메뉴 건너뛰기




Volumn 5, Issue 1, 2015, Pages 1-26

Direct methods for computing single-molecule entropies from molecular simulations

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; IMPORTANCE SAMPLING; MOLECULAR GRAPHICS; MOLECULAR STRUCTURE; MOLECULES;

EID: 84919463511     PISSN: 17590876     EISSN: 17590884     Source Type: Journal    
DOI: 10.1002/wcms.1195     Document Type: Article
Times cited : (48)

References (102)
  • 1
    • 79959385914 scopus 로고    scopus 로고
    • Behind the folding funnel diagram
    • Karplus M. Behind the folding funnel diagram. Nat Chem Biol 2011, 7:401-404.
    • (2011) Nat Chem Biol , vol.7 , pp. 401-404
    • Karplus, M.1
  • 2
    • 70349100806 scopus 로고    scopus 로고
    • Theory of free energy and entropy in noncovalent binding
    • Zhou H-X, Gilson MK. Theory of free energy and entropy in noncovalent binding. Chem Rev 2009, 109:4092-4107.
    • (2009) Chem Rev , vol.109 , pp. 4092-4107
    • Zhou, H.-X.1    Gilson, M.K.2
  • 3
    • 84887749989 scopus 로고    scopus 로고
    • A surprising role for conformational entropy in protein function
    • Wand AJ, Moorman VJ, Harpole KW. A surprising role for conformational entropy in protein function. Top Curr Chem 2013, 337:69-94.
    • (2013) Top Curr Chem , vol.337 , pp. 69-94
    • Wand, A.J.1    Moorman, V.J.2    Harpole, K.W.3
  • 4
    • 84871856768 scopus 로고    scopus 로고
    • Entropies of adsorbed molecules exceed expectations
    • Weaver JF. Entropies of adsorbed molecules exceed expectations. Science 2013, 339:39-40.
    • (2013) Science , vol.339 , pp. 39-40
    • Weaver, J.F.1
  • 5
    • 84868116583 scopus 로고    scopus 로고
    • The entropies of adsorbed molecules
    • Campbell CT, Sellers JRV. The entropies of adsorbed molecules. J Am Chem Soc 2012, 134:18109-18115.
    • (2012) J Am Chem Soc , vol.134 , pp. 18109-18115
    • Campbell, C.T.1    Sellers, J.R.V.2
  • 7
    • 0030961726 scopus 로고    scopus 로고
    • Entropy in protein folding and in protein-protein interactions
    • Brady GP, Sharp KA. Entropy in protein folding and in protein-protein interactions. Curr Opin Struct Biol 1997, 7:215-221.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 215-221
    • Brady, G.P.1    Sharp, K.A.2
  • 8
    • 84873526287 scopus 로고    scopus 로고
    • The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation
    • Wand AJ. The dark energy of proteins comes to light: conformational entropy and its role in protein function revealed by NMR relaxation. Curr Opin Struct Biol 2013, 23:75-81.
    • (2013) Curr Opin Struct Biol , vol.23 , pp. 75-81
    • Wand, A.J.1
  • 9
    • 0003527976 scopus 로고    scopus 로고
    • Sausalito, CA: University Science Books; .
    • McQuarrie D. Statistical Mechanics. Sausalito, CA: University Science Books; 2000.
    • (2000) Statistical Mechanics
    • McQuarrie, D.1
  • 12
    • 77953512913 scopus 로고    scopus 로고
    • Thermodynamic and differential entropy under a change of variables
    • Hnizdo V, Gilson MK. Thermodynamic and differential entropy under a change of variables. Entropy 2010, 12:578-590.
    • (2010) Entropy , vol.12 , pp. 578-590
    • Hnizdo, V.1    Gilson, M.K.2
  • 13
    • 0031058541 scopus 로고    scopus 로고
    • The statistical-thermodynamic basis for computation of binding affinities: a critical review
    • Gilson MK, Given JA, Bush BL, McCammon JA. The statistical-thermodynamic basis for computation of binding affinities: a critical review. Biophys J 1997, 72:1047-1069.
    • (1997) Biophys J , vol.72 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, J.A.4
  • 14
    • 0023475026 scopus 로고
    • Configurational entropy of native proteins
    • Karplus M, Ichiye T, Pettitt BM. Configurational entropy of native proteins. Biophys J 1987, 52:1083-1085.
    • (1987) Biophys J , vol.52 , pp. 1083-1085
    • Karplus, M.1    Ichiye, T.2    Pettitt, B.M.3
  • 15
    • 80051658093 scopus 로고    scopus 로고
    • Entropy calculations of single molecules by combining the rigid-rotor and harmonic-oscillator approximations with conformational entropy estimations from molecular dynamics simulations
    • Suárez E, Díaz N, Suárez D. Entropy calculations of single molecules by combining the rigid-rotor and harmonic-oscillator approximations with conformational entropy estimations from molecular dynamics simulations. J Chem Theory Comput 2011, 7:2638-2653.
    • (2011) J Chem Theory Comput , vol.7 , pp. 2638-2653
    • Suárez, E.1    Díaz, N.2    Suárez, D.3
  • 16
    • 34250311276 scopus 로고    scopus 로고
    • Calculation of entropy and heat capacity of organic compounds in the gas phase. Evaluation of a consistent method without adjustable parameters. Applications to hydrocarbons
    • DeTar DF. Calculation of entropy and heat capacity of organic compounds in the gas phase. Evaluation of a consistent method without adjustable parameters. Applications to hydrocarbons. J Phys Chem A 2007, 111:4464-4477.
    • (2007) J Phys Chem A , vol.111 , pp. 4464-4477
    • DeTar, D.F.1
  • 17
    • 0000638124 scopus 로고    scopus 로고
    • Theoretical ab initio calculation of entropy, heat capacity, and heat content
    • DeTar DF. Theoretical ab initio calculation of entropy, heat capacity, and heat content. J Phys Chem A 1998, 102:5128-5141.
    • (1998) J Phys Chem A , vol.102 , pp. 5128-5141
    • DeTar, D.F.1
  • 18
    • 0035921577 scopus 로고    scopus 로고
    • Use of DFT methods for the calculation of the entropy of gas phase organic molecules: an examination of the quality of results from a simple approach
    • Guthrie JP. Use of DFT methods for the calculation of the entropy of gas phase organic molecules: an examination of the quality of results from a simple approach. J Phys Chem A 2001, 105:8495-8499.
    • (2001) J Phys Chem A , vol.105 , pp. 8495-8499
    • Guthrie, J.P.1
  • 19
    • 0000127140 scopus 로고
    • Method for estimating the configurational entropy of macromolecules
    • Karplus M, Kushick JN. 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
  • 20
    • 0011146589 scopus 로고
    • Corrections to the quasi-harmonic approximation for evaluating molecular entropies
    • Rojas OL, Levy RL, Szabo A. Corrections to the quasi-harmonic 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.L.2    Szabo, A.3
  • 21
    • 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
  • 22
    • 0034323089 scopus 로고    scopus 로고
    • Absolute entropies from molecular dynamics simulation trajectories
    • Schäfer H, Mark AE, van Gunsteren WF. Absolute entropies from molecular dynamics simulation trajectories. J Chem Phys 2000, 113:7809.
    • (2000) J Chem Phys , vol.113 , pp. 7809
    • Schäfer, H.1    Mark, A.E.2    van Gunsteren, W.F.3
  • 23
    • 0035828630 scopus 로고    scopus 로고
    • On the calculation of entropy from covariance matrices of the atomic fluctuations
    • Andricioaei I, Karplus M. On the calculation of entropy from covariance matrices of the atomic fluctuations. J Chem Phys 2001, 115:6289.
    • (2001) J Chem Phys , vol.115 , pp. 6289
    • Andricioaei, I.1    Karplus, M.2
  • 24
    • 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
  • 26
    • 25844492293 scopus 로고    scopus 로고
    • Evaluating the accuracy of the quasi-harmonic approximation
    • Chang C-E, Chen W, Gilson MK. Evaluating the accuracy of the quasi-harmonic 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
  • 27
    • 83455186416 scopus 로고    scopus 로고
    • Configurational entropy: an improvement of the quasi-harmonic approximation using configurational temperature
    • Nguyen PH, Derreumaux P. Configurational entropy: an improvement of the quasi-harmonic approximation using configurational temperature. Phys Chem Chem Phys 2012, 14:877.
    • (2012) Phys Chem Chem Phys , vol.14 , pp. 877
    • Nguyen, P.H.1    Derreumaux, P.2
  • 28
    • 84858014432 scopus 로고    scopus 로고
    • Alternative interdomain configurations of the full-length MMP-2 enzyme explored by molecular dynamics simulations
    • Díaz N, Suárez D. Alternative interdomain configurations of the full-length MMP-2 enzyme explored by molecular dynamics simulations. J Phys Chem B 2012, 116:2677-2686.
    • (2012) J Phys Chem B , vol.116 , pp. 2677-2686
    • Díaz, N.1    Suárez, D.2
  • 29
    • 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 AE, van Gunsteren WF. 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
  • 30
    • 79951471013 scopus 로고    scopus 로고
    • Configurational entropy reallocation and complex loop dynamics of the mosquito-stage Pvs25 protein complexed with the fab fragment of the malaria transmission blocking antibody 2A8
    • Stavrakoudis A, Tsoulos IG. Configurational entropy reallocation and complex loop dynamics of the mosquito-stage Pvs25 protein complexed with the fab fragment of the malaria transmission blocking antibody 2A8. J Chem Theory Comput 2011, 7:515-524.
    • (2011) J Chem Theory Comput , vol.7 , pp. 515-524
    • Stavrakoudis, A.1    Tsoulos, I.G.2
  • 31
    • 84867340614 scopus 로고    scopus 로고
    • On the contribution of linear correlations to quasi-harmonic conformational entropy in proteins
    • Polyansky AA, Kuzmanic A, Hlevnjak M, Zagrovic B. On the contribution of linear correlations to quasi-harmonic conformational entropy in proteins. J Chem Theory Comput 2012, 8:3820-3829.
    • (2012) J Chem Theory Comput , vol.8 , pp. 3820-3829
    • Polyansky, A.A.1    Kuzmanic, A.2    Hlevnjak, M.3    Zagrovic, B.4
  • 32
    • 62649113018 scopus 로고    scopus 로고
    • Correlated motions and interactions at the onset of the DNA-induced partial unfolding of Ets-1
    • Kamberaj H, van der Vaart A. Correlated motions and interactions at the onset of the DNA-induced partial unfolding of Ets-1. Biophys J 2009, 96:1307-1317.
    • (2009) Biophys J , vol.96 , pp. 1307-1317
    • Kamberaj, H.1    van der Vaart, A.2
  • 33
    • 84865063074 scopus 로고    scopus 로고
    • Exploring residue component contributions to dynamical network models of allostery
    • VanWart A, Eargle J, Luthey-Schulten Z, Amaro RE. Exploring residue component contributions to dynamical network models of allostery. J Chem Theory Comput 2012, 8:2949-2961.
    • (2012) J Chem Theory Comput , vol.8 , pp. 2949-2961
    • VanWart, A.1    Eargle, J.2    Luthey-Schulten, Z.3    Amaro, R.E.4
  • 34
    • 16344395749 scopus 로고    scopus 로고
    • Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design
    • Chen W, Chang C-E, Gilson MK. Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design. Biophys J 2004, 87:3035-3049.
    • (2004) Biophys J , vol.87 , pp. 3035-3049
    • Chen, W.1    Chang, C.-E.2    Gilson, M.K.3
  • 35
    • 33846822002 scopus 로고    scopus 로고
    • Ligand configurational entropy and protein binding
    • Chang CA, Chen W, Gilson MK. Ligand configurational entropy and protein binding. Proc Natl Acad Sci U S A 2007, 104:1534-1539.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 1534-1539
    • Chang, C.A.1    Chen, W.2    Gilson, M.K.3
  • 36
    • 46449096350 scopus 로고    scopus 로고
    • Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods
    • Hnizdo V, Tan J, Killian BJ, Gilson MK. Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods. J Comput Chem 2008, 29:1605-1614.
    • (2008) J Comput Chem , vol.29 , pp. 1605-1614
    • Hnizdo, V.1    Tan, J.2    Killian, B.J.3    Gilson, M.K.4
  • 37
    • 68949141761 scopus 로고    scopus 로고
    • Adaptive anisotropic kernels for nonparametric estimation of absolute configurational entropies in high-dimensional configuration spaces
    • Hensen U, Grubmüller H, Lange O. Adaptive anisotropic kernels for nonparametric estimation of absolute configurational entropies in high-dimensional configuration spaces. Phys Rev E 2009, 80:011913.
    • (2009) Phys Rev E , vol.80 , pp. 011913
    • Hensen, U.1    Grubmüller, H.2    Lange, O.3
  • 38
    • 63749108613 scopus 로고    scopus 로고
    • In silico relationship between configurational entropy and soft degrees of freedom in proteins and peptides
    • Li D-W, Brüschweiler R. In silico relationship between configurational entropy and soft degrees of freedom in proteins and peptides. Phys Rev Lett 2009, 102:118108.
    • (2009) Phys Rev Lett , vol.102 , pp. 118108
    • Li, D.-W.1    Brüschweiler, R.2
  • 39
    • 84864261290 scopus 로고    scopus 로고
    • Will molecular dynamics simulations of proteins ever reach equilibrium?
    • Genheden S, Ryde U. Will molecular dynamics simulations of proteins ever reach equilibrium? Phys Chem Chem Phys 2012, 14:8662-8667.
    • (2012) Phys Chem Chem Phys , vol.14 , pp. 8662-8667
    • Genheden, S.1    Ryde, U.2
  • 40
    • 84655171824 scopus 로고    scopus 로고
    • Fragmentation methods: a route to accurate calculations on large systems
    • Gordon MS, Fedorov DG, Pruitt SR, Slipchenko LV. Fragmentation methods: a route to accurate calculations on large systems. Chem Rev 2012, 112:632-672.
    • (2012) Chem Rev , vol.112 , pp. 632-672
    • Gordon, M.S.1    Fedorov, D.G.2    Pruitt, S.R.3    Slipchenko, L.V.4
  • 41
    • 84865200038 scopus 로고    scopus 로고
    • A generalized many-body expansion and a unified view of fragment-based methods in electronic structure theory
    • Richard RM, Herbert JM. A generalized many-body expansion and a unified view of fragment-based methods in electronic structure theory. J Chem Phys 2012, 137:064113.
    • (2012) J Chem Phys , vol.137 , pp. 064113
    • Richard, R.M.1    Herbert, J.M.2
  • 42
    • 0034271164 scopus 로고    scopus 로고
    • Physical nature of higher-order mutual information: Intrinsic correlations and frustration
    • Matsuda H. Physical nature of higher-order mutual information: Intrinsic correlations and frustration. Phys Rev E 2000, 62:3096-3102.
    • (2000) Phys Rev E , vol.62 , pp. 3096-3102
    • Matsuda, H.1
  • 43
    • 34547227692 scopus 로고    scopus 로고
    • Extraction of configurational entropy from molecular simulations via an expansion approximation
    • Killian BJ, Yundenfreund Kravitz J, Gilson MK. Extraction of configurational entropy from molecular simulations via an expansion approximation. J Chem Phys 2007, 127:024107.
    • (2007) J Chem Phys , vol.127 , pp. 024107
    • Killian, B.J.1    Yundenfreund Kravitz, J.2    Gilson, M.K.3
  • 45
    • 84863648167 scopus 로고    scopus 로고
    • Dynamic and thermodynamic signatures of native and non-native protein states with application to the improvement of protein structures
    • Li D-W, Brüschweiler R. Dynamic and thermodynamic signatures of native and non-native protein states with application to the improvement of protein structures. J Chem Theory Comput 2012, 8:2531-2539.
    • (2012) J Chem Theory Comput , vol.8 , pp. 2531-2539
    • Li, D.-W.1    Brüschweiler, R.2
  • 46
    • 84859571593 scopus 로고    scopus 로고
    • Balanced and bias-corrected computation of conformational entropy differences for molecular trajectories
    • Numata J, Knapp E-W. Balanced and bias-corrected computation of conformational entropy differences for molecular trajectories. J Chem Theory Comput 2012, 8:1235-1245.
    • (2012) J Chem Theory Comput , vol.8 , pp. 1235-1245
    • Numata, J.1    Knapp, E.-W.2
  • 48
    • 65449130754 scopus 로고    scopus 로고
    • MIST: Maximum Information Spanning Trees for dimension reduction of biological data sets
    • King BM, Tidor B. MIST: Maximum Information Spanning Trees for dimension reduction of biological data sets. Bioinformatics 2009, 25:1165-1172.
    • (2009) Bioinformatics , vol.25 , pp. 1165-1172
    • King, B.M.1    Tidor, B.2
  • 49
    • 84858068315 scopus 로고    scopus 로고
    • Efficient calculation of molecular configurational entropies using an information theoretic approximation
    • King BM, Silver NW, Tidor B. Efficient calculation of molecular configurational entropies using an information theoretic approximation. J Phys Chem B 2012, 116:2891-2904.
    • (2012) J Phys Chem B , vol.116 , pp. 2891-2904
    • King, B.M.1    Silver, N.W.2    Tidor, B.3
  • 50
    • 84870579518 scopus 로고    scopus 로고
    • Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding
    • Fenley AT, Muddana HS, Gilson MK. Entropy-enthalpy transduction caused by conformational shifts can obscure the forces driving protein-ligand binding. Proc Natl Acad Sci U S A 2012, 109:20006-20011.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 20006-20011
    • Fenley, A.T.1    Muddana, H.S.2    Gilson, M.K.3
  • 51
    • 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
  • 53
    • 67650047673 scopus 로고    scopus 로고
    • Thermodynamic properties of liquid water: an application of a nonparametric approach to computing the entropy of a neat fluid
    • Wang L, Abel R, Friesner RA, Berne BJ. Thermodynamic properties of liquid water: an application of a nonparametric approach to computing the entropy of a neat fluid. J Chem Theory Comput 2009, 5:1462-1473.
    • (2009) J Chem Theory Comput , vol.5 , pp. 1462-1473
    • Wang, L.1    Abel, R.2    Friesner, R.A.3    Berne, B.J.4
  • 54
    • 76649103043 scopus 로고    scopus 로고
    • Methods for calculating the absolute entropy and free energy of biological systems based on ideas from polymer physics
    • Meirovitch H. Methods for calculating the absolute entropy and free energy of biological systems based on ideas from polymer physics. J Mol Recognit 2010, 23:153-172.
    • (2010) J Mol Recognit , vol.23 , pp. 153-172
    • Meirovitch, H.1
  • 55
    • 84885401372 scopus 로고    scopus 로고
    • Absolute free energy of binding and entropy of the FKBP12-FK506 complex: effects of the force field
    • General IJ, Meirovitch H. Absolute free energy of binding and entropy of the FKBP12-FK506 complex: effects of the force field. J Chem Theory Comput 2013, 9:4609-4619.
    • (2013) J Chem Theory Comput , vol.9 , pp. 4609-4619
    • General, I.J.1    Meirovitch, H.2
  • 56
    • 66549092123 scopus 로고    scopus 로고
    • Absolute free energy and entropy of a mobile loop of the enzyme acetylcholinesterase
    • Mihailescu M, Meirovitch H. Absolute free energy and entropy of a mobile loop of the enzyme acetylcholinesterase. J Phys Chem B 2009, 113:7950-7964.
    • (2009) J Phys Chem B , vol.113 , pp. 7950-7964
    • Mihailescu, M.1    Meirovitch, H.2
  • 57
    • 0001064378 scopus 로고
    • Free energy determination of polypeptide conformations generated by molecular dynamics
    • Di Nola A, Berendsen HJC, Edholm O. Free energy determination of polypeptide conformations generated by molecular dynamics. Macromolecules 1984, 17:2044-2050.
    • (1984) Macromolecules , vol.17 , pp. 2044-2050
    • Di Nola, A.1    Berendsen, H.J.C.2    Edholm, O.3
  • 58
    • 79960913321 scopus 로고    scopus 로고
    • Calculation of configurational entropy with a boltzmann-quasiharmonic model: the origin of high-affinity protein-ligand binding
    • Harpole KW, Sharp KA. Calculation of configurational entropy with a boltzmann-quasiharmonic model: the origin of high-affinity protein-ligand binding. J Phys Chem B 2011, 115:9461-9472.
    • (2011) J Phys Chem B , vol.115 , pp. 9461-9472
    • Harpole, K.W.1    Sharp, K.A.2
  • 59
    • 73949098933 scopus 로고    scopus 로고
    • Absolute single-molecule entropies from quasi-harmonic analysis of microsecond molecular dynamics: correction terms and convergence properties
    • Baron R, Hünenberger PH, McCammon JA. Absolute single-molecule entropies from quasi-harmonic analysis of microsecond molecular dynamics: correction terms and convergence properties. J Chem Theory Comput 2009, 5:3150-3160.
    • (2009) J Chem Theory Comput , vol.5 , pp. 3150-3160
    • Baron, R.1    Hünenberger, P.H.2    McCammon, J.A.3
  • 60
    • 34250853492 scopus 로고    scopus 로고
    • Estimating the configurational entropy from molecular dynamics simulations: anharmonicity and correlation corrections to the quasi-harmonic approximation
    • Baron R, van Gunsteren WF, Hünenberger PH. Estimating the configurational entropy from molecular dynamics simulations: anharmonicity and correlation corrections to the quasi-harmonic approximation. Trends Phys Chem 2006, 11:87-122.
    • (2006) Trends Phys Chem , vol.11 , pp. 87-122
    • Baron, R.1    van Gunsteren, W.F.2    Hünenberger, P.H.3
  • 61
    • 48549083172 scopus 로고    scopus 로고
    • Conformational entropy of biomolecules: beyond the quasi-harmonic approximation
    • Numata J, Wan M, Knapp E-W. Conformational entropy of biomolecules: beyond the quasi-harmonic approximation. Genome Inform 2007, 18:192-205.
    • (2007) Genome Inform , vol.18 , pp. 192-205
    • Numata, J.1    Wan, M.2    Knapp, E.-W.3
  • 62
    • 0347602124 scopus 로고    scopus 로고
    • Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
    • Gohlke H, Case DA. Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf. J Comput Chem 2003, 25:238-250.
    • (2003) J Comput Chem , vol.25 , pp. 238-250
    • Gohlke, H.1    Case, D.A.2
  • 63
    • 39749152456 scopus 로고    scopus 로고
    • Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases
    • Stoica I, Sadiq SK, Coveney PV. Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases. J Am Chem Soc 2007, 130:2639-2648.
    • (2007) J Am Chem Soc , vol.130 , pp. 2639-2648
    • Stoica, I.1    Sadiq, S.K.2    Coveney, P.V.3
  • 64
    • 77949416782 scopus 로고    scopus 로고
    • Kinetic and binding effects in peptide substrate selectivity of matrix metalloproteinase-2: molecular dynamics and QM/MM calculations
    • Díaz N, Suárez D, Suárez E. Kinetic and binding effects in peptide substrate selectivity of matrix metalloproteinase-2: molecular dynamics and QM/MM calculations. Proteins 2010, 78:1-11.
    • (2010) Proteins , vol.78 , pp. 1-11
    • Díaz, N.1    Suárez, D.2    Suárez, E.3
  • 65
    • 0036140611 scopus 로고    scopus 로고
    • Determining the shear viscosity of model liquids from molecular dynamics simulations
    • Bess H. Determining the shear viscosity of model liquids from molecular dynamics simulations. J Chem Phys 2002, 116:209-217.
    • (2002) J Chem Phys , vol.116 , pp. 209-217
    • Bess, H.1
  • 66
    • 84857448586 scopus 로고    scopus 로고
    • Influence of the solvent representation on vibrational entropy calculations: generalized born versus distance-dependent dielectric model
    • Kopitz H, Cashman DA, Pfeiffer-Marek S, Gohlke H. Influence of the solvent representation on vibrational entropy calculations: generalized born versus distance-dependent dielectric model. J Comput Chem 2012, 33:1004-1013.
    • (2012) J Comput Chem , vol.33 , pp. 1004-1013
    • Kopitz, H.1    Cashman, D.A.2    Pfeiffer-Marek, S.3    Gohlke, H.4
  • 67
    • 67650851281 scopus 로고    scopus 로고
    • Calculation of free-energy differences by confinement simulations. Application to peptide conformers
    • Cecchini M, Krivov SV, Spichty M, Karplus M. Calculation of free-energy differences by confinement simulations. Application to peptide conformers. J Phys Chem B 2009, 113:9728-9740.
    • (2009) J Phys Chem B , vol.113 , pp. 9728-9740
    • Cecchini, M.1    Krivov, S.V.2    Spichty, M.3    Karplus, M.4
  • 69
    • 58149327312 scopus 로고    scopus 로고
    • An improved method to predict the entropy term with the MM/PBSA approach
    • Kongsted J, Ryde U. An improved method to predict the entropy term with the MM/PBSA approach. J Comput Aided Mol Des 2008, 23:63-71.
    • (2008) J Comput Aided Mol Des , vol.23 , pp. 63-71
    • Kongsted, J.1    Ryde, U.2
  • 70
    • 79251640898 scopus 로고    scopus 로고
    • Ligand entropy in gas-phase, upon solvation and protein complexation. Fast estimation with quasi-Newton Hessian
    • Wlodek S, Skillman AG, Nicholls A. Ligand entropy in gas-phase, upon solvation and protein complexation. Fast estimation with quasi-Newton Hessian. J Chem Theory Comput 2010, 6:2140-2152.
    • (2010) J Chem Theory Comput , vol.6 , pp. 2140-2152
    • Wlodek, S.1    Skillman, A.G.2    Nicholls, A.3
  • 71
    • 84861520787 scopus 로고    scopus 로고
    • Develop and test a solvent accessible surface area-based model in conformational entropy calculations
    • Wang J, Hou T. Develop and test a solvent accessible surface area-based model in conformational entropy calculations. J Chem Inf Model 2012, 52:1199-1212.
    • (2012) J Chem Inf Model , vol.52 , pp. 1199-1212
    • Wang, J.1    Hou, T.2
  • 73
    • 0028871798 scopus 로고
    • Side-chain conformational entropy in protein folding
    • Doig AJ, Sternberg MJE. Side-chain conformational entropy in protein folding. Protein Sci 1995, 4:2247-2251.
    • (1995) Protein Sci , vol.4 , pp. 2247-2251
    • Doig, A.J.1    Sternberg, M.J.E.2
  • 74
    • 33845977740 scopus 로고    scopus 로고
    • On side-chain conformational entropy of proteins
    • Zhang J, Liu JS. On side-chain conformational entropy of proteins. PLoS Comput Biol 2006, 2:e168.
    • (2006) PLoS Comput Biol , vol.2 , pp. e168
    • Zhang, J.1    Liu, J.S.2
  • 75
    • 67650677848 scopus 로고    scopus 로고
    • Calculation of proteins' total side-chain torsional entropy and its influence on protein-ligand interactions
    • DuBay KH, Geissler PL. Calculation of proteins' total side-chain torsional entropy and its influence on protein-ligand interactions. J Mol Biol 2009, 391:484-497.
    • (2009) J Mol Biol , vol.391 , pp. 484-497
    • DuBay, K.H.1    Geissler, P.L.2
  • 76
    • 84880697996 scopus 로고    scopus 로고
    • CENCALC: a computational tool for conformational entropy calculations from molecular simulations
    • Suárez E, Díaz N, Méndez J, Suárez D. CENCALC: a computational tool for conformational entropy calculations from molecular simulations. J Comput Chem 2013, 34:2041-2054.
    • (2013) J Comput Chem , vol.34 , pp. 2041-2054
    • Suárez, E.1    Díaz, N.2    Méndez, J.3    Suárez, D.4
  • 77
    • 84865736993 scopus 로고    scopus 로고
    • Multibody local approximation: application to conformational entropy calculations on biomolecules
    • Suárez E, Suárez D. Multibody local approximation: application to conformational entropy calculations on biomolecules. J Chem Phys 2012, 137:084115.
    • (2012) J Chem Phys , vol.137 , pp. 084115
    • Suárez, E.1    Suárez, D.2
  • 78
    • 79955874370 scopus 로고    scopus 로고
    • Equilibrium sampling in biomolecular simulation
    • Zuckerman DM. Equilibrium sampling in biomolecular simulation. Annu Rev Biophys 2011, 40:41-62.
    • (2011) Annu Rev Biophys , vol.40 , pp. 41-62
    • Zuckerman, D.M.1
  • 80
    • 68949161935 scopus 로고    scopus 로고
    • Entropy inference and the James-Stein estimator, with application to nonlinear gene association networks
    • Hausser J, Strimmer K. Entropy inference and the James-Stein estimator, with application to nonlinear gene association networks. J Mach Learn Res 2009, 10:1469-1484.
    • (2009) J Mach Learn Res , vol.10 , pp. 1469-1484
    • Hausser, J.1    Strimmer, K.2
  • 81
    • 78650129666 scopus 로고    scopus 로고
    • Symmetry numbers for rigid, flexible, and fluxional molecules: theory and applications
    • Gilson MK, Irikura KK. Symmetry numbers for rigid, flexible, and fluxional molecules: theory and applications. J Phys Chem B 2010, 114:16304-16317.
    • (2010) J Phys Chem B , vol.114 , pp. 16304-16317
    • Gilson, M.K.1    Irikura, K.K.2
  • 82
    • 80053513788 scopus 로고    scopus 로고
    • Distinguishability in entropy calculations: chemical reactions, conformational and residual entropy
    • Suárez E. Distinguishability in entropy calculations: chemical reactions, conformational and residual entropy. Entropy 2011, 13:1533-1540.
    • (2011) Entropy , vol.13 , pp. 1533-1540
    • Suárez, E.1
  • 83
    • 84877768087 scopus 로고    scopus 로고
    • Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design
    • Chodera JD, Mobley DL. Entropy-enthalpy compensation: role and ramifications in biomolecular ligand recognition and design. Annu Rev Biophys 2013, 42:121-142.
    • (2013) Annu Rev Biophys , vol.42 , pp. 121-142
    • Chodera, J.D.1    Mobley, D.L.2
  • 84
    • 84856234241 scopus 로고    scopus 로고
    • Evaluation of protein-ligand binding free energy focused on its entropic components
    • Chiba S, Harano Y, Roth R, Kinoshita M, Sakurai M. Evaluation of protein-ligand binding free energy focused on its entropic components. J Comput Chem 2012, 33:550-560.
    • (2012) J Comput Chem , vol.33 , pp. 550-560
    • Chiba, S.1    Harano, Y.2    Roth, R.3    Kinoshita, M.4    Sakurai, M.5
  • 86
    • 67650079411 scopus 로고    scopus 로고
    • Toward accurate microscopic calculation of solvation entropies: extending the restraint release approach to studies of solvation effects
    • Singh N, Warshel A. Toward accurate microscopic calculation of solvation entropies: extending the restraint release approach to studies of solvation effects. J Phys Chem B 2009, 113:7372-7382.
    • (2009) J Phys Chem B , vol.113 , pp. 7372-7382
    • Singh, N.1    Warshel, A.2
  • 87
    • 62849103081 scopus 로고    scopus 로고
    • Understanding and improving free energy calculations in molecular simulations: error analysis and reduction methods
    • Lu N, Woolf TB. Understanding and improving free energy calculations in molecular simulations: error analysis and reduction methods. Free Energy Calculations 2007, 86:199-247.
    • (2007) Free Energy Calculations , vol.86 , pp. 199-247
    • Lu, N.1    Woolf, T.B.2
  • 88
    • 77951247516 scopus 로고    scopus 로고
    • A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes
    • Singh N, Warshel A. A comprehensive examination of the contributions to the binding entropy of protein-ligand complexes. Proteins 2010, 78:1724-1735.
    • (2010) Proteins , vol.78 , pp. 1724-1735
    • Singh, N.1    Warshel, A.2
  • 89
    • 84873686708 scopus 로고    scopus 로고
    • Calculation of molecular entropies using temperature integration
    • Sharp K. Calculation of molecular entropies using temperature integration. J Chem Theory Comput 2013, 9:1164-1172.
    • (2013) J Chem Theory Comput , vol.9 , pp. 1164-1172
    • Sharp, K.1
  • 90
    • 84872850584 scopus 로고    scopus 로고
    • A simplified confinement method for calculating absolute free energies and free energy and entropy differences
    • Ovchinnikov V, Cecchini M, Karplus M. A simplified confinement method for calculating absolute free energies and free energy and entropy differences. J Phys Chem B 2013, 117:750-762.
    • (2013) J Phys Chem B , vol.117 , pp. 750-762
    • Ovchinnikov, V.1    Cecchini, M.2    Karplus, M.3
  • 91
    • 30744434619 scopus 로고    scopus 로고
    • Evaluating the conformational entropy of macromolecules using an energy decomposition approach
    • Ohkubo YZ, Thorpe IF. Evaluating the conformational entropy of macromolecules using an energy decomposition approach. J Chem Phys 2006, 124:024910.
    • (2006) J Chem Phys , vol.124 , pp. 024910
    • Ohkubo, Y.Z.1    Thorpe, I.F.2
  • 92
    • 84877694532 scopus 로고    scopus 로고
    • Conformational entropy of intrinsically disordered protein
    • Chong S-H, Ham S. Conformational entropy of intrinsically disordered protein. J Phys Chem B 2013, 117:5503-5509.
    • (2013) J Phys Chem B , vol.117 , pp. 5503-5509
    • Chong, S.-H.1    Ham, S.2
  • 93
    • 33646945580 scopus 로고    scopus 로고
    • Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution
    • Igumenova TI, Frederick KK, Wand AJ. Characterization of the fast dynamics of protein amino acid side chains using NMR relaxation in solution. Chem Rev 2006, 106:1672-1699.
    • (2006) Chem Rev , vol.106 , pp. 1672-1699
    • Igumenova, T.I.1    Frederick, K.K.2    Wand, A.J.3
  • 95
    • 36448947240 scopus 로고    scopus 로고
    • Toward quantitative interpretation of methyl side-chain dynamics from NMR by molecular dynamics simulations
    • Showalter SA, Johnson E, Rance M, Brüschweiler R. Toward quantitative interpretation of methyl side-chain dynamics from NMR by molecular dynamics simulations. J Am Chem Soc 2007, 129:14146-14147.
    • (2007) J Am Chem Soc , vol.129 , pp. 14146-14147
    • Showalter, S.A.1    Johnson, E.2    Rance, M.3    Brüschweiler, R.4
  • 96
    • 67650529401 scopus 로고    scopus 로고
    • A dictionary for protein side-chain entropies from NMR order parameters
    • Li D-W, Brüschweiler R. A dictionary for protein side-chain entropies from NMR order parameters. J Am Chem Soc 2009, 131:7226-7227.
    • (2009) J Am Chem Soc , vol.131 , pp. 7226-7227
    • Li, D.-W.1    Brüschweiler, R.2
  • 97
    • 84892565996 scopus 로고    scopus 로고
    • Conformational entropies and order parameters: convergence, reproducibility, and transferability
    • Genheden S, Akke M, Ryde U. Conformational entropies and order parameters: convergence, reproducibility, and transferability. J Chem Theory Comput 2014, 10:432-438.
    • (2014) J Chem Theory Comput , vol.10 , pp. 432-438
    • Genheden, S.1    Akke, M.2    Ryde, U.3
  • 98
    • 34447503697 scopus 로고    scopus 로고
    • Conformational entropy in molecular recognition by proteins
    • Frederick KK, Marlow MS, Valentine KG, Wand AJ. Conformational entropy in molecular recognition by proteins. Nature 2007, 448:325-329.
    • (2007) Nature , vol.448 , pp. 325-329
    • Frederick, K.K.1    Marlow, M.S.2    Valentine, K.G.3    Wand, A.J.4
  • 99
    • 84885611062 scopus 로고    scopus 로고
    • Microscopic Insights into the NMR relaxation-based protein conformational entropy meter
    • Kasinath V, Sharp K, Wand AJ. Microscopic Insights into the NMR relaxation-based protein conformational entropy meter. J Am Chem Soc 2013, 135:15092-15100.
    • (2013) J Am Chem Soc , vol.135 , pp. 15092-15100
    • Kasinath, V.1    Sharp, K.2    Wand, A.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.