메뉴 건너뛰기




Volumn 10, Issue 3, 2009, Pages 229-243

Methods for calculating the entropy and free energy and their application to problems involving protein flexibility and ligand binding

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA HELIX; COMPUTER PROGRAM; CONTROLLED STUDY; ENTROPY; LIGAND BINDING; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; METHODOLOGY; MOLECULAR DYNAMICS; MONTE CARLO METHOD; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN STRUCTURE; REVIEW; THERMODYNAMICS; ANIMAL; BIOCHEMISTRY; CHEMISTRY; HUMAN; METABOLISM; PROTEIN BINDING;

EID: 69449086187     PISSN: 13892037     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920309788452209     Document Type: Review
Times cited : (47)

References (142)
  • 1
    • 0024578173 scopus 로고
    • Free energy via molecular simulation: Applications to chemical and biomolecular systems
    • Beveridge, D. L.; DiCapua, F. M. Free energy via molecular simulation: applications to chemical and biomolecular systems. Annu. Rev. Biophys. Biophys. Chem., 1989, 18, 431-492.
    • (1989) Annu. Rev. Biophys. Biophys. Chem , vol.18 , pp. 431-492
    • Beveridge, D.L.1    DiCapua, F.M.2
  • 2
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical Phenomena
    • Kollman, P. A. Free energy calculations: applications to chemical and biochemical Phenomena. Chem. Rev., 1993, 93, 2395-2417.
    • (1993) Chem. Rev , vol.93 , pp. 2395-2417
    • Kollman, P.A.1
  • 3
    • 0009590921 scopus 로고
    • Free energy calculations: A breakthrough for modeling organic chemistry in solution
    • Jorgensen, W. L. Free energy calculations: a breakthrough for modeling organic chemistry in solution. Acc Chem. Res., 1989, 22, 184-189.
    • (1989) Acc Chem. Res , vol.22 , pp. 184-189
    • Jorgensen, W.L.1
  • 4
    • 0032342086 scopus 로고    scopus 로고
    • Calculation of the free energy and entropy of macromolecular systems by computer simulation
    • Lipkowitz, K.B, Boyd, D.B, eds, WileyVCH, New York
    • Meirovitch, H. Calculation of the free energy and entropy of macromolecular systems by computer simulation. In Reviews in Computational Chemistry. (Lipkowitz, K.B., Boyd, D.B., eds.). WileyVCH, New York. 1998, 121-74.
    • (1998) Reviews in Computational Chemistry , pp. 121-174
    • Meirovitch, H.1
  • 5
    • 0031058541 scopus 로고    scopus 로고
    • The statistical thermodynamic basis for computing of binding affinities: A critical review
    • Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. The statistical thermodynamic basis for computing of binding affinities: A critical review. Biophys. J., 1997, 72, 1047-1069.
    • (1997) Biophys. J , vol.72 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, J.A.4
  • 6
    • 0141682863 scopus 로고    scopus 로고
    • Absolute binding free energies: A qualitative approach for their calculation
    • Boresch, S.; Tettinger, F.; Leitgeb, M.; Karplus, M. Absolute binding free energies: A qualitative approach for their calculation. J. Phys. Chem. B, 2003, 107, 9535-9551.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 9535-9551
    • Boresch, S.1    Tettinger, F.2    Leitgeb, M.3    Karplus, M.4
  • 7
    • 34147133371 scopus 로고    scopus 로고
    • Recent developments in methodologies for calculating entropy and free energy of biological systems by computer simulation
    • Meirovitch, H. Recent developments in methodologies for calculating entropy and free energy of biological systems by computer simulation. Curr. Opinion in Struct. Biol., 2007, 17, 181-186.
    • (2007) Curr. Opinion in Struct. Biol , vol.17 , pp. 181-186
    • Meirovitch, H.1
  • 9
    • 33845335781 scopus 로고    scopus 로고
    • Towards predictive ligand design with free-energy based Computational methods?
    • Foloppe, N.; Hubbard, R. Towards predictive ligand design with free-energy based Computational methods?. Curr. Med. Chemistry, 2007, 13, 3583-3608.
    • (2007) Curr. Med. Chemistry , vol.13 , pp. 3583-3608
    • Foloppe, N.1    Hubbard, R.2
  • 11
    • 36849126204 scopus 로고
    • Studies of molecular dynamics. 1. General method
    • Alder, B. J.; Wainwright, T. E. Studies of molecular dynamics. 1. General method. J. Chem. Phys., 1959, 31, 459-466.
    • (1959) J. Chem. Phys , vol.31 , pp. 459-466
    • Alder, B.J.1    Wainwright, T.E.2
  • 12
    • 0017776823 scopus 로고
    • Dynamics of folded proteins
    • McCammon, J. A.; Gelin, B. R.; Karplus, M. Dynamics of folded proteins. Nature, 1977, 267, 585-590.
    • (1977) Nature , vol.267 , pp. 585-590
    • McCammon, J.A.1    Gelin, B.R.2    Karplus, M.3
  • 13
    • 0005635371 scopus 로고
    • On the zero fluctuation of the microscopic free energy and its potential use
    • Meirovitch, H.; Alexandrowicz, Z. On the zero fluctuation of the microscopic free energy and its potential use. J. Stat Phys., 1976, 15, 123-127.
    • (1976) J. Stat Phys , vol.15 , pp. 123-127
    • Meirovitch, H.1    Alexandrowicz, Z.2
  • 14
    • 0001523090 scopus 로고    scopus 로고
    • Simulation of a free energy upper bound, based on the anti-correlation between an approximate free energy functional and its fluctuation
    • Meirovitch, H. Simulation of a free energy upper bound, based on the anti-correlation between an approximate free energy functional and its fluctuation. J. Chem. Phys., 1999, 111, 7215-7224.
    • (1999) J. Chem. Phys , vol.111 , pp. 7215-7224
    • Meirovitch, H.1
  • 15
    • 0023140044 scopus 로고
    • Multiple conformational states of proteins - a molecular dynamics analysis of myoglobin
    • Elber, R.; Karplus, M. Multiple conformational states of proteins - a molecular dynamics analysis of myoglobin. Science, 1987, 235, 318-321.
    • (1987) Science , vol.235 , pp. 318-321
    • Elber, R.1    Karplus, M.2
  • 16
    • 0042091834 scopus 로고
    • Packing structures and transitions in liquids and solids
    • Stillinger, F. H.; Weber, T. A. Packing structures and transitions in liquids and solids. Science, 1984, 225, 983-989.
    • (1984) Science , vol.225 , pp. 983-989
    • Stillinger, F.H.1    Weber, T.A.2
  • 18
    • 0026587998 scopus 로고
    • Structural evidence for induced fit as a mechanism for antibody- antigen recognition
    • Rini, J. M.; Schulze-Gahmen, U.; Wilson, I. A. Structural evidence for induced fit as a mechanism for antibody- antigen recognition. Science, 1992, 255, 959-965.
    • (1992) Science , vol.255 , pp. 959-965
    • Rini, J.M.1    Schulze-Gahmen, U.2    Wilson, I.A.3
  • 22
    • 0023338860 scopus 로고
    • Stability of polypeptides conformational states as determined by computer simulation of the free energy
    • Meirovitch, H.; Vásquez, M.; Scheraga, H. A. Stability of polypeptides conformational states as determined by computer simulation of the free energy. Biopolymers, 1987, 26, 651-671.
    • (1987) Biopolymers , vol.26 , pp. 651-671
    • Meirovitch, H.1    Vásquez, M.2    Scheraga, H.A.3
  • 24
    • 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
    • Meirovitch, H.; Koerber, S. C., Rivier, J.; Hagler, A. T. 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. Biopolymers, 1994, 34, 815-839.
    • (1994) Biopolymers , vol.34 , pp. 815-839
    • Meirovitch, H.1    Koerber, S.C.2    Rivier, J.3    Hagler, A.T.4
  • 25
    • 0030102542 scopus 로고    scopus 로고
    • New theoretical methodology for elucidating the solution structure of peptides from NMR data. III. Solvation effects
    • Meirovitch, H.; Meirovitch, E. New theoretical methodology for elucidating the solution structure of peptides from NMR data. III. Solvation effects. J. Phys. Chem., 1996, 100, 5123-5133.
    • (1996) J. Phys. Chem , vol.100 , pp. 5123-5133
    • Meirovitch, H.1    Meirovitch, E.2
  • 26
    • 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
    • Meirovitch, H.; Hendrickson, T. F. The backbone entropy of loops as a measure of their flexibility. Application to a ras protein simulated by molecular dynamics. Proteins, 1997, 29, 127-140.
    • (1997) Proteins , vol.29 , pp. 127-140
    • Meirovitch, H.1    Hendrickson, T.F.2
  • 27
    • 0033198024 scopus 로고    scopus 로고
    • Free energy based populations of interconverting microstates of a cyclic peptide lead to the experimental NMR data
    • Baysal, C.; Meirovitch, H. Free energy based populations of interconverting microstates of a cyclic peptide lead to the experimental NMR data. Biopolymers, 1999, 50, 329-344.
    • (1999) Biopolymers , vol.50 , pp. 329-344
    • Baysal, C.1    Meirovitch, H.2
  • 28
    • 0034656198 scopus 로고    scopus 로고
    • Ab initio structure prediction of a cyclic pentapeptide in DMSO based on an implicit solvation model
    • Baysal, C.; Meirovitch, H. Ab initio structure prediction of a cyclic pentapeptide in DMSO based on an implicit solvation model. Biopolymers, 2000, 53, 423-433.
    • (2000) Biopolymers , vol.53 , pp. 423-433
    • Baysal, C.1    Meirovitch, H.2
  • 29
    • 3042694216 scopus 로고    scopus 로고
    • Simulation method for calculating the entropy and free energy of peptides and proteins
    • Cheluvaraja, S.; Meirovitch, H. Simulation method for calculating the entropy and free energy of peptides and proteins. Proc. Natl. Acad. Sci. USA, 2004, 101, 9241-9246.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , pp. 9241-9246
    • Cheluvaraja, S.1    Meirovitch, H.2
  • 30
    • 22944464730 scopus 로고    scopus 로고
    • Calculation of the entropy and free energy by the hypothetical scanning Monte Carlo Method: Application to peptides
    • Cheluvaraja, S.; Meirovitch, H. Calculation of the entropy and free energy by the hypothetical scanning Monte Carlo Method: Application to peptides. J. Chem. Phys., 2005, 122, 054903-14.
    • (2005) J. Chem. Phys , vol.122 , pp. 054903-054914
    • Cheluvaraja, S.1    Meirovitch, H.2
  • 31
    • 28944443113 scopus 로고    scopus 로고
    • Calculation of the entropy and free energy from Monte Carlo simulations of a peptide stretched by an external force
    • Cheluvaraja, S.; Meirovitch, H. Calculation of the entropy and free energy from Monte Carlo simulations of a peptide stretched by an external force. J. Phys. Chem. B, 2005, 109, 21963-21970.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 21963-21970
    • Cheluvaraja, S.1    Meirovitch, H.2
  • 32
    • 33746099689 scopus 로고    scopus 로고
    • Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecular dynamics method
    • Cheluvaraja, S.; Meirovitch, H. Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecular dynamics method. J. Chem. Phys., 2006, 125, 024905-13.
    • (2006) J. Chem. Phys , vol.125 , pp. 024905-024913
    • Cheluvaraja, S.1    Meirovitch, H.2
  • 33
    • 0035865992 scopus 로고    scopus 로고
    • Exploring the energy landscape of a beta hairpin in explicit solvent
    • Garcia, A. E.; Sanbonmatsu, K. Y. Exploring the energy landscape of a beta hairpin in explicit solvent. Proteins, 2001, 42, 345-354.
    • (2001) Proteins , vol.42 , pp. 345-354
    • Garcia, A.E.1    Sanbonmatsu, K.Y.2
  • 34
    • 0000106469 scopus 로고
    • Multicanonical algorithms for first order phase transition
    • Berg, B. A.; Neuhaus, T. Multicanonical algorithms for first order phase transition. Phys. Lett. B, 1991, 267, 249-253.
    • (1991) Phys. Lett. B , vol.267 , pp. 249-253
    • Berg, B.A.1    Neuhaus, T.2
  • 35
    • 0037491167 scopus 로고    scopus 로고
    • β-hairpins, ahelices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal β-hairpin of SH3 domain
    • Ikeda, K.; Galzitskaya, O. V.; Nakamura, H.; Higo, J. β-hairpins, ahelices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal β-hairpin of SH3 domain. J. Comput. Chem., 2003, 24, 310-318.
    • (2003) J. Comput. Chem , vol.24 , pp. 310-318
    • Ikeda, K.1    Galzitskaya, O.V.2    Nakamura, H.3    Higo, J.4
  • 36
    • 28644431872 scopus 로고    scopus 로고
    • Free energy landscape and fold mechanism of a β-hairpin in explicit water: A replica exchange molecular dynamics study
    • Nguyen, P. H.; Stock, G.; Mittag, E.; Hu, C. K.; Li, M. S. Free energy landscape and fold mechanism of a β-hairpin in explicit water: a replica exchange molecular dynamics study. Proteins, 2005, 61, 795-808.
    • (2005) Proteins , vol.61 , pp. 795-808
    • Nguyen, P.H.1    Stock, G.2    Mittag, E.3    Hu, C.K.4    Li, M.S.5
  • 37
    • 34547648681 scopus 로고    scopus 로고
    • Collective Langevin dynamics of conformational motions in proteins
    • Lange, O. F.; Grubmüller, H. Collective Langevin dynamics of conformational motions in proteins. J. Chem. Phys., 2006, 124, 214903-18.
    • (2006) J. Chem. Phys , vol.124 , pp. 214903-214918
    • Lange, O.F.1    Grubmüller, H.2
  • 38
    • 36849116054 scopus 로고
    • Machine calculation of thermodynamic properties of a simple fluid
    • MacDonald, I. R.; Singer, K. Machine calculation of thermodynamic properties of a simple fluid. J. Chem. Phys., 1967, 47, 4766-4772.
    • (1967) J. Chem. Phys , vol.47 , pp. 4766-4772
    • MacDonald, I.R.1    Singer, K.2
  • 39
    • 0014665094 scopus 로고
    • Phase transition of the Lennard-Jones system
    • Hansen, J. -P.; Verlet, L. Phase transition of the Lennard-Jones system. Phys. Rev., 1969, 184, 151-161.
    • (1969) Phys. Rev , vol.184 , pp. 151-161
    • Hansen, J.-P.1    Verlet, L.2
  • 40
    • 36849097857 scopus 로고
    • Use of computer experiments to locate the melting transition and calculate the entropy in the solid phase
    • Hoover, W. G.; Ree, F. H. Use of computer experiments to locate the melting transition and calculate the entropy in the solid phase, J. Chem. Phys., 1967, 47, 4873-4878.
    • (1967) J. Chem. Phys , vol.47 , pp. 4873-4878
    • Hoover, W.G.1    Ree, F.H.2
  • 41
    • 70349684413 scopus 로고    scopus 로고
    • Allen, M. P.; Tildesley, D. J. In Computer Simulation of Liquids. Clarenden press, Oxford. 1987.
    • Allen, M. P.; Tildesley, D. J. In Computer Simulation of Liquids. Clarenden press, Oxford. 1987.
  • 42
    • 33646471468 scopus 로고
    • Statistical mechanics of fluid mixtures
    • Kirkwood, J. G. Statistical mechanics of fluid mixtures. J. Chem. Phys., 1935, 3, 300-313.
    • (1935) J. Chem. Phys , vol.3 , pp. 300-313
    • Kirkwood, J.G.1
  • 43
    • 36849122972 scopus 로고
    • High-temperature equation of state by a perturbation method. I. Nonpolar gases
    • Zwanzig, R. W. High-temperature equation of state by a perturbation method. I. Nonpolar gases. J. Chem. Phys., 1954, 22, 1420-1426.
    • (1954) J. Chem. Phys , vol.22 , pp. 1420-1426
    • Zwanzig, R.W.1
  • 44
    • 36849102181 scopus 로고
    • Monte Carlo simulation of vacancies in rare-gas crystals
    • Squire, D. R.; Hoover, W. G. Monte Carlo simulation of vacancies in rare-gas crystals. J. Chem. Phys., 1969, 50, 701-706.
    • (1969) J. Chem. Phys , vol.50 , pp. 701-706
    • Squire, D.R.1    Hoover, W.G.2
  • 45
    • 16444385400 scopus 로고
    • Monte Carlo free energy estimates using non-Boltzmann sampling. Application to the subcritical Lennard- Jones fluid
    • Torrie, G. M.; Valleau, J. P. Monte Carlo free energy estimates using non-Boltzmann sampling. Application to the subcritical Lennard- Jones fluid. Chem. Phys. Lett., 1974, 28, 578-581.
    • (1974) Chem. Phys. Lett , vol.28 , pp. 578-581
    • Torrie, G.M.1    Valleau, J.P.2
  • 46
    • 0342929614 scopus 로고
    • Nonphysical sampling distributions in Monte Carlo free energy estimation: Umbrella sampling
    • Torrie, G. M.; Valleau, J. P. Nonphysical sampling distributions in Monte Carlo free energy estimation: Umbrella sampling. J. Comp. Phys., 1977, 23, 187-199.
    • (1977) J. Comp. Phys , vol.23 , pp. 187-199
    • Torrie, G.M.1    Valleau, J.P.2
  • 47
    • 4243754128 scopus 로고    scopus 로고
    • Nonequilibrium equality for free energy differences
    • Jarzynski, C. Nonequilibrium equality for free energy differences. Phys. Rev. Lett., 1997, 78, 2690-2693.
    • (1997) Phys. Rev. Lett , vol.78 , pp. 2690-2693
    • Jarzynski, C.1
  • 48
    • 33646987405 scopus 로고
    • Optimized Monte Carlo data analysis
    • Ferrenberg, A. M.; Swendsen, R.H. Optimized Monte Carlo data analysis. Phys. Rev. Lett., 1989, 63, 1195-1198.
    • (1989) Phys. Rev. Lett , vol.63 , pp. 1195-1198
    • Ferrenberg, A.M.1    Swendsen, R.H.2
  • 49
    • 84986497803 scopus 로고
    • Multidimensional free energy calculations using the weighted histogram analysis method
    • Kumar, S.; Rosenberg, J. M.; Bouzida, D.; Swendsen, R. H.; Kolmann, P. A. Multidimensional free energy calculations using the weighted histogram analysis method. J. Comput. Chem., 1995, 16, 1339-1350.
    • (1995) J. Comput. Chem , vol.16 , pp. 1339-1350
    • Kumar, S.1    Rosenberg, J.M.2    Bouzida, D.3    Swendsen, R.H.4    Kolmann, P.A.5
  • 50
    • 0001186767 scopus 로고    scopus 로고
    • Method for free energy calculations using iterative technique
    • Kumar, S.; Payne, P. W.; Vásquez, M. Method for free energy calculations using iterative technique. J. Comput Chem., 1996, 17, 1269-1275.
    • (1996) J. Comput Chem , vol.17 , pp. 1269-1275
    • Kumar, S.1    Payne, P.W.2    Vásquez, M.3
  • 51
    • 0001661731 scopus 로고
    • Thermodynamics of aqueous solvation: Solution properties of alcohols and alkanes
    • Fleischman, S. H.; Brooks, III C. L. Thermodynamics of aqueous solvation: Solution properties of alcohols and alkanes. J. Chem. Phys., 1987, 87, 3029-3037.
    • (1987) J. Chem. Phys , vol.87 , pp. 3029-3037
    • Fleischman, S.H.1    Brooks III, C.L.2
  • 53
    • 10844229225 scopus 로고    scopus 로고
    • Calculation of the aqueous solvation energy and entropy, as well as free energy of simple polar solutes
    • Wan, S.; Stote, R. H.; Karplus, M. Calculation of the aqueous solvation energy and entropy, as well as free energy of simple polar solutes. J. Chem. Phys., 2004, 121, 9539-9548.
    • (2004) J. Chem. Phys , vol.121 , pp. 9539-9548
    • Wan, S.1    Stote, R.H.2    Karplus, M.3
  • 54
    • 0027321958 scopus 로고
    • Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches
    • Miyamoto, S.; Kollman, P. A. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches. Proteins, 1993, 16, 226-245.
    • (1993) Proteins , vol.16 , pp. 226-245
    • Miyamoto, S.1    Kollman, P.A.2
  • 55
    • 0027239578 scopus 로고
    • What determines the strength of noncovalent association of ligands to proteins in aqueous solution
    • Miyamoto, S.; Kollman, P. A. What determines the strength of noncovalent association of ligands to proteins in aqueous solution. Proc. Natl. Acad. Sci. USA, 1993, 90, 8402-8406.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 8402-8406
    • Miyamoto, S.1    Kollman, P.A.2
  • 56
    • 0029011701 scopus 로고    scopus 로고
    • Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M. Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman P. A. A second generation force field for the simulation of proteins,nucleic acids, and organic molecules. J. Am. Chem. Soc., 1995, 117, 5179-5197.
    • Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M. Jr.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman P. A. A second generation force field for the simulation of proteins,nucleic acids, and organic molecules. J. Am. Chem. Soc., 1995, 117, 5179-5197.
  • 57
    • 0041784950 scopus 로고    scopus 로고
    • MacKerell, A. D. Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L. Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III, Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wio'rkiewicz-Kuczem, J.; Yin, D.; Karplus, M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B, 1998, 102, 3586-3616.
    • MacKerell, A. D. Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L. Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III, Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wio'rkiewicz-Kuczem, J.; Yin, D.; Karplus, M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B, 1998, 102, 3586-3616.
  • 59
    • 29044442254 scopus 로고    scopus 로고
    • Molecular modeling of organic and biomolecular systems using BOSS and MCPRO
    • Jorgensen, W. L.; Tirado-Rives, J. Molecular modeling of organic and biomolecular systems using BOSS and MCPRO. J. Comput. Chem., 2005, 26, 1689-1700.
    • (2005) J. Comput. Chem , vol.26 , pp. 1689-1700
    • Jorgensen, W.L.1    Tirado-Rives, J.2
  • 62
    • 70349663768 scopus 로고    scopus 로고
    • Ponder, J. W. TINKER, software tools for molecular design, version 4.2. 2004
    • Ponder, J. W. TINKER - software tools for molecular design, version 4.2. 2004.
  • 63
    • 84965088938 scopus 로고    scopus 로고
    • Adaptive integration method for Monte Carlo simulations
    • Fasnacht, M.; Swendsen, R. H.; Rosenberg, J. M. Adaptive integration method for Monte Carlo simulations. Phys. Rev. E, 2004, 69, 056704-15.
    • (2004) Phys. Rev. E , vol.69 , pp. 056704-056715
    • Fasnacht, M.1    Swendsen, R.H.2    Rosenberg, J.M.3
  • 65
    • 33644899039 scopus 로고
    • Simulated Tempering: A New Monte Carlo Scheme
    • Marinari, E.; Parisi, G. Simulated Tempering: a New Monte Carlo Scheme. Europhys Lett., 1992, 19, 451-455.
    • (1992) Europhys Lett , vol.19 , pp. 451-455
    • Marinari, E.1    Parisi, G.2
  • 66
    • 6644221271 scopus 로고    scopus 로고
    • Efficient multiple-range random walk algorithm to calculate the density of states
    • Wang, F.; Landau, D. P. Efficient multiple-range random walk algorithm to calculate the density of states. Phys. Rev. Lett., 2001, 86, 2050-2053.
    • (2001) Phys. Rev. Lett , vol.86 , pp. 2050-2053
    • Wang, F.1    Landau, D.P.2
  • 67
  • 68
    • 17444413356 scopus 로고    scopus 로고
    • Direct calculation of solid-liquid equilibria from density of states Monte Carlo simulations
    • Mastny, E. A.; de Pablo, J. J. Direct calculation of solid-liquid equilibria from density of states Monte Carlo simulations. J. Chem. Phys., 2005, 122, 124109-6.
    • (2005) J. Chem. Phys , vol.122 , pp. 124109-124116
    • Mastny, E.A.1    de Pablo, J.J.2
  • 69
    • 34547853580 scopus 로고    scopus 로고
    • Order-parameter-based Monte Carlo simulation of crystallization
    • Chopra, M.; Müller, M.; de Pablo, J. J. Order-parameter-based Monte Carlo simulation of crystallization. J. Chem. Phys., 2006, 124, 134102-8.
    • (2006) J. Chem. Phys , vol.124 , pp. 134102-134108
    • Chopra, M.1    Müller, M.2    de Pablo, J.J.3
  • 70
    • 0345790274 scopus 로고    scopus 로고
    • Expanded ensemble and replica exchange methods for simulation of protein-like systems
    • Fenwick, M. K.; Escobedo, F. A. Expanded ensemble and replica exchange methods for simulation of protein-like systems. J. Chem. Phys., 2003, 119, 11998-12010.
    • (2003) J. Chem. Phys , vol.119 , pp. 11998-12010
    • Fenwick, M.K.1    Escobedo, F.A.2
  • 71
    • 1642273052 scopus 로고    scopus 로고
    • On the use of Bennett's acceptance ratio method in multi-canonical-type simulations
    • Fenwick, M. K.; Escobedo, F. A. On the use of Bennett's acceptance ratio method in multi-canonical-type simulations. J., Chem. Phys., 2004, 120, 3066-3074.
    • (2004) J., Chem. Phys , vol.120 , pp. 3066-3074
    • Fenwick, M.K.1    Escobedo, F.A.2
  • 72
    • 21244501332 scopus 로고    scopus 로고
    • Multicanonical schemes for mapping out free energy landscapes of single-component and multicomponent systems
    • Gospodinov, I. D.; Escobedo, F. A. Multicanonical schemes for mapping out free energy landscapes of single-component and multicomponent systems. J. Chem. Phys., 2005, 122, 164103-10.
    • (2005) J. Chem. Phys , vol.122 , pp. 164103-164110
    • Gospodinov, I.D.1    Escobedo, F.A.2
  • 73
    • 32044443418 scopus 로고    scopus 로고
    • Abreu, C. R. A.; Escobedo, F. A. A general framework for non-Boltzmann Monte Carlo sampling. J. Chem. Phys., 2006, 124, 054116-12.
    • Abreu, C. R. A.; Escobedo, F. A. A general framework for non-Boltzmann Monte Carlo sampling. J. Chem. Phys., 2006, 124, 054116-12.
  • 74
    • 35948985463 scopus 로고    scopus 로고
    • Optimized expanded ensembles for simulations involving molecular insertions and deletions. II. Open systems
    • Escobedo, F. A. Optimized expanded ensembles for simulations involving molecular insertions and deletions. II. Open systems. J. Chem. Phys., 2007, 127, 174104-12.
    • (2007) J. Chem. Phys , vol.127 , pp. 174104-174112
    • Escobedo, F.A.1
  • 75
    • 5244304444 scopus 로고
    • Efficient estimation of free energy differences from Monte Carlo data
    • Bennett, C. H. Efficient estimation of free energy differences from Monte Carlo data. J. Comput. Phys., 1976, 22, 245-268.
    • (1976) J. Comput. Phys , vol.22 , pp. 245-268
    • Bennett, C.H.1
  • 76
    • 0037961506 scopus 로고    scopus 로고
    • Replica-exchange multi-canonical and multicanonical replica-exchange Monte Carlo simulations of peptides. II. Application to a more complex system
    • Mitsutake, A.; Sugita, Y.; Okamoto, Y. Replica-exchange multi-canonical and multicanonical replica-exchange Monte Carlo simulations of peptides. II. Application to a more complex system. J. Chem. Phys., 2003, 118, 6676-6688.
    • (2003) J. Chem. Phys , vol.118 , pp. 6676-6688
    • Mitsutake, A.1    Sugita, Y.2    Okamoto, Y.3
  • 77
    • 17844365851 scopus 로고    scopus 로고
    • Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent
    • Sugita, Y.; Okamoto, Y. Molecular mechanism for stabilizing a short helical peptide studied by generalized-ensemble simulations with explicit solvent. Biophys. J., 2005, 88, 3180-3190.
    • (2005) Biophys. J , vol.88 , pp. 3180-3190
    • Sugita, Y.1    Okamoto, Y.2
  • 78
    • 33847021237 scopus 로고    scopus 로고
    • Cooperative folding mechanism of a ???-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation
    • Yoda, D. Sugita, Y.; Okamoto, Y. Cooperative folding mechanism of a ???-hairpin peptide studied by a multicanonical replica-exchange molecular dynamics simulation. Proteins, 2007, 66, 846-859.
    • (2007) Proteins , vol.66 , pp. 846-859
    • Yoda, D.1    Sugita, Y.2    Okamoto, Y.3
  • 79
    • 0030819348 scopus 로고    scopus 로고
    • Multicanonical ensemble generated by molecular dynamics simulation for enhanced sampling of peptides
    • Nakajima, N.; Nakamura, H.; Kidera, A. Multicanonical ensemble generated by molecular dynamics simulation for enhanced sampling of peptides. J. Phys. Chem. B, 1997, 101, 817-824.
    • (1997) J. Phys. Chem. B , vol.101 , pp. 817-824
    • Nakajima, N.1    Nakamura, H.2    Kidera, A.3
  • 80
    • 0344121638 scopus 로고    scopus 로고
    • The filling potential method: A method for estimating the free energy surface for protein-ligand docking
    • Fukunishi, Y.; Mikami, Y.; Nakamura, H. The filling potential method: A method for estimating the free energy surface for protein-ligand docking. J. Phys. Chem. B, 2003, 107, 13201-13210.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 13201-13210
    • Fukunishi, Y.1    Mikami, Y.2    Nakamura, H.3
  • 81
    • 9644303223 scopus 로고    scopus 로고
    • Free energy landscapes of small peptides in an implicit solvent model determined by force-biased multicanonical molecular dynamics simulation
    • Watanabe, Y. S.; Kim, J. G.; Fukunishi, Y.; Nakamura, H. Free energy landscapes of small peptides in an implicit solvent model determined by force-biased multicanonical molecular dynamics simulation. Chem. Phys. Lett., 2004, 400, 258-263.
    • (2004) Chem. Phys. Lett , vol.400 , pp. 258-263
    • Watanabe, Y.S.1    Kim, J.G.2    Fukunishi, Y.3    Nakamura, H.4
  • 82
    • 37349000545 scopus 로고    scopus 로고
    • Protein-inhibitor flexible docking by a multicanonical sampling: Native complex structure with the lowest free energy and a free-energy barrier distinguishing the native complex from the others
    • Kamiya, N.; Yonezawa, Y.; Nakamura, H.; Higo, J. Protein-inhibitor flexible docking by a multicanonical sampling: Native complex structure with the lowest free energy and a free-energy barrier distinguishing the native complex from the others. Proteins, 2008, 70, 41-53.
    • (2008) Proteins , vol.70 , pp. 41-53
    • Kamiya, N.1    Yonezawa, Y.2    Nakamura, H.3    Higo, J.4
  • 83
    • 5444249356 scopus 로고
    • Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems. 2004
    • Ytreberg, F. M.; Zuckerman, D. M. Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems. 2004 J. Comput. Chem., 25, 1749-1759.
    • (1749) J. Comput. Chem , vol.25
    • Ytreberg, F.M.1    Zuckerman, D.M.2
  • 84
    • 3042688939 scopus 로고    scopus 로고
    • Single-ensemble nonequilibrium path-sampling estimates of free energy differences
    • Ytreberg, F. M.; Zuckerman, D. M. Single-ensemble nonequilibrium path-sampling estimates of free energy differences. J. Chem. Phys., 2004, 120, 10876-10879.
    • (2004) J. Chem. Phys , vol.120 , pp. 10876-10879
    • Ytreberg, F.M.1    Zuckerman, D.M.2
  • 85
    • 33645666178 scopus 로고    scopus 로고
    • Rare events and convergence of exponentially averaged work values
    • Jarzynski, C. Rare events and convergence of exponentially averaged work values. Phys. Rev. E, 2006, 73, 046105-10.
    • (2006) Phys. Rev. E , vol.73 , pp. 046105-046110
    • Jarzynski, C.1
  • 86
    • 34548080273 scopus 로고    scopus 로고
    • Rosenbluth-sampled nonequilibrium work method for Calculation of free energies in molecular simulation
    • Wu, D.; Kolke, D. A. Rosenbluth-sampled nonequilibrium work method for Calculation of free energies in molecular simulation. J. Chem. Phys., 2005, 122, 204104-13.
    • (2005) J. Chem. Phys , vol.122 , pp. 204104-204113
    • Wu, D.1    Kolke, D.A.2
  • 87
    • 17444372741 scopus 로고    scopus 로고
    • Biased sampling of non-equilibrium trajectories: Can fast switching simulations outperform conventional free energy calculations methods?
    • Oberhofer, H.; Dellago, C.; Geissler, P. Biased sampling of non-equilibrium trajectories: can fast switching simulations outperform conventional free energy calculations methods?. J. Phys. Chem., 2005, 109, 6902-6915.
    • (2005) J. Phys. Chem , vol.109 , pp. 6902-6915
    • Oberhofer, H.1    Dellago, C.2    Geissler, P.3
  • 88
    • 31544454748 scopus 로고    scopus 로고
    • Equilibrium free energies from fast-switching trajectories with large time step
    • Lechner, W.; Oberhofer, H.; Dellago, C.; Geissler, P. Equilibrium free energies from fast-switching trajectories with large time step. J. Chem. Phys., 2006, 124, 044113- 12.
    • (2006) J. Chem. Phys , vol.124 , pp. 044113-44212
    • Lechner, W.1    Oberhofer, H.2    Dellago, C.3    Geissler, P.4
  • 89
    • 34547139165 scopus 로고    scopus 로고
    • A skewed-momenta method to efficiently generate conformational-transition trajectories
    • MacFadyen, J.; Andricioaci, I. A skewed-momenta method to efficiently generate conformational-transition trajectories. J. Chem. Phys., 2005, 123, 074107-9.
    • (2005) J. Chem. Phys , vol.123 , pp. 074107-074109
    • MacFadyen, J.1    Andricioaci, I.2
  • 90
    • 34547648030 scopus 로고    scopus 로고
    • Adib, A., B. Free energy surfaces from nonequilibrium processes without work measurement. J. Chem. Phys., 2006, 124, 144111-5.
    • Adib, A., B. Free energy surfaces from nonequilibrium processes without work measurement. J. Chem. Phys., 2006, 124, 144111-5.
  • 91
    • 23944432199 scopus 로고    scopus 로고
    • Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamics integration
    • Shirts, M. R.; Pande, V. S. Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamics integration. J. Chem. Phys., 2005, 122, 144107-16.
    • (2005) J. Chem. Phys , vol.122 , pp. 144107-144116
    • Shirts, M.R.1    Pande, V.S.2
  • 92
    • 33748267063 scopus 로고    scopus 로고
    • Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics
    • Jayachandran, G.; Shirts, M. R.; Park, S.; Pande, V. J. Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics. J. Chem. Phys., 2006, 125, 084901-12.
    • (2006) J. Chem. Phys , vol.125 , pp. 084901-084912
    • Jayachandran, G.1    Shirts, M.R.2    Park, S.3    Pande, V.J.4
  • 93
    • 33750970530 scopus 로고    scopus 로고
    • Comparison of free energy methods for molecular simulations
    • Ytreberg, F. M.; Swendsen, R. H.; Zuckerman, D. M. Comparison of free energy methods for molecular simulations. J. Chem. Phys., 2006, 125, 184114-11.
    • (2006) J. Chem. Phys , vol.125 , pp. 184114-184211
    • Ytreberg, F.M.1    Swendsen, R.H.2    Zuckerman, D.M.3
  • 94
    • 33644938813 scopus 로고    scopus 로고
    • Potential of mean force for a acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain
    • Zharkg, D.; Gullingsrud, J.; McCammon, J. A. Potential of mean force for a acetylcholine unbinding from the alpha7 nicotinic acetylcholine receptor ligand-binding domain. J. Am. Chem. Soc., 2006, 128, 3019-3026.
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 3019-3026
    • Zharkg, D.1    Gullingsrud, J.2    McCammon, J.A.3
  • 95
    • 33748269730 scopus 로고    scopus 로고
    • Free energy calculations with non-eqvilibrium methods: Applications of the Jarzynski relationship
    • Xiong, H.; Crespo, A.; Marti, M.; Estrin, D.; Roilberg, A. E. Free energy calculations with non-eqvilibrium methods: applications of the Jarzynski relationship. Theor. Chem. Acc., 2006, 116, 338-346.
    • (2006) Theor. Chem. Acc , vol.116 , pp. 338-346
    • Xiong, H.1    Crespo, A.2    Marti, M.3    Estrin, D.4    Roilberg, A.E.5
  • 96
    • 51149216498 scopus 로고
    • Analysis of the contribution of internal vibrations to the statistical weights of equilibrium conformations of macromolecules
    • Go, N.; Scheraga, H. A. Analysis of the contribution of internal vibrations to the statistical weights of equilibrium conformations of macromolecules. J. Chem. Phys., 1969, 51, 4751-4767.
    • (1969) J. Chem. Phys , vol.51 , pp. 4751-4767
    • Go, N.1    Scheraga, H.A.2
  • 97
    • 18344362394 scopus 로고
    • On the use of classical statistical mechanics in the treatment of polymer chain conformation
    • Go, N.; Scheraga, H. A. On the use of classical statistical mechanics in the treatment of polymer chain conformation. Macromolecules, 1976, 9, 535-542.
    • (1976) Macromolecules , vol.9 , pp. 535-542
    • Go, N.1    Scheraga, H.A.2
  • 98
    • 0001182617 scopus 로고
    • Computer simulation of the conformational properties of oligopeptides. Comparison of theoretical methods and analysis of experimental results
    • Hagler, A. T.; Stern, P. S.; Sharon, R.; Becker, J. M.; Naider, F. Computer simulation of the conformational properties of oligopeptides. Comparison of theoretical methods and analysis of experimental results. J Am. Chem. Soc., 1979, 101, 6842-6852.
    • (1979) J Am. Chem. Soc , vol.101 , pp. 6842-6852
    • Hagler, A.T.1    Stern, P.S.2    Sharon, R.3    Becker, J.M.4    Naider, F.5
  • 99
    • 0242411477 scopus 로고    scopus 로고
    • Chang, C. E.; Gilson, M. K. Tork: Conformational analysis method for molecules and complexes. J. Comput. Chem., 2003, 24, 1987-1998.
    • Chang, C. E.; Gilson, M. K. Tork: Conformational analysis method for molecules and complexes. J. Comput. Chem., 2003, 24, 1987-1998.
  • 100
    • 33646062293 scopus 로고    scopus 로고
    • Concepts in receptor optimization: Targeting the RGD peptide
    • Chen, W.; Chang, C. E.; Gilson, M. K. Concepts in receptor optimization: targeting the RGD peptide. J. Am. Chem. Soc., 2005, 128, 4675-4684.
    • (2005) J. Am. Chem. Soc , vol.128 , pp. 4675-4684
    • Chen, W.1    Chang, C.E.2    Gilson, M.K.3
  • 101
    • 0000127140 scopus 로고
    • Method for estimating the configurational entropy of macromolecules
    • Karplus, M.; Kushick, J. N. Method for estimating the configurational entropy of macromolecules. Macromolecules, 1981, 14, 325-332.
    • (1981) Macromolecules , vol.14 , pp. 325-332
    • Karplus, M.1    Kushick, J.N.2
  • 102
    • 0011146589 scopus 로고
    • Corrections to the quasiharmonic approximation for evaluating molecular entropies
    • Rojas, O. L.; Levy, R. M.; Szabo, A. Corrections to the quasiharmonic approximation for evaluating molecular entropies. J. Chem. Phys., 1986, 85, 1037-1043.
    • (1986) J. Chem. Phys , vol.85 , pp. 1037-1043
    • Rojas, O.L.1    Levy, R.M.2    Szabo, A.3
  • 103
    • 0034323089 scopus 로고    scopus 로고
    • Absolute entropies from molecular dynamics simulation trajectories
    • Schäfer, H.; Mark, A.E.; van Gunsteren, W. F. Absolute entropies from molecular dynamics simulation trajectories. J. Chem. Phys., 2000, 113, 7809-7817.
    • (2000) J. Chem. Phys , vol.113 , pp. 7809-7817
    • Schäfer, H.1    Mark, A.E.2    van Gunsteren, W.F.3
  • 104
    • 0035314075 scopus 로고    scopus 로고
    • Entropy calculations on a reversibly folding peptide: Changes in solute free energy cannot explain folding behavior
    • Schäfer, H.; Daura, X.; Mark, A. E.; van Gunsteren, W. F. Entropy calculations on a reversibly folding peptide: Changes in solute free energy cannot explain folding behavior. Proteins, 2001, 43, 45-56.
    • (2001) Proteins , vol.43 , pp. 45-56
    • Schäfer, H.1    Daura, X.2    Mark, A.E.3    van Gunsteren, W.F.4
  • 105
    • 25844492293 scopus 로고    scopus 로고
    • Evaluating the accuracy of the quasiharmonic approximation
    • Chang, C. E.; Chen, W.; Gilson, M. K. Evaluating the accuracy of the quasiharmonic approximation.. J. Chem. Theory. Comput., 2005, 1, 1017-1028.
    • (2005) J. Chem. Theory. Comput , vol.1 , pp. 1017-1028
    • Chang, C.E.1    Chen, W.2    Gilson, M.K.3
  • 106
    • 0001351515 scopus 로고
    • Estimation of absolute and relative entropies of macromolecules using the covariance matrix
    • Schlitter, J. Estimation of absolute and relative entropies of macromolecules using the covariance matrix. Chem. Phys. Lett., 1993, 215, 617-621.
    • (1993) Chem. Phys. Lett , vol.215 , pp. 617-621
    • Schlitter, J.1
  • 107
    • 0035828630 scopus 로고    scopus 로고
    • On the calculation of entropy from covariance matrices of the atomic fluctuations
    • Andricioaei, I.; Kaplus, M. On the calculation of entropy from covariance matrices of the atomic fluctuations. J Chem. Phys., 2001, 115, 6289-6292.
    • (2001) J Chem. Phys , vol.115 , pp. 6289-6292
    • Andricioaei, I.1    Kaplus, M.2
  • 108
    • 17044372385 scopus 로고    scopus 로고
    • Absolute and relative entropies from computer simulation with applications to ligand binding
    • Carlsson, J.; Åqvist, J. Absolute and relative entropies from computer simulation with applications to ligand binding. J. Phys. Chem. B, 2005, 109, 6448-6456.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 6448-6456
    • Carlsson, J.1    Åqvist, J.2
  • 109
    • 33846307768 scopus 로고    scopus 로고
    • 2D entropy of discrete molecular ensembles
    • Wang, J.; Brüschweiler, R. 2D entropy of discrete molecular ensembles. J. Chem. Theory Comput., 2006, 2, 18-24.
    • (2006) J. Chem. Theory Comput , vol.2 , pp. 18-24
    • Wang, J.1    Brüschweiler, R.2
  • 110
    • 38049123863 scopus 로고    scopus 로고
    • Evaluation of configurational entropy methods from peptide folding-unfolding simulation
    • Li, D. W.; Khanlarzadeh, M.; Wang, J.; Huo, S.; Brüschweiler, R. Evaluation of configurational entropy methods from peptide folding-unfolding simulation. J. Phys. Chem. B, 2007, 111, 13807-13813.
    • (2007) J. Phys. Chem. B , vol.111 , pp. 13807-13813
    • Li, D.W.1    Khanlarzadeh, M.2    Wang, J.3    Huo, S.4    Brüschweiler, R.5
  • 111
    • 0001598816 scopus 로고
    • Calculation of entropy with computer simulation methods
    • Meirovitch, H. Calculation of entropy with computer simulation methods. Chem. Phys. Lett., 1977, 45, 389-392.
    • (1977) Chem. Phys. Lett , vol.45 , pp. 389-392
    • Meirovitch, H.1
  • 112
    • 0001251117 scopus 로고
    • Computer simulation of the free energy of polymer chains with excluded volume and with finite interactions
    • Meirovitch, H. Computer simulation of the free energy of polymer chains with excluded volume and with finite interactions. Phys. Rev. A, 1985, 32, 3709-3715.
    • (1985) Phys. Rev. A , vol.32 , pp. 3709-3715
    • Meirovitch, H.1
  • 113
    • 0005546313 scopus 로고
    • Computer simulation of the entropy of continuum chain models: The two dimensional freely-jointed chain of hard disks
    • Meirovitch, H.; Scheraga, H. A. Computer simulation of the entropy of continuum chain models: the two dimensional freely-jointed chain of hard disks. J. Chem. Phys., 1986, 84, 6369-6375.
    • (1986) J. Chem. Phys , vol.84 , pp. 6369-6375
    • Meirovitch, H.1    Scheraga, H.A.2
  • 114
    • 0005648839 scopus 로고
    • Methods for estimating the entropy with computer simulation. The simple cubic Ising lattice
    • Meirovitch, H. Methods for estimating the entropy with computer simulation. The simple cubic Ising lattice. J. Phys. A, 1983, 16, 839-846.
    • (1983) J. Phys. A , vol.16 , pp. 839-846
    • Meirovitch, H.1
  • 115
    • 0035280880 scopus 로고    scopus 로고
    • On the simulation of the entropy of macromolecules with different flexibilities
    • Meirovitch, H. On the simulation of the entropy of macromolecules with different flexibilities. J. Chem. Phys., 2001, 114, 3859-3867.
    • (2001) J. Chem. Phys , vol.114 , pp. 3859-3867
    • Meirovitch, H.1
  • 116
    • 0346058197 scopus 로고    scopus 로고
    • Absolute entropy and free energy of fluids using the hypothetical scanning method. II. Transition probabilities from canonical Monte Carlo simulations of partial systems
    • White, R. P.; Meirovitch, H. Absolute entropy and free energy of fluids using the hypothetical scanning method. II. Transition probabilities from canonical Monte Carlo simulations of partial systems. J. Chem. Phys., 2003, 119, 12096-12105.
    • (2003) J. Chem. Phys , vol.119 , pp. 12096-12105
    • White, R.P.1    Meirovitch, H.2
  • 117
    • 11144269103 scopus 로고    scopus 로고
    • Lower and upper bounds for the absolute free energy by the hypothetical scanning Monte Carlo method: Application to liquid argon and water
    • White, R. P.; Meirovitch, H. Lower and upper bounds for the absolute free energy by the hypothetical scanning Monte Carlo method: Application to liquid argon and water. J. Chem. Phys., 2004, 121, 10889-10904.
    • (2004) J. Chem. Phys , vol.121 , pp. 10889-10904
    • White, R.P.1    Meirovitch, H.2
  • 118
    • 33744803702 scopus 로고    scopus 로고
    • Calculation of the entropy of random coil polymers with the hypothetical scanning Monte Carlo Method
    • White, R. P.; Meirovitch, H. Calculation of the entropy of random coil polymers with the hypothetical scanning Monte Carlo Method. J. Chem. Phys., 2005, 123, 214908-11.
    • (2005) J. Chem. Phys , vol.123 , pp. 214908-214911
    • White, R.P.1    Meirovitch, H.2
  • 119
    • 34547555286 scopus 로고    scopus 로고
    • Free volume hypothetical scanning molecular dynamics method for the absolute free energy of liquids
    • White, R. P.; Meirovitch, H. Free volume hypothetical scanning molecular dynamics method for the absolute free energy of liquids. J. Chem. Phys., 2006, 124, 204108-13.
    • (2006) J. Chem. Phys , vol.124 , pp. 204108-204113
    • White, R.P.1    Meirovitch, H.2
  • 120
    • 38749088637 scopus 로고    scopus 로고
    • Stability of the free and bound microstates of a mobile loop of α-amylase obtained from the absolute entropy and free energy
    • Cheluvaraja, S.; Meirovitch, H. Stability of the free and bound microstates of a mobile loop of α-amylase obtained from the absolute entropy and free energy. J. Chem. Theory Comput., 2008, 4, 192-208.
    • (2008) J. Chem. Theory Comput , vol.4 , pp. 192-208
    • Cheluvaraja, S.1    Meirovitch, H.2
  • 121
    • 49649089718 scopus 로고    scopus 로고
    • Entropy and free energy of a mobile loop in explicit water
    • Cheluvaraja, S.; Mihailescu, M.; Meirovitch, H. Entropy and free energy of a mobile loop in explicit water. J. Phys. Chem., 2008, 112, 9512-9522.
    • (2008) J. Phys. Chem , vol.112 , pp. 9512-9522
    • Cheluvaraja, S.1    Mihailescu, M.2    Meirovitch, H.3
  • 122
    • 4043180889 scopus 로고
    • A new method for simulation of real chains. Scanning future steps
    • Meirovitch, H. A new method for simulation of real chains. Scanning future steps. J. Phys. A, 1982, 15, L735-L740.
    • (1982) J. Phys. A , vol.15
    • Meirovitch, H.1
  • 123
    • 0001563695 scopus 로고
    • Statistical properties of the scanning simulation method for polymer chains
    • Meirovitch, H. Statistical properties of the scanning simulation method for polymer chains. J. Chem. Phys., 1988, 89, 2514-2522.
    • (1988) J. Chem. Phys , vol.89 , pp. 2514-2522
    • Meirovitch, H.1
  • 124
    • 0024066981 scopus 로고
    • Stability of polypeptides conformational states: II. The free energy of the statistical coil obtained by the scanning simulation method
    • Meirovitch, H.; Vásquez, M.; Scheraga, H. A. Stability of polypeptides conformational states: II. The free energy of the statistical coil obtained by the scanning simulation method. Biopolymers, 1988, 27, 1189-1204.
    • (1988) Biopolymers , vol.27 , pp. 1189-1204
    • Meirovitch, H.1    Vásquez, M.2    Scheraga, H.A.3
  • 125
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 1983, 79, 926-935.
    • (1983) J. Chem. Phys , vol.79 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Madura, J.D.3
  • 126
    • 0346186095 scopus 로고    scopus 로고
    • Absolute entropy and free energy of fluids using the hypothetical scanning method. I. Calculation of transition probabilities from local grand canonical partition functions
    • Szarecka, A.; White, R. P.; Meirovitch, H. Absolute entropy and free energy of fluids using the hypothetical scanning method. I. Calculation of transition probabilities from local grand canonical partition functions. J. Chem. Phys., 2003, 119, 12084-12095.
    • (2003) J. Chem. Phys , vol.119 , pp. 12084-12095
    • Szarecka, A.1    White, R.P.2    Meirovitch, H.3
  • 127
    • 0030268102 scopus 로고    scopus 로고
    • Partition functions and equilibrium measures in two-dimensional and quasi- three-dimensional turbulence
    • Chorin, A. J. Partition functions and equilibrium measures in two-dimensional and quasi- three-dimensional turbulence. Phys. Fluids, 1996, 8, 2656-2660
    • (1996) Phys. Fluids , vol.8 , pp. 2656-2660
    • Chorin, A.J.1
  • 128
    • 33847642496 scopus 로고    scopus 로고
    • Nearest- neighbor nonparametric method for estimating the configurational entropy of complex molecules
    • Hnizdo, V.; Darian, E.; Fedorowicz, A; Demchuk, E.; Li, S.; Singh, H. Nearest- neighbor nonparametric method for estimating the configurational entropy of complex molecules. J. Comput. Chem., 2007, 28, 655-668.
    • (2007) J. Comput. Chem , vol.28 , pp. 655-668
    • Hnizdo, V.1    Darian, E.2    Fedorowicz, A.3    Demchuk, E.4    Li, S.5    Singh, H.6
  • 129
    • 34547227692 scopus 로고    scopus 로고
    • Extraction of configurational entropy firom molecular simulations via an expansion approximation
    • Killian, B. J.; Kravitz, J. Y.; Gilson, M. K. Extraction of configurational entropy firom molecular simulations via an expansion approximation. J. Chem. Phys., 2007, 127, 024107-16.
    • (2007) J. Chem. Phys , vol.127 , pp. 024107-024116
    • Killian, B.J.1    Kravitz, J.Y.2    Gilson, M.K.3
  • 130
    • 0025698293 scopus 로고
    • Absolute free energies in biomolecular systems. Macromolecules
    • Stoessel, J. P.; Novak, P. Absolute free energies in biomolecular systems. Macromolecules. Macromolecules, 1990, 23, 1961-1965.
    • (1990) Macromolecules , vol.23 , pp. 1961-1965
    • Stoessel, J.P.1    Novak, P.2
  • 131
    • 33748807193 scopus 로고    scopus 로고
    • An efficient path-independent method for free energy calculations
    • Tyka, M. D.; Clarke, A. R.; Sessions, R. B. An efficient path-independent method for free energy calculations. J. Phys. Chem. B, 2006, 110, 17212-17220.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 17212-17220
    • Tyka, M.D.1    Clarke, A.R.2    Sessions, R.B.3
  • 132
    • 34547648559 scopus 로고    scopus 로고
    • Simple estimation of absolute free energies for biomolecules
    • Ytreberg, F. M.; Zuckerman, D. M. Simple estimation of absolute free energies for biomolecules. J. Chem. Phys., 2006, 124, 104105-5.
    • (2006) J. Chem. Phys , vol.124 , pp. 104105-104105
    • Ytreberg, F.M.1    Zuckerman, D.M.2
  • 133
    • 36549092427 scopus 로고
    • A Monte Carlo method for determining free energy differences and transition state theory rate constants
    • Voter, A. F. A Monte Carlo method for determining free energy differences and transition state theory rate constants. J. Chem. Phys., 1985, 82, 1890-1899.
    • (1985) J. Chem. Phys , vol.82 , pp. 1890-1899
    • Voter, A.F.1
  • 134
    • 19944364561 scopus 로고    scopus 로고
    • Peptide conformational. equilibria computed via a single-stage shifting protocol
    • Ytreberg, F. M.; Zuckerman, D. M. Peptide conformational. equilibria computed via a single-stage shifting protocol. J. Phys. Chem. B, 2005, 109, 9096-9103.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 9096-9103
    • Ytreberg, F.M.1    Zuckerman, D.M.2
  • 135
    • 23744508332 scopus 로고    scopus 로고
    • Absolute free energy calculations by thermodynamic integration in four spatial dimensions
    • Rodinger, T.; Howell, P. L.; Pomes, R. Absolute free energy calculations by thermodynamic integration in four spatial dimensions. J. Chem. Phys., 2005, 123, 034104-11.
    • (2005) J. Chem. Phys , vol.123 , pp. 034104-034111
    • Rodinger, T.1    Howell, P.L.2    Pomes, R.3
  • 136
    • 2342648012 scopus 로고    scopus 로고
    • Ensemble variance in free energy calculations by thermodynamic integration: Theory, optimal "alchemical" path, and practical solutions
    • Blondel, A. Ensemble variance in free energy calculations by thermodynamic integration: theory, optimal "alchemical" path, and practical solutions. J. Comput. Chem., 2004, 25, 985-993.
    • (2004) J. Comput. Chem , vol.25 , pp. 985-993
    • Blondel, A.1
  • 137
    • 36049018890 scopus 로고    scopus 로고
    • On the calculation of absolute free energy from molecular- dynamics or Monte Carlo data
    • Huang, L.; Makarov, D. E. On the calculation of absolute free energy from molecular- dynamics or Monte Carlo data. J. Chem. Phys., 2006, 124, 064108-9.
    • (2006) J. Chem. Phys , vol.124 , pp. 064108-064109
    • Huang, L.1    Makarov, D.E.2
  • 138
    • 18744379773 scopus 로고    scopus 로고
    • Estimation of the absolute intemal-rotation entropy of molecules with two torsional degrees of freedom from stochastic simulations
    • Darian, E.; Hnizdo, V.; Fedorowicz, A.; Singh, H.; Demchuck, E. Estimation of the absolute intemal-rotation entropy of molecules with two torsional degrees of freedom from stochastic simulations. J. Comput. Chem., 2005, 26, 651-660.
    • (2005) J. Comput. Chem , vol.26 , pp. 651-660
    • Darian, E.1    Hnizdo, V.2    Fedorowicz, A.3    Singh, H.4    Demchuck, E.5
  • 139
    • 30744434619 scopus 로고    scopus 로고
    • Evaluating the conformational entropy of macromolecules using an energy decomposition approach
    • Ohkubo, Y. Z.; Thorpe, I. F. Evaluating the conformational entropy of macromolecules using an energy decomposition approach. J. Chem. Phys., 2006, 124, 024910-6.
    • (2006) J. Chem. Phys , vol.124 , pp. 024910-024916
    • Ohkubo, Y.Z.1    Thorpe, I.F.2
  • 140
    • 33646178918 scopus 로고    scopus 로고
    • Calculation of absolute protein-ligand binding affinity using path and endpoint approaches
    • Lee, M. S.; Olson, M. A. Calculation of absolute protein-ligand binding affinity using path and endpoint approaches. Biophys. J., 2006, 90, 864-877.
    • (2006) Biophys. J , vol.90 , pp. 864-877
    • Lee, M.S.1    Olson, M.A.2
  • 141
    • 18744372751 scopus 로고    scopus 로고
    • Calculation of absolute protein-ligand binding free energy from computer simulation
    • Woo, H. J.; Roux, B. Calculation of absolute protein-ligand binding free energy from computer simulation. Proc. Natl. Acad. Sci. USA, 2005, 102, 6825-6830.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , pp. 6825-6830
    • Woo, H.J.1    Roux, B.2
  • 142
    • 33644776045 scopus 로고    scopus 로고
    • Toward accurate ab initio QM/MM calculations of free energy profiles of enzymatic reactions
    • Rosta, E.; Klähn, M.; Warshel, A. Toward accurate ab initio QM/MM calculations of free energy profiles of enzymatic reactions. J. Phys. Chem. B, 2006, 110, 2934-2941.
    • (2006) J. Phys. Chem. B , vol.110 , pp. 2934-2941
    • Rosta, E.1    Klähn, M.2    Warshel, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.