-
3
-
-
7044239742
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
14
-
-
25844507555
-
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
-
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
-
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
-
(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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
35
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79: 926-935.
-
(1983)
J Chem Phys
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
36
-
-
33846037322
-
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
-
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
-
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
-
-
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.
-
-
-
-
40
-
-
27344454932
-
Gromacs: Fast, flexible, and free
-
van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, et al. (2005) Gromacs: Fast, flexible, and free. J Comp Chem 26: 1701-1718.
-
(2005)
J Comp Chem
, vol.26
, pp. 1701-1718
-
-
van der Spoel, D.1
Lindahl, E.2
Hess, B.3
Groenhof, G.4
Mark, A.E.5
-
41
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81: 3684-3690.
-
(1984)
J Chem Phys
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
van Gunsteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
43
-
-
84986440341
-
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
-
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
|