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Volumn 5, Issue 2, 2010, Pages

Estimating absolute configurational entropies of macromolecules: The minimally coupled subspace approach

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE DERIVATIVE; ALKANE DERIVATIVE; BUTANE; DECANE; DIALANINE; HEPTANE; HEXANE; NONANE; OCTANE; PENTANE; TATA BINDING PROTEIN; UNCLASSIFIED DRUG; PEPTIDE;

EID: 77949608591     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0009179     Document Type: Article
Times cited : (61)

References (44)
  • 3
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • Kollman P (1993) Free energy calculations: Applications to chemical and biochemical phenomena. Chem Rev 93: 2395-2417.
    • (1993) Chem Rev , vol.93 , pp. 2395-2417
    • Kollman, P.1
  • 4
    • 34147133371 scopus 로고    scopus 로고
    • Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation
    • Meirovitch H (2007) Recent developments in methodologies for calculating the entropy and free energy of biological systems by computer simulation. Curr Opin Struct Biol 17: 181-186.
    • (2007) Curr Opin Struct Biol , vol.17 , pp. 181-186
    • Meirovitch, H.1
  • 6
    • 3042694216 scopus 로고    scopus 로고
    • Simulation method for calculating the entropy and free energy of peptides and proteins
    • Cheluvaraja S, Meirovitch H (2004) Simulation method for calculating the entropy and free energy of peptides and proteins. PNAS 101: 9241-9246.
    • (2004) PNAS , vol.101 , pp. 9241-9246
    • Cheluvaraja, S.1    Meirovitch, H.2
  • 7
    • 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 (2006) Calculation of the entropy and free energy of peptides by molecular dynamics simulations using the hypothetical scanning molecular dynamics method. J Chem Phys 125: 024905.
    • (2006) J Chem Phys , vol.125 , pp. 024905
    • Cheluvaraja, S.1    Meirovitch, H.2
  • 8
    • 0000127140 scopus 로고
    • Method for estimating the configurational entropy of macromolecules
    • Karplus M, Kushick JN (1981) Method for estimating the configurational entropy of macromolecules. Macromolecules 14: 325-332.
    • (1981) Macromolecules , vol.14 , pp. 325-332
    • Karplus, M.1    Kushick, J.N.2
  • 9
    • 0001351515 scopus 로고
    • Estimation of absolute and relative entropies of macromolecules using the covariance matrix
    • Schlitter J (1993) Estimation of absolute and relative entropies of macromolecules using the covariance matrix. Chemical Physics Letters 215: 617-621.
    • (1993) Chemical Physics Letters , vol.215 , pp. 617-621
    • Schlitter, J.1
  • 10
    • 0036725277 scopus 로고    scopus 로고
    • Molecular dynamics simulations of biomolecules
    • Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nat Struct Mol Biol 9: 646-652.
    • (2002) Nat Struct Mol Biol , vol.9 , pp. 646-652
    • Karplus, M.1    McCammon, J.A.2
  • 11
    • 25844492293 scopus 로고    scopus 로고
    • Evaluating the accuracy of the quasiharmonic approximation
    • Chang C, Chen W, Gilson M (2005) Evaluating the accuracy of the quasiharmonic approximation. J Chem Theory Comput 1: 1017-1028.
    • (2005) J Chem Theory Comput , vol.1 , pp. 1017-1028
    • Chang, C.1    Chen, W.2    Gilson, M.3
  • 12
    • 33846822002 scopus 로고    scopus 로고
    • Ligand configurational entropy and protein binding
    • Chang C, Chen W, Gilson MK (2007) Ligand configurational entropy and protein binding. PNAS 104: 1534-1539.
    • (2007) PNAS , vol.104 , pp. 1534-1539
    • Chang, C.1    Chen, W.2    Gilson, M.K.3
  • 13
  • 14
    • 25844507555 scopus 로고    scopus 로고
    • The entropic cost of protein-protein association: A case study on acetylcholinesterase binding to fasciculin-2
    • Minh DDL, Bui JM, Chang C, Jain T, Swanson JMJ, et al. (2005) The entropic cost of protein-protein association: A case study on acetylcholinesterase binding to fasciculin-2. Biophys J 89: 25-27.
    • (2005) Biophys J , vol.89 , pp. 25-27
    • Minh, D.D.L.1    Bui, J.M.2    Chang, C.3    Jain, T.4    Swanson, J.M.J.5
  • 15
    • 33744818146 scopus 로고    scopus 로고
    • Conformational and dynamical properties of disaccharides in water: A molecular dynamics study
    • Pereira CS, Kony D, Baron R, Müller M, van Gunsteren WF, et al. (2006) Conformational and dynamical properties of disaccharides in water: a molecular dynamics study. Biophysical Journal 90: 4337-4344.
    • (2006) Biophysical Journal , vol.90 , pp. 4337-4344
    • Pereira, C.S.1    Kony, D.2    Baron, R.3    Müller, M.4    van Gunsteren, W.F.5
  • 16
    • 33646426637 scopus 로고    scopus 로고
    • Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates
    • Baron R, deVries A, Hünenberger P, van Gunsteren W (2006) Comparison of atomic-level and coarse-grained models for liquid hydrocarbons from molecular dynamics configurational entropy estimates. J Phys Chem B 110: 8464-8473.
    • (2006) J Phys Chem B , vol.110 , pp. 8464-8473
    • Baron, R.1    deVries, A.2    Hünenberger, P.3    van Gunsteren, W.4
  • 17
    • 43649103922 scopus 로고    scopus 로고
    • (thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding
    • Baron R, McCammon JA (2008) (thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding. ChemPhysChem 9: 983-988.
    • (2008) ChemPhysChem , vol.9 , pp. 983-988
    • Baron, R.1    McCammon, J.A.2
  • 18
    • 0031337279 scopus 로고    scopus 로고
    • Evaluation of the molecular configuration integral in all degrees of freedom for the direct calculation of conformational free energies: Prediction of the anomeric free energy of monosaccharides
    • Kolossvary I (1997) Evaluation of the molecular configuration integral in all degrees of freedom for the direct calculation of conformational free energies: Prediction of the anomeric free energy of monosaccharides. J Phys Chem A 101: 9900-9905.
    • (1997) J Phys Chem A , vol.101 , pp. 9900-9905
    • Kolossvary, I.1
  • 19
    • 0037473066 scopus 로고    scopus 로고
    • Calculation of molecular configuration integrals
    • Chang C, Potter M, Gilson M (2003) Calculation of molecular configuration integrals. J Phys Chem B 107: 1048-1055.
    • (2003) J Phys Chem B , vol.107 , pp. 1048-1055
    • Chang, C.1    Potter, M.2    Gilson, M.3
  • 20
    • 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 W, Hünenberger P (2006) Estimating the configurational entropy from molecular dynamics simulations: anharmonicity and correlation corrections to the quasi-harmonic approximation. Trends Phys Chem 11: 87-122.
    • (2006) Trends Phys Chem , vol.11 , pp. 87-122
    • Baron, R.1    van Gunsteren, W.2    Hünenberger, P.3
  • 21
    • 68949141761 scopus 로고    scopus 로고
    • Adaptive anisotropic kernels for nonparametric estimation of absolute configurational entropies in highdimensional configuration spaces
    • Hensen U, Grubmüller H, Lange OF (2009) Adaptive anisotropic kernels for nonparametric estimation of absolute configurational entropies in highdimensional configuration spaces. Phys Rev E 80: 011913.
    • (2009) Phys Rev E , vol.80 , pp. 011913
    • Hensen, U.1    Grubmüller, H.2    Lange, O.F.3
  • 22
    • 33748807193 scopus 로고    scopus 로고
    • An efficient, path-independent method for free-energy calculations
    • Tyka M, Clarke A, Sessions R (2006) An efficient, path-independent method for free-energy calculations. J Phys Chem B 110: 17212-17220.
    • (2006) J Phys Chem B , vol.110 , pp. 17212-17220
    • Tyka, M.1    Clarke, A.2    Sessions, R.3
  • 25
    • 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, et al. (2007) Nearest-neighbor nonparametric method for estimating the configurational entropy of complex molecules. J Comp Chem 28: 655-668.
    • (2007) J Comp Chem , vol.28 , pp. 655-668
    • Hnizdo, V.1    Darian, E.2    Fedorowicz, A.3    Demchuk, E.4    Li, S.5
  • 27
    • 39749132831 scopus 로고    scopus 로고
    • Full correlation analysis of conformational protein dynamics
    • Lange OF, Grubmüller H (2008) Full correlation analysis of conformational protein dynamics. Proteins 70: 1294-1312.
    • (2008) Proteins , vol.70 , pp. 1294-1312
    • Lange, O.F.1    Grubmüller, H.2
  • 28
    • 33644847828 scopus 로고    scopus 로고
    • Generalized correlation for biomolecular dynamics
    • Lange OF, Grubmüller H (2006) Generalized correlation for biomolecular dynamics. Proteins 62: 1053-1061.
    • (2006) Proteins , vol.62 , pp. 1053-1061
    • Lange, O.F.1    Grubmüller, H.2
  • 29
    • 0000116263 scopus 로고
    • Direct entropy calculation from computer simulation of liquids
    • Baranyai A, Evans DJ (1989) Direct entropy calculation from computer simulation of liquids. Phys Rev A 40: 3817-3822.
    • (1989) Phys Rev A , vol.40 , pp. 3817-3822
    • Baranyai, A.1    Evans, D.J.2
  • 30
    • 0342880932 scopus 로고    scopus 로고
    • Information content of signals using correlation function expansions of the entropy
    • Attard P, Jepps OG, Marčelja S (1997) Information content of signals using correlation function expansions of the entropy. Phys Rev E 56: 4052-4067.
    • (1997) Phys Rev E , vol.56 , pp. 4052-4067
    • Attard, P.1    Jepps, O.G.2    Marčelja, S.3
  • 31
    • 77949573928 scopus 로고    scopus 로고
    • Statistical Physics
    • on the, World Scientific, chapter Markov Superposition Expansion for the Entropy and Correlation Functions in Two and Three Dimensions
    • Attard P (1999) Statistical Physics on the Eve of the Twenty-First Century, World Scientific, chapter Markov Superposition Expansion for the Entropy and Correlation Functions in Two and Three Dimensions.
    • (1999) Eve of the Twenty-First Century
    • Attard, P.1
  • 32
    • 34547227692 scopus 로고    scopus 로고
    • Extraction of configurational entropy from molecular simulations via an expansion approximation
    • Killian BJ, Kravitz JY, Gilson MK (2007) Extraction of configurational entropy from molecular simulations via an expansion approximation. J Chem Phys 127: 024107.
    • (2007) J Chem Phys , vol.127 , pp. 024107
    • Killian, B.J.1    Kravitz, J.Y.2    Gilson, M.K.3
  • 33
    • 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 (2008) Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods. J Comp Chem 29: 1605-1614.
    • (2008) J Comp Chem , vol.29 , pp. 1605-1614
    • Hnizdo, V.1    Tan, J.2    Killian, B.J.3    Gilson, M.K.4
  • 34
    • 0035913529 scopus 로고    scopus 로고
    • Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
    • Kaminski G, Friesner R, Tirado-Rives J, Jorgensen W (2001) Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 105: 6474-6487.
    • (2001) J Phys Chem B , vol.105 , pp. 6474-6487
    • Kaminski, G.1    Friesner, R.2    Tirado-Rives, J.3    Jorgensen, W.4
  • 36
    • 33846037322 scopus 로고    scopus 로고
    • Estimation of absolute solvent and solvation shell entropies via permutation reduction
    • Reinhard F, Grubmüller H (2007) Estimation of absolute solvent and solvation shell entropies via permutation reduction. J Chem Phys 126: 014102.
    • (2007) J Chem Phys , vol.126 , pp. 014102
    • Reinhard, F.1    Grubmüller, H.2
  • 37
    • 0036140611 scopus 로고    scopus 로고
    • Determining the shear viscosity of model liquids from molecular dynamics simulations
    • Hess B (2002) Determining the shear viscosity of model liquids from molecular dynamics simulations. J Chem Phys 116: 209-217.
    • (2002) J Chem Phys , vol.116 , pp. 209-217
    • Hess, B.1
  • 38
    • 7544226311 scopus 로고    scopus 로고
    • PRODRG - a tool for high-throughput crystallography of protein-ligand complexes
    • Schüttelkopf AW, van Aalten DMF (2004) PRODRG - a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallographica D 60: 1355-1363.
    • (2004) Acta Crystallographica D , vol.60 , pp. 1355-1363
    • Schüttelkopf, A.W.1    van Aalten, D.M.F.2
  • 39
    • 77949604606 scopus 로고    scopus 로고
    • van Gunsteren WF, Daura X, Mark AE (1998) GROMOS force field. Encyclopaedia of computational chemistry edition. pp 1211-1216.
    • van Gunsteren WF, Daura X, Mark AE (1998) GROMOS force field. Encyclopaedia of computational chemistry edition. pp 1211-1216.
  • 43
    • 84986440341 scopus 로고
    • Settle: An analytical version of the shake and rattle algorithm for rigid water models
    • Miyamoto S, Kollman PA (1992) Settle: An analytical version of the shake and rattle algorithm for rigid water models. J Comp Chem 13: 952-962.
    • (1992) J Comp Chem , vol.13 , pp. 952-962
    • Miyamoto, S.1    Kollman, P.A.2
  • 44
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N log(N) method for Ewald sums in large systems
    • Darden T, York D, Pedersen L (1993) Particle mesh Ewald: An N log(N) method for Ewald sums in large systems. J Chem Phys 98: 10089-10092.
    • (1993) J Chem Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3


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