
    • (1984) Science , vol.225 , pp. 983
    • Stillinger, F.H.1    Weber, T.A.2
  • 94
    • 0023140044 scopus 로고
    • Multiple Conformational States of Proteins: A Molecular Dynamics Analysis of Myoglobin
    • R. Elber and M. Karplus, Science, 235, 318 (1987). Multiple Conformational States of Proteins: A Molecular Dynamics Analysis of Myoglobin.
    • (1987) Science , vol.235 , pp. 318
    • Elber, R.1    Karplus, M.2
  • 95
    • 0000717285 scopus 로고
    • Minimization of Polypeptide Energy. V. Theoretical Aspects
    • K. D. Gibson and H. A. Scheraga, J. Physiol. Chem. Phys., 1, 109 (1969). Minimization of Polypeptide Energy. V. Theoretical Aspects.
    • (1969) J. Physiol. Chem. Phys. , vol.1 , pp. 109
    • Gibson, K.D.1    Scheraga, H.A.2
  • 96
    • 18344362394 scopus 로고
    • On the Use of Classical Statistical Mechanics in the Treatment of Polymer Chain Conformation
    • N. Gō and H. A. Scheraga, Macromolecules, 9, 535 (1976). On the Use of Classical Statistical Mechanics in the Treatment of Polymer Chain Conformation.
    • (1976) Macromolecules , vol.9 , pp. 535
    • Go, N.1    Scheraga, H.A.2
  • 97
    • 0028331255 scopus 로고
    • Normal Mode Analysis of Protein Dynamics
    • D. A. Case, Curr. Opin. Struct. Biol. 4, 285 (1994). Normal Mode Analysis of Protein Dynamics.
    • (1994) Curr. Opin. Struct. Biol. , vol.4 , pp. 285
    • Case, D.A.1
  • 98
    • 0014946546 scopus 로고
    • Molecular Theory of the Helix-Coil Transition of Polyamino Acids. II. Numerical Evaluations of s and σ for Polyglycine and Poly-L-alanine in the Absence (for s and σ) and Presence (for σ) of Solvent
    • M. Gō, N. Gō, and H. A. Scheraga, J. Chem. Phys., 52, 2060 (1970). Molecular Theory of the Helix-Coil Transition of Polyamino Acids. II. Numerical Evaluations of s and σ for Polyglycine and Poly-L-alanine in the Absence (for s and σ) and Presence (for σ) of Solvent.
    • (1970) J. Chem. Phys. , vol.52 , pp. 2060
    • Go, M.1    Go, N.2    Scheraga, H.A.3
  • 99
    • 0346756916 scopus 로고
    • Conformational Energy Calculations. Thermodynamic Parameters of the Helix-Coil Transition for Poly(L-lysine) in Aqueous Salt Solution
    • F. T. Hesselink, T. Ooi, and H. A. Scheraga, Macromolecules, 6, 541 (1973). Conformational Energy Calculations. Thermodynamic Parameters of the Helix-Coil Transition for Poly(L-lysine) in Aqueous Salt Solution.
    • (1973) Macromolecules , vol.6 , pp. 541
    • Hesselink, F.T.1    Ooi, T.2    Scheraga, H.A.3
  • 100
    • 0016089450 scopus 로고
    • Molecular Theory of the Helix-Coil Transition of Polyamino Acids. IV. Evaluation and Analysis of s for Poly(L-valine) in the Absence and Presence of Water
    • M. Gō, T. T. Hesselink, N. Gō, and H. A. Scheraga, Macromolecules, 7, 459 (1974). Molecular Theory of the Helix-Coil Transition of Polyamino Acids. IV. Evaluation and Analysis of s for Poly(L-valine) in the Absence and Presence of Water.
    • (1974) Macromolecules , vol.7 , pp. 459
    • Go, M.1    Hesselink, T.T.2    Go, N.3    Scheraga, H.A.4
  • 101
    • 0021508484 scopus 로고
    • Molecular Theory of the Helix-Coil Transition of Polyamino Acids. V. Explanation of the Different Conformational Behavior of Valine, Isoleucine, and Leucine in Aqueous Solution
    • M. Gō and H. A. Scheraga, Biopolymers, 23, 1961 (1984). Molecular Theory of the Helix-Coil Transition of Polyamino Acids. V. Explanation of the Different Conformational Behavior of Valine, Isoleucine, and Leucine in Aqueous Solution.
    • (1984) Biopolymers , vol.23 , pp. 1961
    • Go, M.1    Scheraga, H.A.2
  • 102
    • 0000831441 scopus 로고
    • A Free Energy Based Monte Carlo Minimization Procedure for Macromolecules
    • M. Vásquez, E. Meirovitch, and H. Meirovitch, J. Phys. Chem., 98, 9380 (1994). A Free Energy Based Monte Carlo Minimization Procedure for Macromolecules.
    • (1994) J. Phys. Chem. , vol.98 , pp. 9380
    • Vásquez, M.1    Meirovitch, E.2    Meirovitch, H.3
  • 103
    • 0029272157 scopus 로고
    • New Theoretical Methodology for Elucidating the Solution Structure of Peptides from NMR Data. 1. The Relative Contribution of Low-Energy Microstates to the Partition Function
    • H. Meirovitch, E. Meirovitch, and J. Lee, J. Phys. Chem., 99, 4847 (1995). New Theoretical Methodology for Elucidating the Solution Structure of Peptides from NMR Data. 1. The Relative Contribution of Low-Energy Microstates to the Partition Function.
    • (1995) J. Phys. Chem. , vol.99 , pp. 4847
    • Meirovitch, H.1    Meirovitch, E.2    Lee, J.3
  • 104
    • 0001442134 scopus 로고    scopus 로고
    • Efficiency of Monte Carlo Minimization Procedures and Their Use in the Analysis of NMR Data Obtained from Flexible Peptides
    • H. Meirovitch and E. Meirovitch, J. Comput. Chem., 18, 240 (1997). Efficiency of Monte Carlo Minimization Procedures and Their Use in the Analysis of NMR Data Obtained from Flexible Peptides.
    • (1997) J. Comput. Chem. , vol.18 , pp. 240
    • Meirovitch, H.1    Meirovitch, E.2
  • 105
    • 0026644295 scopus 로고
    • Conformational Analysis of the Highly Potent Constrained Gonadotropin-Releasing Hormone Antagonist. 2. Molecular Dynamics Simulations
    • J. Rizo, S. C. Koerber, R. J. Bienstock, J. Rivier, A. T. Hagler, and L. M. Gierasch, J. Am. Chem. Soc., 114, 2860 (1992). Conformational Analysis of the Highly Potent Constrained Gonadotropin-Releasing Hormone Antagonist. 2. Molecular Dynamics Simulations.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 2860
    • Rizo, J.1    Koerber, S.C.2    Bienstock, R.J.3    Rivier, J.4    Hagler, A.T.5    Gierasch, L.M.6
  • 107
    • 0023769808 scopus 로고
    • Structure and Energetics of Ligand Binding to Proteins: Escherichia coli Dihydrofolate Reductase-Trimethoprim, a Drug-Receptor System
    • P. Dauber-Osguthorpe, V. A. Roberts, D. J. Osguthorpe, J. Wolff, M. Genest, and A. T. Hagler, Proteins, 4, 31 (1988). Structure and Energetics of Ligand Binding to Proteins: Escherichia coli Dihydrofolate Reductase-Trimethoprim, A Drug-Receptor System.
    • (1988) Proteins , vol.4 , pp. 31
    • Dauber-Osguthorpe, P.1    Roberts, V.A.2    Osguthorpe, D.J.3    Wolff, J.4    Genest, M.5    Hagler, A.T.6
  • 108
    • 0022399917 scopus 로고
    • Transition from B to Z DNA: Contribution of Internal Fluctuations to the Configurational Entropy Difference
    • K. K. Irikura, B. Tidor, B. R. Brooks, and M. Karplus, Science, 229, 571 (1985). Transition from B to Z DNA: Contribution of Internal Fluctuations to the Configurational Entropy Difference.
    • (1985) Science , vol.229 , pp. 571
    • Irikura, K.K.1    Tidor, B.2    Brooks, B.R.3    Karplus, M.4
  • 109
    • 0027390460 scopus 로고
    • The Contribution of Cross-Links to Protein Stability: A Normal Mode Analysis of the Configurational Entropy of the Native State
    • B. Tidor and M. Karplus, Proteins, 15, 71 (1993). The Contribution of Cross-Links to Protein Stability: A Normal Mode Analysis of the Configurational Entropy of the Native State.
    • (1993) Proteins , vol.15 , pp. 71
    • Tidor, B.1    Karplus, M.2
  • 110
    • 0028360307 scopus 로고
    • The Contribution of Vibrational Entropy to Molecular Association. The Dimerization of Insulin
    • B. Tidor and M. Karplus, J. Mol. Biol., 238, 405 (1994). The Contribution of Vibrational Entropy to Molecular Association. The Dimerization of Insulin.
    • (1994) J. Mol. Biol. , vol.238 , pp. 405
    • Tidor, B.1    Karplus, M.2
  • 112
    • 0016273821 scopus 로고
    • Classical Statistical Mechanics of Constraints: A Theorem and Application to Polymers
    • M. Fixman, Proc. Natl. Acad. Sci. U.S.A., 71, 3050 (1974). Classical Statistical Mechanics of Constraints: A Theorem and Application to Polymers.
    • (1974) Proc. Natl. Acad. Sci. U.S.A. , vol.71 , pp. 3050
    • Fixman, M.1
  • 113
    • 0000961995 scopus 로고
    • Evaluation of Configurational Entropy for Proteins: Application to Molecular Dynamics Simulations of α-Helix
    • R. M. Levy, M. Karplus, J. Kushick, and D. Perahia, Macromolecules, 17, 1370 (1984). Evaluation of Configurational Entropy for Proteins: Application to Molecular Dynamics Simulations of α-Helix.
    • (1984) Macromolecules , vol.17 , pp. 1370
    • Levy, R.M.1    Karplus, M.2    Kushick, J.3    Perahia, D.4
  • 114
    • 0011146589 scopus 로고
    • Corrections to the Quasiharmonic Approximation for Evaluating Molecular Entropies
    • O. L. Rojas, R. M. Levy, and A. Szabo, J. Chem. Phys., 85, 1037 (1986). Corrections to the Quasiharmonic Approximation for Evaluating Molecular Entropies.
    • (1986) J. Chem. Phys. , vol.85 , pp. 1037
    • Rojas, O.L.1    Levy, R.M.2    Szabo, A.3
  • 115
    • 0000980795 scopus 로고
    • Quasi-Harmonic Method for Calculating Vibrational Spectra from Classical Simulations on Multidimensional Anharmonic Potential Surfaces
    • R. M. Levy, O. L. Rojas, and R. A. Friesner, J. Phys. Chem., 88, 4233 (1984). Quasi-Harmonic Method for Calculating Vibrational Spectra from Classical Simulations on Multidimensional Anharmonic Potential Surfaces.
    • (1984) J. Phys. Chem. , vol.88 , pp. 4233
    • Levy, R.M.1    Rojas, O.L.2    Friesner, R.A.3
  • 116
    • 0001064378 scopus 로고
    • Free Energy Determination of Polypeptide Conformations Generated by Molecular Dynamics
    • A. DiNola, H. J. C. Berendsen, and O. Edholm, Macromolecules, 17, 2044 (1984). Free Energy Determination of Polypeptide Conformations Generated by Molecular Dynamics.
    • (1984) Macromolecules , vol.17 , pp. 2044
    • DiNola, A.1    Berendsen, H.J.C.2    Edholm, O.3
  • 117
    • 0001766043 scopus 로고
    • An Optimized Harmonic Reference System for the Evaluation of Discretized Path Integrals
    • R. A. Friesner and R. M. Levy, J. Chem. Phys., 80, 4488 (1984). An Optimized Harmonic Reference System for the Evaluation of Discretized Path Integrals.
    • (1984) J. Chem. Phys. , vol.80 , pp. 4488
    • Friesner, R.A.1    Levy, R.M.2
  • 118
    • 84946455932 scopus 로고
    • Entropy Estimation from Simulations of Non-Diffusive Systems
    • O. Edholm and H. J. C. Berendsen, Mol. Phys., 51, 1011 (1984). Entropy Estimation from Simulations of Non-Diffusive Systems.
    • (1984) Mol. Phys. , vol.51 , pp. 1011
    • Edholm, O.1    Berendsen, H.J.C.2
  • 119
    • 0004919929 scopus 로고
    • Monte Carlo Study of Entropy for Face-Centered-Cubic Ising Antiferromagnet
    • K. Binder, Z. Phys. B, 45, 61 (1981). Monte Carlo Study of Entropy for Face-Centered-Cubic Ising Antiferromagnet.
    • (1981) Z. Phys. B , vol.45 , pp. 61
    • Binder, K.1
  • 120
    • 0028486119 scopus 로고
    • Concentrated, Semiflexible Lattice Chain Systems and Criticism of the Scanning Technique
    • M. L. Mansfield, Macromolecules, 27, 4699 (1994). Concentrated, Semiflexible Lattice Chain Systems and Criticism of the Scanning Technique.
    • (1994) Macromolecules , vol.27 , pp. 4699
    • Mansfield, M.L.1
  • 121
    • 0346126176 scopus 로고    scopus 로고
    • A Response to Mansfield's Paper "Concentrated, Semiflexible Lattice Chain Systems and Criticism of the Scanning Method."
    • H. Meirovitch, Macromolecules, 29, 475 (1996). A Response to Mansfield's Paper "Concentrated, Semiflexible Lattice Chain Systems and Criticism of the Scanning Method."
    • (1996) Macromolecules , vol.29 , pp. 475
    • Meirovitch, H.1
  • 122
    • 0001838445 scopus 로고
    • Calculation of Thermodynamic Properties of Liquid Argon from Lennard-Jones Parameters by Monte Carlo Method
    • I. R. McDonald and K. Singer, Discuss. Faraday Soc., 43, 40 (1967). Calculation of Thermodynamic Properties of Liquid Argon from Lennard-Jones Parameters by Monte Carlo Method.
    • (1967) Discuss. Faraday Soc. , vol.43 , pp. 40
    • McDonald, I.R.1    Singer, K.2
  • 123
    • 0346756913 scopus 로고
    • Monte Carlo Recursion Evaluation of Free Energy
    • Z. Li and H. A. Scheraga, J. Phys. Chem., 92, 2633 (1988). Monte Carlo Recursion Evaluation of Free Energy.
    • (1988) J. Phys. Chem. , vol.92 , pp. 2633
    • Li, Z.1    Scheraga, H.A.2
  • 124
    • 0011887786 scopus 로고
    • Calculation of the Free Energy of Liquid Water by the Monte Carlo Recursion Method
    • Z. Li and H. A. Scheraga, Chem. Phys. Lett., 154, 516 (1989). Calculation of the Free Energy of Liquid Water by the Monte Carlo Recursion Method.
    • (1989) Chem. Phys. Lett. , vol.154 , pp. 516
    • Li, Z.1    Scheraga, H.A.2
  • 125
    • 0000968363 scopus 로고
    • Phase Transition in the Lennard-Jones System. II. High Temperature Limit
    • J.-P. Hansen, Phys. Rev. A, 2, 221 (1970). Phase Transition in the Lennard-Jones System. II. High Temperature Limit.
    • (1970) Phys. Rev. A , vol.2 , pp. 221
    • Hansen, J.-P.1
  • 126
    • 0000081005 scopus 로고
    • Perturbation Theory and Equation of State for Fluids
    • D. Levesque and L. Verlet, Phys. Rev., 182, 307 (1969). Perturbation Theory and Equation of State for Fluids.
    • (1969) Phys. Rev. , vol.182 , pp. 307
    • Levesque, D.1    Verlet, L.2
  • 128
    • 0346126174 scopus 로고
    • The Free Energy of Spheres with Dipoles: Monte Carlo with Multistage Sampling
    • G. N. Patey and J. P. Valleau, Chem. Phys. Lett., 21, 297 (1973). The Free Energy of Spheres with Dipoles: Monte Carlo with Multistage Sampling.
    • (1973) Chem. Phys. Lett. , vol.21 , pp. 297
    • Patey, G.N.1    Valleau, J.P.2
  • 129
    • 0000903604 scopus 로고    scopus 로고
    • Solid-Solid and Liquid-Solid Phase Equilibria for the Restricted Primitive Model
    • B. Smit, K. Esselnik, and D. Frenkel, Mol. Phys., 87, 159 (1996). Solid-Solid and Liquid-Solid Phase Equilibria for the Restricted Primitive Model.
    • (1996) Mol. Phys. , vol.87 , pp. 159
    • Smit, B.1    Esselnik, K.2    Frenkel, D.3
  • 130
    • 0001144878 scopus 로고    scopus 로고
    • The Vapour Pressure of Glassy Crystals of Dimers
    • R. K. Bowles and R. J. Speedy, Mol. Phys., 87, 1349 (1996). The Vapour Pressure of Glassy Crystals of Dimers.
    • (1996) Mol. Phys. , vol.87 , pp. 1349
    • Bowles, R.K.1    Speedy, R.J.2
  • 131
    • 0042124254 scopus 로고    scopus 로고
    • Excess Properties of Dipolar and Non-Polar Fluid Mixtures from NpT Molecular Dynamics Simulations
    • C. Kriebel, A. Müller, J. Winkelmann, and J. Fischer, Mol. Phys., 87, 151 (1996). Excess Properties of Dipolar and Non-Polar Fluid Mixtures from NpT Molecular Dynamics Simulations.
    • (1996) Mol. Phys. , vol.87 , pp. 151
    • Kriebel, C.1    Müller, A.2    Winkelmann, J.3    Fischer, J.4
  • 132
    • 36749109235 scopus 로고
    • The Surface Tension of Water: A Monte Carlo Calculation Using an Umbrella Sampling Algorithm
    • H. L. Scott and C. Y. Lee, J. Chem. Phys., 73, 4591 (1980). The Surface Tension of Water: A Monte Carlo Calculation Using an Umbrella Sampling Algorithm.
    • (1980) J. Chem. Phys. , vol.73 , pp. 4591
    • Scott, H.L.1    Lee, C.Y.2
  • 133
    • 0000172525 scopus 로고
    • Excess Free Energy of Different Water Models Computed by Monte Carlo Methods
    • M. Mezei, Mol. Phys., 47, 1307 (1982). Excess Free Energy of Different Water Models Computed by Monte Carlo Methods.
    • (1982) Mol. Phys. , vol.47 , pp. 1307
    • Mezei, M.1
  • 134
    • 0000292706 scopus 로고
    • Monte Carlo Calculation of the Free Energy Difference between Hard and Soft Core Diatomic Liquids
    • G. Jacucci and N. Quirke, Mol. Phys., 40, 1005 (1980). Monte Carlo Calculation of the Free Energy Difference Between Hard and Soft Core Diatomic Liquids.
    • (1980) Mol. Phys. , vol.40 , pp. 1005
    • Jacucci, G.1    Quirke, N.2
  • 135
    • 0000891929 scopus 로고
    • Energy Difference Functions in Monte Carlo Simulations. Application to (1) The Calculation of the Free Energy of Liquid Nitrogen, (2) The Fluctuation of Monte Carlo Averages
    • N. Quirke and G. Jacucci, Mol. Phys., 45, 823 (1982). Energy Difference Functions in Monte Carlo Simulations. Application to (1) The Calculation of the Free Energy of Liquid Nitrogen, (2) The Fluctuation of Monte Carlo Averages.
    • (1982) Mol. Phys. , vol.45 , pp. 823
    • Quirke, N.1    Jacucci, G.2
  • 136
    • 36749108636 scopus 로고
    • A Monte Carlo Simulation of the Hydrophobic Interaction
    • C. Pangali, M. Rao, and B. J. Berne, J. Chem. Phys., 71, 2975 (1979). A Monte Carlo Simulation of the Hydrophobic Interaction.
    • (1979) J. Chem. Phys. , vol.71 , pp. 2975
    • Pangali, C.1    Rao, M.2    Berne, B.J.3
  • 138
    • 36549092427 scopus 로고
    • A Monte Carlo Method for Determining Free-Energy Differences and Transition State Theory Rate Constants
    • A. F. Voter, J. Chem. Phys., 82, 1890 (1985). A Monte Carlo Method for Determining Free-Energy Differences and Transition State Theory Rate Constants.
    • (1985) J. Chem. Phys. , vol.82 , pp. 1890
    • Voter, A.F.1
  • 139
    • 0001087856 scopus 로고
    • Calculation of Free Energy Surfaces Using the Methods of Thermodynamic Perturbation Theory
    • D. J. Tobias and C. L. Brooks III, Chem. Phys. Lett., 142, 472 (1987). Calculation of Free Energy Surfaces Using the Methods of Thermodynamic Perturbation Theory.
    • (1987) Chem. Phys. Lett. , vol.142 , pp. 472
    • Tobias, D.J.1    Brooks C.L. III2
  • 140
    • 0001626776 scopus 로고
    • Adaptive Umbrella Sampling: Self-Consistent Determination of the Non-Boltzmann Bias
    • M. Mezei, J. Comput. Phys., 68, 237 (1987). Adaptive Umbrella Sampling: Self-Consistent Determination of the Non-Boltzmann Bias.
    • (1987) J. Comput. Phys. , vol.68 , pp. 237
    • Mezei, M.1
  • 141
    • 0000087970 scopus 로고
    • An Adaptive Umbrella Sampling Procedure in Conformational Analysis Using Molecular Dynamics and Its Application to Glycol
    • (a) R. W. W. Hooft, B. P. van Eijck, and J. Kroon, J. Chem. Phys., 97, 6690 (1992). An Adaptive Umbrella Sampling Procedure in Conformational Analysis Using Molecular Dynamics and Its Application to Glycol.
    • (1992) J. Chem. Phys. , vol.97 , pp. 6690
    • Hooft, R.W.W.1    Van Eijck, B.P.2    Kroon, J.3
  • 142
    • 0000430018 scopus 로고
    • Use of Molecular Dynamics Methods in Conformational Analysis. Glycol. A Model Study
    • (b) R. W. W. Hooft, B. P. van Eijck, and J. Kroon, J. Chem. Phys., 97, 3639 (1992). Use of Molecular Dynamics Methods in Conformational Analysis. Glycol. A Model Study.
    • (1992) J. Chem. Phys. , vol.97 , pp. 3639
    • Hooft, R.W.W.1    Van Eijck, B.P.2    Kroon, J.3
  • 143
    • 11744353229 scopus 로고
    • The Computation of a Potential of Mean Force: Choice of the Biasing Potential in the Umbrella Sampling Technique
    • T. C. Beutler and W. F. van Gunsteren, J. Chem. Phys., 100, 1492 (1994). The Computation of a Potential of Mean Force: Choice of the Biasing Potential in the Umbrella Sampling Technique.
    • (1994) J. Chem. Phys. , vol.100 , pp. 1492
    • Beutler, T.C.1    Van Gunsteren, W.F.2
  • 144
    • 4243327836 scopus 로고
    • Umbrella Sampling Along Linear Combinations of Generalized Coordinates. Theory and Application to a Glycine Dipeptide
    • T. C. Beutler and W. F. van Gunsteren, Chem. Phys. Lett., 237, 308 (1995). Umbrella Sampling Along Linear Combinations of Generalized Coordinates. Theory and Application to a Glycine Dipeptide.
    • (1995) Chem. Phys. Lett. , vol.237 , pp. 308
    • Beutler, T.C.1    Van Gunsteren, W.F.2
  • 145
    • 0000071835 scopus 로고    scopus 로고
    • Motion and Conformation of Side Chains in Peptides. A Comparison of 2D Umbrella-Sampling Molecular Dynamics and NMR Results
    • T. C. Beutler, T. Bremi, R. R. Ernst, and W. F. van Gunsteren, J. Phys. Chem., 100, 2637 (1996). Motion and Conformation of Side Chains in Peptides. A Comparison of 2D Umbrella-Sampling Molecular Dynamics and NMR Results.
    • (1996) J. Phys. Chem. , vol.100 , pp. 2637
    • Beutler, T.C.1    Bremi, T.2    Ernst, R.R.3    Van Gunsteren, W.F.4
  • 146
    • 33845377761 scopus 로고
    • Monte Carlo Determination of the Free Energy and Internal Energy of Hydration for the Ala Dipeptide at 25°C
    • M. Mezei, P. K. Mehrotra, and D. L. Beveridge, J. Am. Chem. Soc., 107, 2239 (1985). Monte Carlo Determination of the Free Energy and Internal Energy of Hydration for the Ala Dipeptide at 25°C.
    • (1985) J. Am. Chem. Soc. , vol.107 , pp. 2239
    • Mezei, M.1    Mehrotra, P.K.2    Beveridge, D.L.3
  • 147
    • 84986519238 scopus 로고
    • The Weighted Histogram Analysis Method for Free Energy Calculations on Biomolecules. I. The Method
    • (a) S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg, J. Comput. Chem., 13, 1011 (1992). The Weighted Histogram Analysis Method for Free Energy Calculations on Biomolecules. I. The Method.
    • (1992) J. Comput. Chem. , vol.13 , pp. 1011
    • Kumar, S.1    Bouzida, D.2    Swendsen, R.H.3    Kollman, P.A.4    Rosenberg, J.M.5
  • 148
    • 0000764091 scopus 로고
    • Constant-Temperature Free Energy Surfaces for Physical and Chemical Processes
    • (b) E. M. Boczko and C. L. Brooks III, J. Phys. Chem., 97, 4509 (1993). Constant-Temperature Free Energy Surfaces for Physical and Chemical Processes.
    • (1993) J. Phys. Chem. , vol.97 , pp. 4509
    • Boczko, E.M.1    Brooks C.L. III2
  • 149
    • 0001186767 scopus 로고    scopus 로고
    • Method for Free Energy Calculations Using Iterative Techniques
    • (c) S. Kumar, P. W. Payne, and M. Vásquez J. Comput. Chem., 17, 1269 (1996). Method for Free Energy Calculations Using Iterative Techniques.
    • (1996) J. Comput. Chem. , vol.17 , pp. 1269
    • Kumar, S.1    Payne, P.W.2    Vásquez, M.3
  • 150
    • 0029151245 scopus 로고
    • First-Principles Calculation of the Folding Free Energy of a Three-Helix Bundle Protein
    • (d) E. M. Boczko and C. L. Brooks III, Science, 269, 393 (1995). First-Principles Calculation of the Folding Free Energy of a Three-Helix Bundle Protein.
    • (1995) Science , vol.269 , pp. 393
    • Boczko, E.M.1    Brooks C.L. III2
  • 151
    • 0000307978 scopus 로고
    • Sodium Chloride Ion Pair Interaction in Water: Computer Simulation
    • M. Berkowitz, O. A. Karim, J. A. McCammon, and P. J. Rossky, Chem. Phys. Lett., 105, 577 (1984). Sodium Chloride Ion Pair Interaction in Water: Computer Simulation.
    • (1984) Chem. Phys. Lett. , vol.105 , pp. 577
    • Berkowitz, M.1    Karim, O.A.2    McCammon, J.A.3    Rossky, P.J.4
  • 152
    • 0001362721 scopus 로고
    • Solvation Structure of Sodium Chloride Ion Pair in Water
    • A. C. Belch, M. Berkowitz, and J. A. McCammon, J. Am. Chem. Soc., 108, 1755 (1986). Solvation Structure of Sodium Chloride Ion Pair in Water.
    • (1986) J. Am. Chem. Soc. , vol.108 , pp. 1755
    • Belch, A.C.1    Berkowitz, M.2    McCammon, J.A.3
  • 153
    • 26644438864 scopus 로고
    • Potential of Mean Force by Constrained Molecular Dynamics: A Sodium Chloride Ion-Pair in Water
    • E. Guàrdia, R. Rey, and J. A. Padró, Chem. Phys., 155, 187 (1991). Potential of Mean Force by Constrained Molecular Dynamics: A Sodium Chloride Ion-Pair in Water.
    • (1991) Chem. Phys. , vol.155 , pp. 187
    • Guàrdia, E.1    Rey, R.2    Padró, J.A.3
  • 154
    • 0011108916 scopus 로고
    • Computer Simulations of NaCl Association in Polarizable Water
    • D. E. Smith and L. X. Dang, J. Chem. Phys., 100, 3757 (1994). Computer Simulations of NaCl Association in Polarizable Water.
    • (1994) J. Chem. Phys. , vol.100 , pp. 3757
    • Smith, D.E.1    Dang, L.X.2
  • 155
    • 0000257331 scopus 로고
    • - Ion Pair in Supercritical Water
    • - Ion Pair in Supercritical Water.
    • (1994) J. Phys. Chem. , vol.98 , pp. 6049
    • Gao, J.1
  • 156
    • 36449003242 scopus 로고
    • The Potentials of Mean Force of Sodium Chloride and Sodium Dimethylphosphate in Water: An Application of Adaptive Umbrella Sampling
    • R. A. Friedman and M. Mezei, J. Chem. Phys., 102, 419 (1995). The Potentials of Mean Force of Sodium Chloride and Sodium Dimethylphosphate in Water: An Application of Adaptive Umbrella Sampling.
    • (1995) J. Chem. Phys. , vol.102 , pp. 419
    • Friedman, R.A.1    Mezei, M.2
  • 157
    • 0001340742 scopus 로고
    • The Effect of Water Models on the Interaction of the Sodium Chloride Ion Pair in Water: Molecular Dynamics Simulations
    • L. X. Dang, J. E. Rice, and P. A. Kollman, J. Chem. Phys., 93, 7528 (1990). The Effect of Water Models on the Interaction of the Sodium Chloride Ion Pair in Water: Molecular Dynamics Simulations.
    • (1990) J. Chem. Phys. , vol.93 , pp. 7528
    • Dang, L.X.1    Rice, J.E.2    Kollman, P.A.3
  • 158
    • 0000939663 scopus 로고
    • Potential of Mean Force by Thermodynamic Integration: Molecular Dynamics Simulation of Decomplexation
    • J. V. Eerden, W. J. Briels, S. Harkema, and D. Feil, Chem. Phys. Lett., 164, 370 (1989). Potential of Mean Force by Thermodynamic Integration: Molecular Dynamics Simulation of Decomplexation.
    • (1989) Chem. Phys. Lett. , vol.164 , pp. 370
    • Eerden, J.V.1    Briels, W.J.2    Harkema, S.3    Feil, D.4
  • 159
    • 0001453671 scopus 로고    scopus 로고
    • Use of the Grand Canonical Ensemble in Potential of Mean Force Calculations
    • H. Resat, M. Mezei, and J. A. McCammon, J. Phys. Chem., 100, 1426 (1996). Use of the Grand Canonical Ensemble in Potential of Mean Force Calculations.
    • (1996) J. Phys. Chem. , vol.100 , pp. 1426
    • Resat, H.1    Mezei, M.2    McCammon, J.A.3
  • 162
    • 0000315520 scopus 로고
    • Free Energies of Association for the Sodium-Dimethyl Phosphate Ion Pair in Aqueous Solution
    • S. E. Huston and P. J. Rossky, J. Phys. Chem., 93, 7888 (1989). Free Energies of Association for the Sodium-Dimethyl Phosphate Ion Pair in Aqueous Solution.
    • (1989) J. Phys. Chem. , vol.93 , pp. 7888
    • Huston, S.E.1    Rossky, P.J.2
  • 163
    • 0011774940 scopus 로고
    • Potential of Mean Force for a Sodium Dimethyl Phosphate Ion Pair in Aqueous Solution: A Further Test of the Extended RISM Theory
    • S.-w. Chen and P. J. Rossky, J. Phys. Chem., 97, 6078 (1993). Potential of Mean Force for a Sodium Dimethyl Phosphate Ion Pair in Aqueous Solution: A Further Test of the Extended RISM Theory.
    • (1993) J. Phys. Chem. , vol.97 , pp. 6078
    • Chen, S.-W.1    Rossky, P.J.2
  • 164
    • 36549099461 scopus 로고
    • Molecular Dynamics with Internal Coordinate Constraints
    • D. J. Tobias and C. L. Brooks III, J. Chem. Phys., 89, 5115 (1988). Molecular Dynamics with Internal Coordinate Constraints.
    • (1988) J. Chem. Phys. , vol.89 , pp. 5115
    • Tobias, D.J.1    Brooks C.L. III2
  • 165
    • 0031021793 scopus 로고    scopus 로고
    • The Sensitivity of Conformational Free Energies of the Alanine Dipeptide to Atomic Site Charges
    • H. Resat, P. V. Maye, and M. Mezei, Biopolymers, 41, 73 (1997). The Sensitivity of Conformational Free Energies of the Alanine Dipeptide to Atomic Site Charges.
    • (1997) Biopolymers , vol.41 , pp. 73
    • Resat, H.1    Maye, P.V.2    Mezei, M.3
  • 166
    • 0000435390 scopus 로고    scopus 로고
    • Comparison of Continuum and Explicit Models of Solvation: Potentials of Mean Force for Alanine Dipeptide
    • T. J. Marrone, M. K. Gilson, and J. A. McCammon, J. Phys. Chem., 100, 1439 (1996). Comparison of Continuum and Explicit Models of Solvation: Potentials of Mean Force for Alanine Dipeptide.
    • (1996) J. Phys. Chem. , vol.100 , pp. 1439
    • Marrone, T.J.1    Gilson, M.K.2    McCammon, J.A.3
  • 167
    • 0028397360 scopus 로고
    • Conformational Transitions of a Dipeptide in Water: Effects of Imposed Pathways Using Umbrella Sampling Techniques
    • F. Fraternali and W. F. van Gunsteren, Biopolymers, 34, 347 (1994). Conformational Transitions of a Dipeptide in Water: Effects of Imposed Pathways Using Umbrella Sampling Techniques.
    • (1994) Biopolymers , vol.34 , pp. 347
    • Fraternali, F.1    Van Gunsteren, W.F.2
  • 168
    • 36549099690 scopus 로고
    • The Thermodynamics of Solvophobic Effects: A Molecular-Dynamics Study of n-Butane in Carbon Tetrachloride and Water
    • D. J. Tobias and C. L. Brooks III, J. Chem. Phys., 92, 2582 (1990). The Thermodynamics of Solvophobic Effects: A Molecular-Dynamics Study of n-Butane in Carbon Tetrachloride and Water.
    • (1990) J. Chem. Phys. , vol.92 , pp. 2582
    • Tobias, D.J.1    Brooks C.L. III2
  • 169
    • 0000683623 scopus 로고
    • Comparison of Free Energy Surfaces for Extended-Atom and All-Atom Models of n-Butane
    • C. D. Bell and S. C. Harvey, J. Phys. Chem., 90, 6595 (1986). Comparison of Free Energy Surfaces for Extended-Atom and All-Atom Models of n-Butane.
    • (1986) J. Phys. Chem. , vol.90 , pp. 6595
    • Bell, C.D.1    Harvey, S.C.2
  • 170
    • 0039952187 scopus 로고
    • Use of Statistical Perturbation Theory for Computing Solvent Effects in Molecular Conformation. Butane in Water
    • W. L. Jorgensen and J. K. Buckner, J. Phys. Chem., 91, 6083 (1987). Use of Statistical Perturbation Theory for Computing Solvent Effects in Molecular Conformation. Butane in Water.
    • (1987) J. Phys. Chem. , vol.91 , pp. 6083
    • Jorgensen, W.L.1    Buckner, J.K.2
  • 171
    • 0025767212 scopus 로고
    • Thermodynamics and Mechanism of α Helix Initiation in Alanine and Valine Peptides
    • D. J. Tobias and C. L. Brooks III, Biochemistry, 30, 6059 (1991). Thermodynamics and Mechanism of α Helix Initiation in Alanine and Valine Peptides.
    • (1991) Biochemistry , vol.30 , pp. 6059
    • Tobias, D.J.1    Brooks C.L. III2
  • 172
    • 0025679019 scopus 로고
    • Reverse Turns in Blocked Dipeptides Are Intrinsically Unstable in Water
    • D. J. Tobias, S. F. Sneddon, and C. L. Brooks III, J. Mol. Biol., 216, 783 (1990). Reverse Turns in Blocked Dipeptides Are Intrinsically Unstable in Water.
    • (1990) J. Mol. Biol. , vol.216 , pp. 783
    • Tobias, D.J.1    Sneddon, S.F.2    Brooks C.L. III3
  • 173
    • 0025882246 scopus 로고
    • Ion Transport in a Model Gramicidin Channel Structure and Thermodynamics
    • B. Roux and M. Karplus, Biophys. J., 59, 961 (1991). Ion Transport in a Model Gramicidin Channel Structure and Thermodynamics.
    • (1991) Biophys. J. , vol.59 , pp. 961
    • Roux, B.1    Karplus, M.2
  • 174
    • 0025327526 scopus 로고
    • Molecular Dynamics Simulation Study of the Free Energy of Association of 9-Methyladenine and 1-Methylthymine Bases in Water
    • L. X. Dang and P. A. Kollman, J. Am Chem. Soc., 112, 503 (1990). Molecular Dynamics Simulation Study of the Free Energy of Association of 9-Methyladenine and 1-Methylthymine Bases in Water.
    • (1990) J. Am Chem. Soc. , vol.112 , pp. 503
    • Dang, L.X.1    Kollman, P.A.2
  • 175
    • 0007836334 scopus 로고
    • Dynamics of Reactions in Polar Solvents. Semi-classical Trajectory Studies of Electron-Transfer and Proton-Transfer Reactions
    • A. Warshel, J. Phys. Chem., 86, 2218 (1982). Dynamics of Reactions in Polar Solvents. Semi-classical Trajectory Studies of Electron-Transfer and Proton-Transfer Reactions.
    • (1982) J. Phys. Chem. , vol.86 , pp. 2218
    • Warshel, A.1
  • 176
    • 0009545384 scopus 로고
    • Simulating the Energetics and Dynamics of Enzymatic Reactions
    • Working Group on Specificity in Biological Interactions, C. Chagas and B. Pullman, Eds.
    • A. Warshel, Working Group on Specificity in Biological Interactions, C. Chagas and B. Pullman, Eds., Pontificiae Academiae Scientiarum Scripta Varia, 55, 59 (1983). Simulating the Energetics and Dynamics of Enzymatic Reactions.
    • (1983) Pontificiae Academiae Scientiarum Scripta Varia , vol.55 , pp. 59
    • Warshel, A.1
  • 178
    • 0024278562 scopus 로고
    • Evaluation of Catalytic Free Energies in Genetically Modified Proteins
    • (b) A. Warshel, F. Sussman, and J.-K. Hwang, J. Mol. Biol., 201, 139 (1988). Evaluation of Catalytic Free Energies in Genetically Modified Proteins.
    • (1988) J. Mol. Biol. , vol.201 , pp. 139
    • Warshel, A.1    Sussman, F.2    Hwang, J.-K.3
  • 179
    • 0000344271 scopus 로고
    • Free-Energy Cost of Bending n-Dodecane in Aqueous Solution. Influence of the Hydrophobic Effect and Solvent Exposed Area
    • A. Wallqvist and D. G. Covell, J. Phys. Chem., 99, 13118 (1995). Free-Energy Cost of Bending n-Dodecane in Aqueous Solution. Influence of the Hydrophobic Effect and Solvent Exposed Area.
    • (1995) J. Phys. Chem. , vol.99 , pp. 13118
    • Wallqvist, A.1    Covell, D.G.2
  • 181
    • 36849108317 scopus 로고
    • Perturbation Theory and Equation of State for Fluids: The Square-Well Potential
    • J. A. Barker and D. Henderson, J. Chem. Phys., 47, 2856 (1967). Perturbation Theory and Equation of State for Fluids: The Square-Well Potential.
    • (1967) J. Chem. Phys. , vol.47 , pp. 2856
    • Barker, J.A.1    Henderson, D.2
  • 182
    • 34250318301 scopus 로고
    • Perturbation Theory and Equation of State for Fluids. II. A Successful Theory of Liquids
    • J. A. Barker and D. Henderson, J. Chem. Phys., 47, 4714 (1967). Perturbation Theory and Equation of State for Fluids. II. A Successful Theory of Liquids.
    • (1967) J. Chem. Phys. , vol.47 , pp. 4714
    • Barker, J.A.1    Henderson, D.2
  • 183
    • 0004967772 scopus 로고
    • A Monte Carlo Study of Water Clusters
    • M. R. Mruzik, Chem. Phys. Lett., 48, 171 (1977). A Monte Carlo Study of Water Clusters.
    • (1977) Chem. Phys. Lett. , vol.48 , pp. 171
    • Mruzik, M.R.1
  • 184
    • 33947094574 scopus 로고
    • Ab Initio Calculation of the Free Energy of Water
    • M. Mezei, S. Swaminathan, and D. L. Beveridge, J. Am Chem. Soc., 100, 3255 (1978). Ab Initio Calculation of the Free Energy of Water.
    • (1978) J. Am Chem. Soc. , vol.100 , pp. 3255
    • Mezei, M.1    Swaminathan, S.2    Beveridge, D.L.3
  • 186
    • 0345514077 scopus 로고
    • Monte Carlo Free Energy Calculations on Dilute Solutions in the Isothermal-Isobaric Ensemble
    • J. C. Owicki and H. A. Scheraga, J. Phys. Chem., 82, 1257 (1978). Monte Carlo Free Energy Calculations on Dilute Solutions in the Isothermal-Isobaric Ensemble.
    • (1978) J. Phys. Chem. , vol.82 , pp. 1257
    • Owicki, J.C.1    Scheraga, H.A.2
  • 187
    • 0344227487 scopus 로고
    • Thermodynamics of Cavity Formation in Water, a Molecular Dynamics Study
    • J. P. M. Postma, H. J. C. Berendsen, and J. R. Haak, Faraday Symp. Chem. Soc., 17, 55 (1982). Thermodynamics of Cavity Formation in Water, a Molecular Dynamics Study.
    • (1982) Faraday Symp. Chem. Soc. , vol.17 , pp. 55
    • Postma, J.P.M.1    Berendsen, H.J.C.2    Haak, J.R.3
  • 188
    • 0019889036 scopus 로고
    • a, Proton Transfer Reactions, and General Acid Catalysis Reactions in Enzymes
    • a, Proton Transfer Reactions, and General Acid Catalysis Reactions in Enzymes.
    • (1981) Biochemistry , vol.20 , pp. 3167
    • Warshel, A.1
  • 189
    • 0021582448 scopus 로고
    • Ligand-Receptor Interactions
    • B. L. Tembe and J. A. McCammon, Comput. Chem., 8, 281 (1984). Ligand-Receptor Interactions.
    • (1984) Comput. Chem. , vol.8 , pp. 281
    • Tembe, B.L.1    McCammon, J.A.2
  • 190
    • 0004504539 scopus 로고
    • Monte Carlo Simulation of Differences in Free Energies of Hydration
    • W. L. Jorgensen and C. Ravimohan, J. Chem. Phys., 83, 3050 (1985). Monte Carlo Simulation of Differences in Free Energies of Hydration.
    • (1985) J. Chem. Phys. , vol.83 , pp. 3050
    • Jorgensen, W.L.1    Ravimohan, C.2
  • 191
    • 33845377546 scopus 로고
    • Hydration of Chloride and Bromide Anions. Determination of Relative Free Energy by Computer Simulation
    • T. P. Lybrand, I. Gosh, and J. A. McCammon, J. Am. Chem. Soc., 107, 7793 (1985). Hydration of Chloride and Bromide Anions. Determination of Relative Free Energy by Computer Simulation.
    • (1985) J. Am. Chem. Soc. , vol.107 , pp. 7793
    • Lybrand, T.P.1    Gosh, I.2    McCammon, J.A.3
  • 192
    • 0022666945 scopus 로고
    • Theoretical Calculation of Relative Binding Affinity in Host-Guest Systems
    • T. P. Lybrand, J. A. McCammon, and G. Wipff, Proc. Natl. Acad. Sci. U.S.A., 83, 833 (1986). Theoretical Calculation of Relative Binding Affinity in Host-Guest Systems.
    • (1986) Proc. Natl. Acad. Sci. U.S.A. , vol.83 , pp. 833
    • Lybrand, T.P.1    McCammon, J.A.2    Wipff, G.3
  • 193
    • 0001051042 scopus 로고
    • Thermodynamics of Ionic Solvation: Monte Carlo Simulations of Aqueous Chloride and Bromide Ions
    • C. L. Brooks III, J. Phys. Chem., 90, 6680 (1986). Thermodynamics of Ionic Solvation: Monte Carlo Simulations of Aqueous Chloride and Bromide Ions.
    • (1986) J. Phys. Chem. , vol.90 , pp. 6680
    • Brooks C.L. III1
  • 194
    • 0023346161 scopus 로고
    • Free Energy Calculations by Computer Simulation
    • P. A. Bash, U. C. Singh, R. Langridge, and P. A. Kollman, Science, 236, 564 (1987). Free Energy Calculations by Computer Simulation.
    • (1987) Science , vol.236 , pp. 564
    • Bash, P.A.1    Singh, U.C.2    Langridge, R.3    Kollman, P.A.4
  • 196
    • 0001486087 scopus 로고
    • Dynamics and Design of Enzymes and Inhibitors
    • C. F. Wong and J. A. McCammon, J. Am. Chem. Soc., 108, 3830 (1986). Dynamics and Design of Enzymes and Inhibitors.
    • (1986) J. Am. Chem. Soc. , vol.108 , pp. 3830
    • Wong, C.F.1    McCammon, J.A.2
  • 197
    • 85005687495 scopus 로고
    • The Free Energy of Xenon Binding to Myoglobin from Molecular Dynamics Simulation
    • J. Hermans and S. Shankar, Isr. J. Chem., 27, 225 (1986). The Free Energy of Xenon Binding to Myoglobin from Molecular Dynamics Simulation.
    • (1986) Isr. J. Chem. , vol.27 , pp. 225
    • Hermans, J.1    Shankar, S.2
  • 198
    • 0344260608 scopus 로고
    • Influence of Hamiltonian Parametrization on Convergence of Kirkwood Free Energy Calculations
    • A. J. Cross, Chem. Phys. Lett., 128, 198 (1986). Influence of Hamiltonian Parametrization on Convergence of Kirkwood Free Energy Calculations.
    • (1986) Chem. Phys. Lett. , vol.128 , pp. 198
    • Cross, A.J.1
  • 199
    • 0001320763 scopus 로고
    • Studies on Free Energy Calculations. I. Thermodynamic Integration Using Polynomial Path
    • H. Resat and M. Mezei, J. Chem. Phys., 99, 6052 (1993). Studies on Free Energy Calculations. I. Thermodynamic Integration Using Polynomial Path.
    • (1993) J. Chem. Phys. , vol.99 , pp. 6052
    • Resat, H.1    Mezei, M.2
  • 200
    • 0000249851 scopus 로고
    • Avoiding Singularities and Numerical Instabilities in Free Energy Calculations Based on Molecular Simulations
    • T. C. Beutler, A. E. Mark, R. C. van Schaik, P. R. Gerber, and W. F. van Gunsteren, Chem. Phys. Lett., 222, 529 (1994). Avoiding Singularities and Numerical Instabilities in Free Energy Calculations Based on Molecular Simulations.
    • (1994) Chem. Phys. Lett. , vol.222 , pp. 529
    • Beutler, T.C.1    Mark, A.E.2    Van Schaik, R.C.3    Gerber, P.R.4    Van Gunsteren, W.F.5
  • 201
    • 0000433021 scopus 로고
    • A New Method for Carrying Out Energy Perturbation Calculations: Dynamically Modified Windows
    • D. A. Pearlman and P. A. Kollman, J. Chem. Phys., 90, 2461 (1989). A New Method for Carrying Out Energy Perturbation Calculations: Dynamically Modified Windows.
    • (1989) J. Chem. Phys. , vol.90 , pp. 2461
    • Pearlman, D.A.1    Kollman, P.A.2
  • 202
    • 33845277848 scopus 로고
    • Calculation of the Free Energy of Association of Nucleic Acid Bases in Vacuo and Water Solution
    • P. Cieplak and P. A. Kollman, J. Am. Chem. Soc., 100, 3734 (1988). Calculation of the Free Energy of Association of Nucleic Acid Bases in Vacuo and Water Solution.
    • (1988) J. Am. Chem. Soc. , vol.100 , pp. 3734
    • Cieplak, P.1    Kollman, P.A.2
  • 203
    • 36549092795 scopus 로고
    • Efficient Computation of Absolute Free Energy of Binding by Computer Simulations. Application to the Methane Dimer in Water
    • W. Jorgensen, J. K. Buckner, S. Boudon, and J. Tirado-Rives, J. Chem. Phys., 89, 3742 (1988). Efficient Computation of Absolute Free Energy of Binding by Computer Simulations. Application to the Methane Dimer in Water.
    • (1988) J. Chem. Phys. , vol.89 , pp. 3742
    • Jorgensen, W.1    Buckner, J.K.2    Boudon, S.3    Tirado-Rives, J.4
  • 205
    • 0025732376 scopus 로고
    • Simulation Analysis of the Stability Mutant R96H of T4 Lysozyme
    • B. Tidor and M. Karplus, Biochemistry, 30, 3217 (1991). Simulation Analysis of the Stability Mutant R96H of T4 Lysozyme.
    • (1991) Biochemistry , vol.30 , pp. 3217
    • Tidor, B.1    Karplus, M.2
  • 207
    • 0027502336 scopus 로고
    • Molecular Dynamic Study of the Stability of Staphylococcal Nuclease Mutants: Component Analysis of the Free Energy Difference of Denaturation
    • N. Yamaotsu, I. Moriguchi, P. A. Kollman, and S. Hirono, Biochim. Biophys. Acta, 1163, 81 (1993). Molecular Dynamic Study of the Stability of Staphylococcal Nuclease Mutants: Component Analysis of the Free Energy Difference of Denaturation.
    • (1993) Biochim. Biophys. Acta , vol.1163 , pp. 81
    • Yamaotsu, N.1    Moriguchi, I.2    Kollman, P.A.3    Hirono, S.4
  • 208
    • 0001661731 scopus 로고
    • Thermodynamics of Aqueous Solvation: Solution Properties of Alcohols and Alkanes
    • C. L. Brooks III, J. Chem. Phys., 87, 3029 (1987). Thermodynamics of Aqueous Solvation: Solution Properties of Alcohols and Alkanes.
    • (1987) J. Chem. Phys. , vol.87 , pp. 3029
    • Brooks C.L. III1
  • 209
    • 0028334097 scopus 로고
    • Decomposition of the Free Energy of a System in Terms of Specific Interactions. Implication for Theoretical and Experimental Studies
    • A. E. Mark and W. F. van Gunsteren, J. Mol. Biol., 240, 167 (1994). Decomposition of the Free Energy of a System in Terms of Specific Interactions. Implication for Theoretical and Experimental Studies.
    • (1994) J. Mol. Biol. , vol.240 , pp. 167
    • Mark, A.E.1    Van Gunsteren, W.F.2
  • 211
    • 0000115003 scopus 로고
    • A Local Reaction Field Method for Fast Evaluation of Long-Range Electrostatic Interactions in Molecular Simulations
    • (b) F. S. Lee and A. Warshel, J. Chem. Phys., 97, 3100 (1992). A Local Reaction Field Method for Fast Evaluation of Long-Range Electrostatic Interactions in Molecular Simulations.
    • (1992) J. Chem. Phys. , vol.97 , pp. 3100
    • Lee, F.S.1    Warshel, A.2
  • 212
    • 0025996871 scopus 로고
    • Proline in α-Helix: Stability and Conformation Studied by Dynamics Simulation
    • R. H. Yun, A. G. Anderson, and J. Hermans, Proteins, 10, 219 (1991). Proline in α-Helix: Stability and Conformation Studied by Dynamics Simulation.
    • (1991) Proteins , vol.10 , pp. 219
    • Yun, R.H.1    Anderson, A.G.2    Hermans, J.3
  • 213
    • 0026050172 scopus 로고
    • Conformational Equilibria of Valine Studied by Dynamics Simulation
    • R. H. Yun and J. Hermans, Protein Eng., 4, 761 (1991). Conformational Equilibria of Valine Studied by Dynamics Simulation.
    • (1991) Protein Eng. , vol.4 , pp. 761
    • Yun, R.H.1    Hermans, J.2
  • 214
    • 0026748637 scopus 로고
    • Differential Helix Propensity of Small Apolar Side Chains Studied by Molecular Dynamics Simulations
    • J. Hermans, A. G. Anderson, and R. H. Yun, Biochemistry, 31, 5646 (1992). Differential Helix Propensity of Small Apolar Side Chains Studied by Molecular Dynamics Simulations.
    • (1992) Biochemistry , vol.31 , pp. 5646
    • Hermans, J.1    Anderson, A.G.2    Yun, R.H.3
  • 215
    • 0024343071 scopus 로고
    • Free Energy Component Analysis: A Study of Glutamic Acid 165 → Aspartic Acid 165 Mutation in Triosephosphate Isomerase
    • V. Daggett, F. Brown, and P. A. Kollman, J. Am. Chem. Soc., 111, 8247 (1989). Free Energy Component Analysis: A Study of Glutamic Acid 165 → Aspartic Acid 165 Mutation in Triosephosphate Isomerase.
    • (1989) J. Am. Chem. Soc. , vol.111 , pp. 8247
    • Daggett, V.1    Brown, F.2    Kollman, P.A.3
  • 216
    • 0024365336 scopus 로고
    • Hidden Thermodynamics of Mutant Proteins: A Molecular Dynamics Analysis
    • J. Gao, K. Kuczwra, B. Tidor, and M. Karplus, Science, 244, 1069 (1989). Hidden Thermodynamics of Mutant Proteins: A Molecular Dynamics Analysis.
    • (1989) Science , vol.244 , pp. 1069
    • Gao, J.1    Kuczwra, K.2    Tidor, B.3    Karplus, M.4
  • 217
    • 0026596911 scopus 로고
    • Calculations of Antibody-Antigen Interactions: Microscopic and Semi-Microscopic Evaluation of the Free Energies of Binding of Phosphorylcholine Analogs to McPC603
    • (a) F. S. Lee, Z.-T. Chu, M. B. Bolger, and A. Warshel, Protein Eng., 5, 215, (1992). Calculations of Antibody-Antigen Interactions: Microscopic and Semi-Microscopic Evaluation of the Free Energies of Binding of Phosphorylcholine Analogs to McPC603.
    • (1992) Protein Eng. , vol.5 , pp. 215
    • Lee, F.S.1    Chu, Z.-T.2    Bolger, M.B.3    Warshel, A.4
  • 218
    • 0026641163 scopus 로고
    • Thermodynamics of Protein-Peptide Interactions in the Ribonuclease-S System Studied by Molecular Dynamics and Free Energy Calculations
    • (b) T. Simonson and A. Brünger, Biochemistry, 31, 8661 (1992). Thermodynamics of Protein-Peptide Interactions in the Ribonuclease-S System Studied by Molecular Dynamics and Free Energy Calculations.
    • (1992) Biochemistry , vol.31 , pp. 8661
    • Simonson, T.1    Brünger, A.2
  • 219
    • 0040543046 scopus 로고
    • When Are Free Energy Components Meaningful?
    • P. E. Smith and W. F. van Gunsteren, J. Phys. Chem., 98, 13735 (1994). When Are Free Energy Components Meaningful?
    • (1994) J. Phys. Chem. , vol.98 , pp. 13735
    • Smith, P.E.1    Van Gunsteren, W.F.2
  • 220
    • 0027968902 scopus 로고
    • Free Energy Simulations: The Meaning of the Individual Contributions from Component Analysis
    • S. Boresch, G. Archontis, and M. Karplus, Proteins, 20, 25 (1994). Free Energy Simulations: The Meaning of the Individual Contributions from Component Analysis.
    • (1994) Proteins , vol.20 , pp. 25
    • Boresch, S.1    Archontis, G.2    Karplus, M.3
  • 221
    • 0029584358 scopus 로고
    • The Meaning of Component Analysis: Decomposition of the Free Energy in Terms of Specific Interactions
    • S. Boresch and M. Karplus, J. Mol. Biol. 254, 801 (1995). The Meaning of Component Analysis: Decomposition of the Free Energy in Terms of Specific Interactions.
    • (1995) J. Mol. Biol. , vol.254 , pp. 801
    • Boresch, S.1    Karplus, M.2
  • 222
    • 84986532462 scopus 로고
    • Free Energy Difference Calculations by Thermodynamic Integration: Difficulties in Obtaining a Precise Value
    • M. J. Mitchell and J. A. McCammon, J. Comput. Chem., 12, 271 (1991). Free Energy Difference Calculations by Thermodynamic Integration: Difficulties in Obtaining a Precise Value.
    • (1991) J. Comput. Chem. , vol.12 , pp. 271
    • Mitchell, M.J.1    McCammon, J.A.2
  • 223
    • 0000318631 scopus 로고
    • Calculation of Relative Free Energy via Indirect Pathways
    • A. E. Mark, W. F. van Gunsteren, and H. J. C. Berendsen, J. Chem. Phys., 94, 3808 (1991). Calculation of Relative Free Energy via Indirect Pathways.
    • (1991) J. Chem. Phys. , vol.94 , pp. 3808
    • Mark, A.E.1    Van Gunsteren, W.F.2    Berendsen, H.J.C.3
  • 224
    • 0008025298 scopus 로고
    • Convergence Properties of Free Energy Calculations: α-Cyclodextrin Complexes as a Case Study
    • A. E. Mark, S. P. van Helden, P. E. Smith, L. H. M. Janssen, and W. F. van Gunsteren, J. Am. Chem. Soc., 116, 6293 (1994). Convergence Properties of Free Energy Calculations: α-Cyclodextrin Complexes as a Case Study.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 6293
    • Mark, A.E.1    Van Helden, S.P.2    Smith, P.E.3    Janssen, L.H.M.4    Van Gunsteren, W.F.5
  • 225
    • 84986468475 scopus 로고
    • Precision of Free Energies Calculated by Molecular Dynamics Simulations of Peptides in Solution
    • J. Hermans, R. H. Yun, and A. G. Anderson, J. Comput. Chem., 13, 429 (1992). Precision of Free Energies Calculated by Molecular Dynamics Simulations of Peptides in Solution.
    • (1992) J. Comput. Chem. , vol.13 , pp. 429
    • Hermans, J.1    Yun, R.H.2    Anderson, A.G.3
  • 226
    • 0026503819 scopus 로고
    • Application of Free Energy Simulations to the Binding of a Transition-State-Analog Inhibitor to HIV Protease
    • A. Tropsha and J. Hermans, Protein Eng., 5, 29 (1992). Application of Free Energy Simulations to the Binding of a Transition-State-Analog Inhibitor to HIV Protease.
    • (1992) Protein Eng. , vol.5 , pp. 29
    • Tropsha, A.1    Hermans, J.2
  • 227
    • 0346663418 scopus 로고
    • Simple Analysis of Noise and Hysteresis in (Slow Growth) Free Energy Simulations
    • J. Hermans, J. Phys. Chem., 98, 13735 (1994). Simple Analysis of Noise and Hysteresis in (Slow Growth) Free Energy Simulations.
    • (1994) J. Phys. Chem. , vol.98 , pp. 13735
    • Hermans, J.1
  • 228
    • 0000886606 scopus 로고
    • Elimination of Errors in Free Energy Calculations Due to the Lag between the Hamiltonian and the System Configuration
    • R. H. Wood, J. Phys. Chem., 95, 4838 (1991). Elimination of Errors in Free Energy Calculations Due to the Lag Between the Hamiltonian and the System Configuration.
    • (1991) J. Phys. Chem. , vol.95 , pp. 4838
    • Wood, R.H.1
  • 229
    • 0029792731 scopus 로고    scopus 로고
    • Atomic Scale Analysis of the Solvation Thermodynamics of Hydrophobic Hydration
    • S. R. Durell and A. Wallqvist, Biophys. J., 254, 1695 (1996). Atomic Scale Analysis of the Solvation Thermodynamics of Hydrophobic Hydration.
    • (1996) Biophys. J. , vol.254 , pp. 1695
    • Durell, S.R.1    Wallqvist, A.2
  • 230
    • 0000656021 scopus 로고
    • Studies on Free Energy Calculations. II. A Theoretical Approach to Molecular Solvation
    • H. Resat and M. Mezei, J. Chem. Phys., 101, 6126 (1994). Studies on Free Energy Calculations. II. A Theoretical Approach to Molecular Solvation.
    • (1994) J. Chem. Phys. , vol.101 , pp. 6126
    • Resat, H.1    Mezei, M.2
  • 231
    • 0006379192 scopus 로고
    • Change of Bond Length in Free Energy Simulations: Algorithmic Improvements, but When Is It Necessary?
    • L. Wang and J. Hermans, J. Chem. Phys., 100, 9129 (1994). Change of Bond Length in Free Energy Simulations: Algorithmic Improvements, But When Is It Necessary?
    • (1994) J. Chem. Phys. , vol.100 , pp. 9129
    • Wang, L.1    Hermans, J.2
  • 232
    • 84986432938 scopus 로고
    • Generalized Alteration of Structure and Parameters: A New Method for Free-Energy Perturbations in Systems Containing Flexible Degrees of Freedom
    • D. L. Severance, J. W. Essex, and W. L. Jorgensen, J. Comput. Chem., 16, 311 (1995). Generalized Alteration of Structure and Parameters: A New Method for Free-Energy Perturbations in Systems Containing Flexible Degrees of Freedom.
    • (1995) J. Comput. Chem. , vol.16 , pp. 311
    • Severance, D.L.1    Essex, J.W.2    Jorgensen, W.L.3
  • 233
    • 0001412107 scopus 로고
    • Investigation of Solvent Effects on Pericyclic Reactions by Computer Simulations
    • W. L. Jorgensen, J. F. Blake, D. Lim, and D. L. Severance, J. Chem. Soc., Faraday Trans., 90, 1727 (1994). Investigation of Solvent Effects on Pericyclic Reactions by Computer Simulations.
    • (1994) J. Chem. Soc., Faraday Trans. , vol.90 , pp. 1727
    • Jorgensen, W.L.1    Blake, J.F.2    Lim, D.3    Severance, D.L.4
  • 234
    • 0038332026 scopus 로고
    • Elucidation of Transition Structures and Solvent Effects for the Mislow-Evans Rearrangement of Allylic Sulfoxides
    • D. K. Jones-Hertzog and W. L. Jorgensen, J. Am. Chem. Soc., 117, 9077 (1995). Elucidation of Transition Structures and Solvent Effects for the Mislow-Evans Rearrangement of Allylic Sulfoxides.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 9077
    • Jones-Hertzog, D.K.1    Jorgensen, W.L.2
  • 235
    • 0029790271 scopus 로고    scopus 로고
    • Monte Carlo Investigations of Solvent Effects on the Chorismate to Prephenate Rearrangement
    • H. A. Carlson and W. L. Jorgensen, J. Am. Chem. Soc., 118, 8475 (1996). Monte Carlo Investigations of Solvent Effects on the Chorismate to Prephenate Rearrangement.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 8475
    • Carlson, H.A.1    Jorgensen, W.L.2
  • 236
    • 0001351418 scopus 로고
    • Importance of Polarization for Dipolar Solutes in Low-Dielectric Media: 1,2-Dichloroethane and Water in Cyclohexane
    • W. L. Jorgensen, N. A. McDonald, M. Selmi, and P. R. Rablen, J. Am. Chem. Soc., 117, 11809 (1995). Importance of Polarization for Dipolar Solutes in Low-Dielectric Media: 1,2-Dichloroethane and Water in Cyclohexane.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 11809
    • Jorgensen, W.L.1    McDonald, N.A.2    Selmi, M.3    Rablen, P.R.4
  • 237
    • 0007425562 scopus 로고    scopus 로고
    • Computation of Gibbs Free Energies of Hydration for Simple Aromatic Molecules: A Comparative Study Using Monte Carlo and Molecular Dynamics Computer Simulation Techniques
    • T. Z. M. Denti, T. C. Beutler, W. F. van Gunsteren, and F. Diederich, J. Phys. Chem., 100, 4256 (1996). Computation of Gibbs Free Energies of Hydration for Simple Aromatic Molecules: A Comparative Study Using Monte Carlo and Molecular Dynamics Computer Simulation Techniques.
    • (1996) J. Phys. Chem. , vol.100 , pp. 4256
    • Denti, T.Z.M.1    Beutler, T.C.2    Van Gunsteren, W.F.3    Diederich, F.4
  • 238
    • 0030062224 scopus 로고    scopus 로고
    • Free Energies of Transfer of Trp Analogs from Chloroform to Water: Comparison of Theory and Experiment and the Importance of Adequate Treatment of Electrostatic and Internal Interactions
    • X. Daura, P. H. Hünenberger, A. E. Mark, E. Querol, F. X. Avilés, and W. F. van Gunsteren, J. Am Chem. Soc., 188, 6285 (1996). Free Energies of Transfer of Trp Analogs from Chloroform to Water: Comparison of Theory and Experiment and the Importance of Adequate Treatment of Electrostatic and Internal Interactions.
    • (1996) J. Am Chem. Soc. , vol.188 , pp. 6285
    • Daura, X.1    Hünenberger, P.H.2    Mark, A.E.3    Querol, E.4    Avilés, F.X.5    Van Gunsteren, W.F.6
  • 239
    • 0029864838 scopus 로고    scopus 로고
    • Salting in Peptides: Conformationally Dependent Solubilities and Phase Behavior of a Tripeptide Zwitterion in Electrolyte Solution
    • J. S. Perkyns, Y. Wang, and M. Pettitt, J. Am. Chem. Soc., 118, 1164 (1996). Salting in Peptides: Conformationally Dependent Solubilities and Phase Behavior of a Tripeptide Zwitterion in Electrolyte Solution.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 1164
    • Perkyns, J.S.1    Wang, Y.2    Pettitt, M.3
  • 240
    • 0000402269 scopus 로고
    • Free Energy Simulation Studies on the Hydration of Tetramethylurea and Tetramethylthiourea
    • M. Mezei and G. Jancsó, Chem. Phys. Lett., 239, 237 (1995). Free Energy Simulation Studies on the Hydration of Tetramethylurea and Tetramethylthiourea.
    • (1995) Chem. Phys. Lett. , vol.239 , pp. 237
    • Mezei, M.1    Jancsó, G.2
  • 242
    • 0346663416 scopus 로고
    • Cooperativity of Water-Solute Interactions at Hydrophilic Surface
    • A. Wallqvist and D. G. Covell J. Phys. Chem., 99, 5705 (1995). Cooperativity of Water-Solute Interactions at Hydrophilic Surface.
    • (1995) J. Phys. Chem. , vol.99 , pp. 5705
    • Wallqvist, A.1    Covell, D.G.2
  • 243
    • 0001656183 scopus 로고    scopus 로고
    • Free Energy Simulations: Correcting for Electrostatic Cutoffs by Use of the Poisson Equation
    • H. Resat and J. A. McCammon, J. Chem. Phys., 104, 7645 (1996). Free Energy Simulations: Correcting for Electrostatic Cutoffs by Use of the Poisson Equation.
    • (1996) J. Chem. Phys. , vol.104 , pp. 7645
    • Resat, H.1    McCammon, J.A.2
  • 244
    • 0030018635 scopus 로고    scopus 로고
    • Computer Simulations of the Solvent Dependence of Apolar Association Strength: Gibbs Free Energy Calculations on a Cyclophane-Pyrene Complex in Water and Chloroform
    • T. Z. M. Denti, W. F. van Gunsteren, and F. Diederich, J. Am. Chem. Soc., 118, 6044 (1996). Computer Simulations of the Solvent Dependence of Apolar Association Strength: Gibbs Free Energy Calculations on a Cyclophane-Pyrene Complex in Water and Chloroform.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 6044
    • Denti, T.Z.M.1    Van Gunsteren, W.F.2    Diederich, F.3
  • 245
    • 0028950191 scopus 로고
    • Investigations into the Stereochemistry of Cyclophane-Steroid Complexes Via Monte Carlo Simulations
    • H. A. Carlson and W. L. Jorgensen, Tetrahedron, 51, 449 (1995). Investigations into the Stereochemistry of Cyclophane-Steroid Complexes Via Monte Carlo Simulations.
    • (1995) Tetrahedron , vol.51 , pp. 449
    • Carlson, H.A.1    Jorgensen, W.L.2
  • 246
    • 0001032416 scopus 로고
    • Conformation and Dynamics of 18-Crown-6, Cryptand 222, and Their Cation Complexes in Acetonitrile Studied by Molecular Dynamics Simulations
    • L. Troxler and G. Wipff, J. Am. Chem. Soc., 116, 1468 (1994). Conformation and Dynamics of 18-Crown-6, Cryptand 222, and Their Cation Complexes in Acetonitrile Studied by Molecular Dynamics Simulations.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 1468
    • Troxler, L.1    Wipff, G.2
  • 247
    • 0005044910 scopus 로고
    • Structure and Binding for Complexes of Rebek's Acridine Diacid with Pyrazine, Quinoxaline, and Pyridine from Monte Carlo Simulations with an All-Atom Force Field
    • E. M. Duffy and W. L. Jorgensen, J. Am. Chem. Soc., 116, 6337 (1994). Structure and Binding for Complexes of Rebek's Acridine Diacid with Pyrazine, Quinoxaline, and Pyridine from Monte Carlo Simulations with an All-Atom Force Field.
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 6337
    • Duffy, E.M.1    Jorgensen, W.L.2
  • 248
    • 0027510416 scopus 로고
    • Modeling the Complexation of Substituted Benzenes by a Cyclophane Host in Water
    • W. L. Jorgensen and T. B. Nguyen, Proc. Natl. Acad. Sci. U.S.A., 90, 1194 (1993). Modeling the Complexation of Substituted Benzenes by a Cyclophane Host in Water.
    • (1993) Proc. Natl. Acad. Sci. U.S.A. , vol.90 , pp. 1194
    • Jorgensen, W.L.1    Nguyen, T.B.2
  • 249
    • 0027227315 scopus 로고
    • The Nature of the Ion Binding Interactions in EF-Hand Peptide Analog: Free Energy Simulation of Asp to Asn Mutations
    • B. Prod'hom and M. Karplus, Protein Eng., 6, 585 (1993). The Nature of the Ion Binding Interactions in EF-Hand Peptide Analog: Free Energy Simulation of Asp to Asn Mutations.
    • (1993) Protein Eng. , vol.6 , pp. 585
    • Prod'hom, B.1    Karplus, M.2
  • 250
    • 0344791934 scopus 로고
    • Relative Free Energies of Folding and Refolding of Model Secondary Structure Elements in Aqueous Solution
    • R. S. Hodes and J. A. Smith, Eds., ESCOM, Leidon
    • A. Tropsha, Y. Yan, S. E. Schneider, L. Li, and B. W. Erickson, in Peptides: Chemistry, Structure and Biology, R. S. Hodes and J. A. Smith, Eds., ESCOM, Leidon, 1994, pp. 883-885. Relative Free Energies of Folding and Refolding of Model Secondary Structure Elements in Aqueous Solution.
    • (1994) Peptides: Chemistry, Structure and Biology , pp. 883-885
    • Tropsha, A.1    Yan, Y.2    Schneider, S.E.3    Li, L.4    Erickson, B.W.5
  • 251
    • 0000713003 scopus 로고
    • Determination of the Chemical Potential of Polymeric Systems from Monte Carlo Simulations
    • S. K. Kumar, I. Szleifer, and A. Z. Panagiotopoulos, Phys. Rev. Lett., 66, 2935 (1991). Determination of the Chemical Potential of Polymeric Systems from Monte Carlo Simulations.
    • (1991) Phys. Rev. Lett. , vol.66 , pp. 2935
    • Kumar, S.K.1    Szleifer, I.2    Panagiotopoulos, A.Z.3
  • 252
    • 0028847038 scopus 로고
    • Thermodynamic Parameters for the Helix-Coil Transition of Oligopeptides: Molecular Dynamics Simulation with the Peptide Growth Method
    • L. Wang, T. O'Connell, A. Tropsha, and J. Hermans, Proc. Natl. Acad. Sci. U.S.A., 92, 10924 (1995). Thermodynamic Parameters for the Helix-Coil Transition of Oligopeptides: Molecular Dynamics Simulation with the Peptide Growth Method.
    • (1995) Proc. Natl. Acad. Sci. U.S.A. , vol.92 , pp. 10924
    • Wang, L.1    O'Connell, T.2    Tropsha, A.3    Hermans, J.4
  • 253
    • 0030271002 scopus 로고    scopus 로고
    • Energetic Decomposition of the α-Helix-Coil Equilibrium of a Dynamic Model System
    • L. Wang, T. O'Connell, A. Tropsha, and J. Hermans, Biopolymers, 39, 479 (1996). Energetic Decomposition of the α-Helix-Coil Equilibrium of a Dynamic Model System.
    • (1996) Biopolymers , vol.39 , pp. 479
    • Wang, L.1    O'Connell, T.2    Tropsha, A.3    Hermans, J.4
  • 254
    • 36449009782 scopus 로고
    • Predictions of Free Energy Differences from a Single Simulation of the Initial State
    • P. E. Smith and W. F. van Gunsteren, J. Chem. Phys., 100, 577 (1994). Predictions of Free Energy Differences from a Single Simulation of the Initial State.
    • (1994) J. Chem. Phys. , vol.100 , pp. 577
    • Smith, P.E.1    Van Gunsteren, W.F.2
  • 255
    • 0000762204 scopus 로고    scopus 로고
    • Cumulant Expansion of the Free Energy: Application to Free Energy Derivatives and Component Analysis
    • G. Archontis and M. Karplus, J. Chem. Phys., 105, 11246 (1996). Cumulant Expansion of the Free Energy: Application to Free Energy Derivatives and Component Analysis.
    • (1996) J. Chem. Phys. , vol.105 , pp. 11246
    • Archontis, G.1    Karplus, M.2
  • 256
    • 5544264558 scopus 로고
    • Gaussian Fluctuation Formula for Electrostatic Free-Energy Changes in Solution
    • R. M. Levy, M. Belhadj, and D. B. Kitchen, J. Chem. Phys. 95, 3627 (1991). Gaussian Fluctuation Formula for Electrostatic Free-Energy Changes in Solution.
    • (1991) J. Chem. Phys. , vol.95 , pp. 3627
    • Levy, R.M.1    Belhadj, M.2    Kitchen, D.B.3
  • 257
    • 0030134642 scopus 로고    scopus 로고
    • Estimating the Relative Free Energy of Different Molecular States with Respect to a Single Reference State
    • H. Liu, A. E. Mark, and W. F. van Gunsteren, J. Phys. Chem., 100, 9485 (1996). Estimating the Relative Free Energy of Different Molecular States with Respect to a Single Reference State.
    • (1996) J. Phys. Chem. , vol.100 , pp. 9485
    • Liu, H.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 258
    • 0029435083 scopus 로고
    • Rapid Non-Empirical Approaches for Estimating Relative Binding Free Energies
    • A. E. Mark, Y. Xu, H. Liu, and W. F. van Gunsteren, Acta Biochim. Polon., 42, 525 (1995). Rapid Non-Empirical Approaches for Estimating Relative Binding Free Energies.
    • (1995) Acta Biochim. Polon. , vol.42 , pp. 525
    • Mark, A.E.1    Xu, Y.2    Liu, H.3    Van Gunsteren, W.F.4
  • 259
    • 33845282688 scopus 로고
    • Microscopic Examination of Free-Energy Relationships for Electron Transfer in Polar Solvents
    • J.-K. Hwang and A. Warshel, J. Am. Chem. Soc., 109, 715 (1987). Microscopic Examination of Free-Energy Relationships for Electron Transfer in Polar Solvents.
    • (1987) J. Am. Chem. Soc. , vol.109 , pp. 715
    • Hwang, J.-K.1    Warshel, A.2
  • 261
    • 0010884753 scopus 로고
    • On the Theory of Oxidation-Reduction Reactions Involving Electron Transfer
    • R. A. Marcus, J. Chem. Phys., 24, 966 (1956). On the Theory of Oxidation-Reduction Reactions Involving Electron Transfer.
    • (1956) J. Chem. Phys. , vol.24 , pp. 966
    • Marcus, R.A.1
  • 262
    • 0009869207 scopus 로고
    • Electrostatic Free Energy and Other Properties of States Having Non-Equilibrium Polarization
    • R. A. Marcus, J. Chem. Phys., 24, 979 (1956). Electrostatic Free Energy and Other Properties of States Having Non-Equilibrium Polarization.
    • (1956) J. Chem. Phys. , vol.24 , pp. 979
    • Marcus, R.A.1
  • 263
    • 0000671518 scopus 로고    scopus 로고
    • a's as Ionizable Residues in Proteins: Semi-Microscopic and Microscopic Approaches
    • a's as Ionizable Residues in Proteins: Semi-Microscopic and Microscopic Approaches.
    • (1997) J. Phys. Chem. B , vol.101 , pp. 4458
    • Sham, Y.Y.1    Chu, Z.T.2    Warshel, A.3
  • 264
    • 0028155689 scopus 로고
    • A New Method for Predicting Binding Affinity in Computer-Aided Drug Design
    • J. Åqvist, C. Medina, and J.-E. Samuelsson, Protein Eng., 7, 385 (1994). A New Method for Predicting Binding Affinity in Computer-Aided Drug Design.
    • (1994) Protein Eng. , vol.7 , pp. 385
    • Åqvist, J.1    Medina, C.2    Samuelsson, J.-E.3
  • 265
    • 0029557441 scopus 로고
    • Estimation of Binding Free Energies for HIV Proteinase Inhibitors by Molecular Dynamics Simulations
    • T. Hansson and J. Åqvist, Protein Eng., 8, 1137 (1995). Estimation of Binding Free Energies for HIV Proteinase Inhibitors by Molecular Dynamics Simulations.
    • (1995) Protein Eng. , vol.8 , pp. 1137
    • Hansson, T.1    Åqvist, J.2
  • 266
    • 0030134110 scopus 로고    scopus 로고
    • On the Validity of Electrostatic Linear Response in Polar Solvents
    • J. Åqvist and T. Hansson, J. Phys. Chem., 100, 9512 (1996). On the Validity of Electrostatic Linear Response in Polar Solvents.
    • (1996) J. Phys. Chem. , vol.100 , pp. 9512
    • Åqvist, J.1    Hansson, T.2
  • 267
    • 0028945948 scopus 로고
    • Sugar Recognition by a Glucose/Galactose Receptor. Evaluation of Binding Energetics from Molecular Dynamics Simulations
    • J. Åqvist and S. L. Mowbray, J. Biol. Chem., 270, 9978 (1995). Sugar Recognition by a Glucose/Galactose Receptor. Evaluation of Binding Energetics from Molecular Dynamics Simulations.
    • (1995) J. Biol. Chem. , vol.270 , pp. 9978
    • Åqvist, J.1    Mowbray, S.L.2
  • 268
    • 0001382020 scopus 로고    scopus 로고
    • Calculation of Absolute Binding Free Energies for Charged Ligands and Effects of Long-Range Electrostatic Interactions
    • J. Åqvist, J. Comput. Chem., 17, 1587 (1996). Calculation of Absolute Binding Free Energies for Charged Ligands and Effects of Long-Range Electrostatic Interactions.
    • (1996) J. Comput. Chem. , vol.17 , pp. 1587
    • Åqvist, J.1
  • 269
    • 0001389474 scopus 로고
    • An Extended Linear Response Method for Determining Free Energies of Hydration
    • H. A. Carlson and W. L. Jorgensen, J. Phys. Chem., 99, 10667 (1995). An Extended Linear Response Method for Determining Free Energies of Hydration.
    • (1995) J. Phys. Chem. , vol.99 , pp. 10667
    • Carlson, H.A.1    Jorgensen, W.L.2
  • 270
    • 0242677212 scopus 로고
    • Calculation of Electrostatic Free Energy Differences with a Time-Saving Approximate Method
    • G. King and R. A. Barford, J. Phys. Chem., 97, 8798 (1993). Calculation of Electrostatic Free Energy Differences with a Time-Saving Approximate Method.
    • (1993) J. Phys. Chem. , vol.97 , pp. 8798
    • King, G.1    Barford, R.A.2
  • 271
    • 0242364982 scopus 로고    scopus 로고
    • Calculations of Free Energy Differences for Computer Simulations of Initial and Final States
    • G. Hummer and A. Szabo, J. Chem. Phys., 105, 2004 (1996). Calculations of Free Energy Differences for Computer Simulations of Initial and Final States.
    • (1996) J. Chem. Phys. , vol.105 , pp. 2004
    • Hummer, G.1    Szabo, A.2
  • 272
    • 0039949211 scopus 로고
    • The Scanning Method with a Mean-Field Parameter: Computer Simulation Study of the Critical Exponents of Self-Avoiding Walks on a Square Lattice
    • H. Meirovitch, Macromolecules, 18, 563 (1985). The Scanning Method with a Mean-Field Parameter: Computer Simulation Study of the Critical Exponents of Self-Avoiding Walks on a Square Lattice.
    • (1985) Macromolecules , vol.18 , pp. 563
    • Meirovitch, H.1
  • 273
    • 0024066981 scopus 로고
    • Stability of Polypeptides Conformational States. II. The Free Energy of the Statistical Coil Obtained by the Scanning Simulation Method
    • H. Meirovitch, M. Vásquez, and H. A. Scheraga, Biopolymers, 27, 1189 (1988). Stability of Polypeptides Conformational States. II. The Free Energy of the Statistical Coil Obtained by the Scanning Simulation Method.
    • (1988) Biopolymers , vol.27 , pp. 1189
    • Meirovitch, H.1    Vásquez, M.2    Scheraga, H.A.3
  • 274
    • 0009702786 scopus 로고
    • Free Energy and Stability of Macromolecules Studied by the Scanning Method
    • H. Meirovitch, M. Vásquez, and H. A. Scheraga, J. Chem. Phys., 92, 1248 (1990). Free Energy and Stability of Macromolecules Studied by the Scanning Method.
    • (1990) J. Chem. Phys. , vol.92 , pp. 1248
    • Meirovitch, H.1    Vásquez, M.2    Scheraga, H.A.3
  • 275
    • 0347293647 scopus 로고
    • The Scanning Simulation Method for Macromolecules
    • H. Meirovitch, Int. J. Mod. Phys. C, 1, 119 (1990). The Scanning Simulation Method for Macromolecules.
    • (1990) Int. J. Mod. Phys. C , vol.1 , pp. 119
    • Meirovitch, H.1
  • 276
    • 0038406062 scopus 로고
    • Entropy, Pressure and Chemical Potential of Multiple Chain Systems from Computer Simulation. I. Application of the Scanning Method
    • H. Meirovitch, J. Chem. Phys., 97, 5803 (1992). Entropy, Pressure and Chemical Potential of Multiple Chain Systems from Computer Simulation. I. Application of the Scanning Method.
    • (1992) J. Chem. Phys. , vol.97 , pp. 5803
    • Meirovitch, H.1
  • 277
    • 0005546313 scopus 로고
    • Computer Simulation of the Entropy of Continuum Chain Models: The Two-Dimensional Freely-Jointed Chain of Hard Disks
    • H. Meirovitch and H. A. Scheraga, J. Chem. Phys., 84, 6369 (1986). Computer Simulation of the Entropy of Continuum Chain Models: The Two-Dimensional Freely-Jointed Chain of Hard Disks.
    • (1986) J. Chem. Phys. , vol.84 , pp. 6369
    • Meirovitch, H.1    Scheraga, H.A.2
  • 278
    • 0005623645 scopus 로고
    • Entropy, Pressure and Chemical Potential of Multiple Chain Systems from Computer Simulation. II. Application of the Metropolis and the Hypothetical Scanning Method
    • H. Meirovitch, J. Chem. Phys., 97, 5816 (1992). Entropy, Pressure and Chemical Potential of Multiple Chain Systems from Computer Simulation. II. Application of the Metropolis and the Hypothetical Scanning Method.
    • (1992) J. Chem. Phys. , vol.97 , pp. 5816
    • Meirovitch, H.1
  • 279
    • 0023338860 scopus 로고
    • Stability of Polypeptide Conformational States as Determined by Computer Simulation of the Free Energy
    • H. Meirovitch, M. Vásquez, and H. A. Scheraga, Biopolymers, 26, 651 (1987). Stability of Polypeptide Conformational States as Determined by Computer Simulation of the Free Energy.
    • (1987) Biopolymers , vol.26 , pp. 651
    • Meirovitch, H.1    Vásquez, M.2    Scheraga, H.A.3
  • 281
    • 36149045396 scopus 로고
    • An Approximate Stochastic Process for Computer Simulation of the Ising Model at Equilibrium
    • H. Meirovitch, J. Phys. A, 15, 2063 (1982). An Approximate Stochastic Process for Computer Simulation of the Ising Model at Equilibrium.
    • (1982) J. Phys. A , vol.15 , pp. 2063
    • Meirovitch, H.1
  • 282
    • 0346663396 scopus 로고
    • unpublished results
    • H. Meirovitch, unpublished results, 1986.
    • (1986)
    • Meirovitch, H.1
  • 283
    • 0000760421 scopus 로고
    • Direct Dynamical Calculation of Entropy and Free Energy by Adiabatic Switching
    • M. Watanabe and W. P. Reinhardt, Phys. Rev. Lett., 65, 3301 (1990). Direct Dynamical Calculation of Entropy and Free Energy by Adiabatic Switching.
    • (1990) Phys. Rev. Lett. , vol.65 , pp. 3301
    • Watanabe, M.1    Reinhardt, W.P.2
  • 284
    • 0001294503 scopus 로고
    • Comment on "Monte Carlo Simulation of a First-Order Transition for Protein Folding."
    • B. A. Berg, U. H. E. Hansmann, and Y. Okamoto, J. Phys. Chem., 99, 2236 (1995). Comment on "Monte Carlo Simulation of a First-Order Transition for Protein Folding."
    • (1995) J. Phys. Chem. , vol.99 , pp. 2236
    • Berg, B.A.1    Hansmann, U.H.E.2    Okamoto, Y.3
  • 285
    • 0029342240 scopus 로고
    • Thermodynamics of Helix-Coil Transitions Studied by Multicanonical Algorithms
    • Y. Okamoto and U. H. E. Hansmann, J. Phys. Chem., 99, 11276 (1995). Thermodynamics of Helix-Coil Transitions Studied by Multicanonical Algorithms.
    • (1995) J. Phys. Chem. , vol.99 , pp. 11276
    • Okamoto, Y.1    Hansmann, U.H.E.2
  • 286
    • 43949158791 scopus 로고
    • Comparative Study of Multicanonical and Simulated Annealing Algorithms in the Protein Folding Problem
    • U. H. E. Hansmann and Y. Okamoto, Physica A, 212, 415 (1994). Comparative Study of Multicanonical and Simulated Annealing Algorithms in the Protein Folding Problem.
    • (1994) Physica A , vol.212 , pp. 415
    • Hansmann, U.H.E.1    Okamoto, Y.2
  • 287
    • 0030572603 scopus 로고    scopus 로고
    • Molecular Dynamics, Langevin and Hybrid Monte Carlo Simulations in Multicanonical Ensemble
    • U. H. E. Hansmann, Y. Okamoto, and F. Eisenmenger, Chem. Phys. Lett., 259, 321 (1996). Molecular Dynamics, Langevin and Hybrid Monte Carlo Simulations in Multicanonical Ensemble.
    • (1996) Chem. Phys. Lett. , vol.259 , pp. 321
    • Hansmann, U.H.E.1    Okamoto, Y.2    Eisenmenger, F.3
  • 288
    • 0142013225 scopus 로고    scopus 로고
    • Numerical Comparisons of Three Recently Proposed Algorithms in the Protein Folding Problem
    • U. H. E. Hansmann and Y. Okamoto, J. Comput. Chem., 18, 920 (1997). Numerical Comparisons of Three Recently Proposed Algorithms in the Protein Folding Problem.
    • (1997) J. Comput. Chem. , vol.18 , pp. 920
    • Hansmann, U.H.E.1    Okamoto, Y.2
  • 289
    • 33751158061 scopus 로고
    • Statistical Thermodynamics of Protein Folding: Sequence Dependence
    • M.-H. Hao and H. A. Scheraga, J. Phys. Chem., 98, 9882 (1994). Statistical Thermodynamics of Protein Folding: Sequence Dependence.
    • (1994) J. Phys. Chem. , vol.98 , pp. 9882
    • Hao, M.-H.1    Scheraga, H.A.2
  • 290
    • 11744314103 scopus 로고
    • Statistical Thermodynamics of Protein Folding: Comparison of Mean Field Theory with Monte Carlo Simulation
    • M.-H. Hao and H. A. Scheraga, J. Chem. Phys., 102, 1334 (1995). Statistical Thermodynamics of Protein Folding: Comparison of Mean Field Theory with Monte Carlo Simulation.
    • (1995) J. Chem. Phys. , vol.102 , pp. 1334
    • Hao, M.-H.1    Scheraga, H.A.2
  • 291
    • 0029945395 scopus 로고    scopus 로고
    • How Optimization of Potential Functions Affects Protein Folding
    • M.-H. Hao and H. A. Scheraga, Proc. Natl. Acad. Sci. U.S.A., 93, 4984 (1996). How Optimization of Potential Functions Affects Protein Folding.
    • (1996) Proc. Natl. Acad. Sci. U.S.A. , vol.93 , pp. 4984
    • Hao, M.-H.1    Scheraga, H.A.2
  • 292
    • 0000829596 scopus 로고    scopus 로고
    • Optimizing Potential Functions for Protein Folding
    • M.-H. Hao and H. A. Scheraga, J. Phys. Chem., 100, 14540 (1996). Optimizing Potential Functions for Protein Folding.
    • (1996) J. Phys. Chem. , vol.100 , pp. 14540
    • Hao, M.-H.1    Scheraga, H.A.2
  • 293
    • 0009501831 scopus 로고
    • Dielectric Properties and Phase Transitions of Water between Conducting Plates
    • M. Watanabe, A. M. Brodsky, and W. P. Reinhardt, J. Phys. Chem., 95, 4593 (1991). Dielectric Properties and Phase Transitions of Water Between Conducting Plates.
    • (1991) J. Phys. Chem. , vol.95 , pp. 4593
    • Watanabe, M.1    Brodsky, A.M.2    Reinhardt, W.P.3
  • 294
    • 0000464094 scopus 로고
    • Variational Path Optimization and Upper and Lower Bounds of Free Energy Changes via Finite Time Minimization of External Work
    • W. P. Reinhardt and J. E. Hunter III, J. Chem. Phys., 97, 1599 (1992). Variational Path Optimization and Upper and Lower Bounds of Free Energy Changes via Finite Time Minimization of External Work.
    • (1992) J. Chem. Phys. , vol.97 , pp. 1599
    • Reinhardt, W.P.1    Hunter J.E. III2
  • 295
    • 0001541834 scopus 로고
    • A Finite Time Variational Method for Determining Optimal Path and Obtaining Bounds on Free Energy Changes from Computer Simulations
    • J. E. Hunter III, W. P. Reinhardt, and T. F. Davis, J. Chem. Phys., 99, 6856 (1993). A Finite Time Variational Method for Determining Optimal Path and Obtaining Bounds on Free Energy Changes from Computer Simulations.
    • (1993) J. Chem. Phys. , vol.99 , pp. 6856
    • Hunter J.E. III1    Reinhardt, W.P.2    Davis, T.F.3
  • 296
    • 0040696353 scopus 로고
    • Variational Upper and Lower Bounds on Quantum Free Energy and Energy Differences via Path Integral Monte Carlo
    • G. J. Hogenson and W. P. Reinhardt, J. Chem. Phys., 102, 4151 (1995). Variational Upper and Lower Bounds on Quantum Free Energy and Energy Differences via Path Integral Monte Carlo.
    • (1995) J. Chem. Phys. , vol.102 , pp. 4151
    • Hogenson, G.J.1    Reinhardt, W.P.2
  • 297
    • 0001464311 scopus 로고    scopus 로고
    • A Thermodynamic Distance Criterion of Optimality for the Calculation of Free Energy Changes from Computer Simulations
    • J. C. Schön, J. Chem. Phys., 105, 10072 (1996). A Thermodynamic Distance Criterion of Optimality for the Calculation of Free Energy Changes from Computer Simulations.
    • (1996) J. Chem. Phys. , vol.105 , pp. 10072
    • Schön, J.C.1
  • 298
    • 36849102835 scopus 로고
    • Monte Carlo Estimation of the Free Energy by Multistage Sampling
    • J. P. Valleau and D. N. Card, J. Chem. Phys., 57, 5457 (1972). Monte Carlo Estimation of the Free Energy by Multistage Sampling.
    • (1972) J. Chem. Phys. , vol.57 , pp. 5457
    • Valleau, J.P.1    Card, D.N.2
  • 299
    • 0001212413 scopus 로고
    • A New Method for the Partition Function of Discrete Systems with Application to the 3D Ising Model
    • G. Bhanot, S. Black, P. Carter, and R. Salvador, Phys. Lett. B, 183, 331 (1987). A New Method for the Partition Function of Discrete Systems with Application to the 3D Ising Model.
    • (1987) Phys. Lett. B , vol.183 , pp. 331
    • Bhanot, G.1    Black, S.2    Carter, P.3    Salvador, R.4
  • 300
    • 4243819810 scopus 로고
    • New Monte Carlo Technique for Studying Phase Transition
    • A. M. Ferrenberg and R. H. Swendsen, Phys. Rev. Lett., 61, 2635 (1988). New Monte Carlo Technique for Studying Phase Transition.
    • (1988) Phys. Rev. Lett. , vol.61 , pp. 2635
    • Ferrenberg, A.M.1    Swendsen, R.H.2
  • 301
  • 302
    • 0002688755 scopus 로고
    • Modern Methods of Analyzing Monte Carlo Computer Simulations
    • R. H. Swendsen, Physica A, 194, 53 (1993). Modern Methods of Analyzing Monte Carlo Computer Simulations.
    • (1993) Physica A , vol.194 , pp. 53
    • Swendsen, R.H.1
  • 303
    • 4244000244 scopus 로고
    • Direct Calculation of Absolute Free Energy for Lattice Systems by Monte Carlo Sampling of Finite Size Dependence
    • K. K. Mon, Phys. Rev. Lett., 54, 2671 (1985). Direct Calculation of Absolute Free Energy for Lattice Systems by Monte Carlo Sampling of Finite Size Dependence.
    • (1985) Phys. Rev. Lett. , vol.54 , pp. 2671
    • Mon, K.K.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.