-
1
-
-
0001492503
-
Computation of free energy in practice: Choice of approximations and accuracy limiting factors
-
van Gunsteren, W. F., Weiner, P. K. and Wilkinson, A. J. (Eds.), ESCOM Science Publishers, Leiden, The Netherlands
-
van Gunsteren, W. F., Beutler, T. C., Fraternali, F., King, P. M., Mark, A. E. and Smith, P. E. (1993). "Computation of free energy in practice: choice of approximations and accuracy limiting factors", In: van Gunsteren, W. F., Weiner, P. K. and Wilkinson, A. J. (Eds.), Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications, 2, 315-348. ESCOM Science Publishers, Leiden, The Netherlands.
-
(1993)
Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications
, vol.2
, pp. 315-348
-
-
Van Gunsteren, W.F.1
Beutler, T.C.2
Fraternali, F.3
King, P.M.4
Mark, A.E.5
Smith, P.E.6
-
4
-
-
0024578173
-
Free-energy via molecular simulation -applications to chemical and biomolecular systems
-
Beveridge, D. L. and DiCapua, F. M. (1989). "Free-energy via molecular simulation -applications to chemical and biomolecular systems", Annu. Rev. Biophys. Biophys. Chem., 18, 431.
-
(1989)
Annu. Rev. Biophys. Biophys. Chem.
, vol.18
, pp. 431
-
-
Beveridge, D.L.1
DiCapua, F.M.2
-
6
-
-
0001577491
-
Free energy perturbation calculations
-
von Ragué Schleyer, P., Allinger, N. L., Clark, T., Gasteiger, J., Kollman, P. A., Schaefer III, H. F. and Schreiner, P. R. (Eds.), Wiley, Chichester
-
Mark, A. E. (1998). "Free energy perturbation calculations", In: von Ragué Schleyer, P., Allinger, N. L., Clark, T., Gasteiger, J., Kollman, P. A., Schaefer III, H. F. and Schreiner, P. R. (Eds.), Encyclopaedia of Computational Chemistry, 2, 1070-1083. Wiley, Chichester.
-
(1998)
Encyclopaedia of Computational Chemistry
, vol.2
, pp. 1070-1083
-
-
Mark, A.E.1
-
7
-
-
0001737514
-
Free energy via molecular simulation: A primer
-
van Gunsteren, W. F., Weiner, P. K. and Wilkinson, A. J. (Eds.), Escom Science Publisher, Leiden
-
King, P. M. (1993). "Free energy via molecular simulation: A primer", In: van Gunsteren, W. F., Weiner, P. K. and Wilkinson, A. J. (Eds.), Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications, 2, 267-314. Escom Science Publisher, Leiden.
-
(1993)
Computer Simulation of Biomolecular Systems, Theoretical and Experimental Applications
, vol.2
, pp. 267-314
-
-
King, P.M.1
-
8
-
-
0242677212
-
Calculation of electrostatic free-energy differences with a time-saving approximate method
-
King, G. and Barford, R. A. (1993). "Calculation of electrostatic free-energy differences with a time-saving approximate method", J. Phys. Chem., 97, 8798.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 8798
-
-
King, G.1
Barford, R.A.2
-
9
-
-
5544264558
-
Gaussian fluctuation formula for electrostatic free-energy changes in solution
-
Levy, R. M., Belhadj, M. and Kitchen, D. B. (1991). "Gaussian fluctuation formula for electrostatic free-energy changes in solution", J. Chem. Phys., 95, 3627.
-
(1991)
J. Chem. Phys.
, vol.95
, pp. 3627
-
-
Levy, R.M.1
Belhadj, M.2
Kitchen, D.B.3
-
10
-
-
36449009782
-
Predictions of free energy differences from a single simulation of the initial state
-
Smith, P. E. and van Gunsteren, W. F. (1994). "Predictions of free energy differences from a single simulation of the initial state", J. Chem. Phys., 100, 577.
-
(1994)
J. Chem. Phys.
, vol.100
, pp. 577
-
-
Smith, P.E.1
Van Gunsteren, W.F.2
-
11
-
-
0028155689
-
A new method for predicting binding affinity in computer-aided drug design
-
Åqvist, J., Medina, C. and Samuelsson, J.-E. (1994). "A new method for predicting binding affinity in computer-aided drug design", Protein Eng., 7, 385.
-
(1994)
Protein Eng.
, vol.7
, pp. 385
-
-
Åqvist, J.1
Medina, C.2
Samuelsson, J.-E.3
-
12
-
-
0242364982
-
Calculation of free-energy differences from computer simulations of initial and final states
-
Hummer, G. and Szabo, A. (1996). "Calculation of free-energy differences from computer simulations of initial and final states", J. Chem. Phys., 105, 2004.
-
(1996)
J. Chem. Phys.
, vol.105
, pp. 2004
-
-
Hummer, G.1
Szabo, A.2
-
13
-
-
0001692244
-
A-dynamics: A new approach to free energy calculations
-
Kong, X. J. and Brooks III, C. L. (1996). "A-dynamics: A new approach to free energy calculations", J. Chem. Phys., 105, 2414.
-
(1996)
J. Chem. Phys.
, vol.105
, pp. 2414
-
-
Kong, X.J.1
Brooks C.L. III2
-
14
-
-
0030134642
-
Estimating the relative free energy of different molecular states with respect to a single reference state
-
Liu, H., Mark, A. E. and van Gunsteren, W. F. (1996). "Estimating the relative free energy of different molecular states with respect to a single reference state", J. Phys. Chem., 100, 9485.
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 9485
-
-
Liu, H.1
Mark, A.E.2
Van Gunsteren, W.F.3
-
15
-
-
0001272783
-
Estimating relative free energies from a single ensemble: Hydration free energies
-
Schäfer, H., van Gunsteren, W. F. and Mark, A. E. (1999). "Estimating relative free energies from a single ensemble: Hydration free energies", J. Comput. Chem., 20, 1604.
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 1604
-
-
Schäfer, H.1
Van Gunsteren, W.F.2
Mark, A.E.3
-
16
-
-
0001389474
-
An extended linear-response method for determining free-energies of hydration
-
Carlson, H. A. and Jörgensen, W. L. (1999). "An extended linear-response method for determining free-energies of hydration", J. Phys. Chem., 99, 10667.
-
(1999)
J. Phys. Chem.
, vol.99
, pp. 10667
-
-
Carlson, H.A.1
Jörgensen, W.L.2
-
17
-
-
0030062224
-
Free energies of transfer of Trp analogs from chloroform to water: Comparison of theory and experiment and the importance of adequate treatment of electrostatic and internal interactions
-
Daura, X., Hünenberger, P. H., Mark, A. E., Querol, E., Avilés, F. X. and van Gunsteren, W. F. (1996). "Free energies of transfer of Trp analogs from chloroform to water: Comparison of theory and experiment and the importance of adequate treatment of electrostatic and internal interactions", J. Am. Chem. Soc., 118, 6285.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 6285
-
-
Daura, X.1
Hünenberger, P.H.2
Mark, A.E.3
Querol, E.4
Avilés, F.X.5
Van Gunsteren, W.F.6
-
18
-
-
0001127721
-
Free energies of solvation in chloroform and water from a linear response approach
-
McDonald, N. A., Carlson, H. A. and Jörgensen, W. L. (1997). "Free energies of solvation in chloroform and water from a linear response approach", J. Phys. Org. Chem., 10, 563.
-
(1997)
J. Phys. Org. Chem.
, vol.10
, pp. 563
-
-
McDonald, N.A.1
Carlson, H.A.2
Jörgensen, W.L.3
-
19
-
-
0032481614
-
Rapid screening of binding affinities: Application of the A-dynamics method to a trypsin-inhibitor system
-
Guo, Z. Y. and Brooks III, C. L. (1998). "Rapid screening of binding affinities: Application of the A-dynamics method to a trypsin-inhibitor system", J. Am. Chem. Soc., 120, 1920.
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 1920
-
-
Guo, Z.Y.1
Brooks C.L. III2
-
20
-
-
0346052295
-
Generalized linear response method: Application to hydration free energy calculations
-
Chen, X. and Tropsha, A. (1999). "Generalized linear response method: Application to hydration free energy calculations", J. Comput. Chem., 20, 749.
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 749
-
-
Chen, X.1
Tropsha, A.2
-
21
-
-
33646471468
-
Statistical mechanics of fluid mixtures
-
Kirkwood, J. G. (1935). "Statistical mechanics of fluid mixtures", J. Chem. Phys., 3, 300.
-
(1935)
J. Chem. Phys.
, vol.3
, pp. 300
-
-
Kirkwood, J.G.1
-
22
-
-
36849122972
-
High-temperature equation of state by a perturbation method. I. Nonpolar gases
-
Zwanzig, R. W. (1954). "High-temperature equation of state by a perturbation method. I. Nonpolar gases", J. Chem. Phys., 22, 1420.
-
(1954)
J. Chem. Phys.
, vol.22
, pp. 1420
-
-
Zwanzig, R.W.1
-
23
-
-
0344227487
-
Thermodynamics of cavity formation in water: A molecular dynamics study
-
Postma, J. P. M., Berendsen, H. J. C. and Haak, J. R. (1982). "Thermodynamics of cavity formation in water: A molecular dynamics study", Faraday Symp. Chem. Soc., 17, 55.
-
(1982)
Faraday Symp. Chem. Soc.
, vol.17
, pp. 55
-
-
Postma, J.P.M.1
Berendsen, H.J.C.2
Haak, J.R.3
-
24
-
-
0003544049
-
-
Vdf Hochschulverlag AG an der ETH Zürich, Zürich
-
van Gunsteren, W. F., Billeter, S. R., Eising, A. A., Hünenberger, P. H., Krüger, P., Mark, A. E., Scott, W. R. P. and Tironi, I. G. (1996). Biomolecular Simulation: The GROMOS96 Manual and User Guide, Vdf Hochschulverlag AG an der ETH Zürich, Zürich.
-
(1996)
Biomolecular Simulation: The GROMOS96 Manual and User Guide
-
-
Van Gunsteren, W.F.1
Billeter, S.R.2
Eising, A.A.3
Hünenberger, P.H.4
Krüger, P.5
Mark, A.E.6
Scott, W.R.P.7
Tironi, I.G.8
-
25
-
-
0002775934
-
Interaction models for water in relation to protein hydration
-
Pullman, B. (Ed.), Reidel, Dordrecht
-
Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F. and Hermans, J. (1981). "Interaction models for water in relation to protein hydration", In: Pullman, B. (Ed.), Intermolecular Forces, pp. 331-342. Reidel, Dordrecht.
-
(1981)
Intermolecular Forces
, pp. 331-342
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Hermans, J.4
-
26
-
-
0008819754
-
The GROMOS biomolecular simulation program package
-
Scott, W. R. P., Hünenberger, P. H., Tironi, I. G., Mark, A. E., Billeter, S. R., Fennen, J., Torda, A. E., Huber, T., Krüger, P. and van Gunsteren, W. F. (1999). "The GROMOS biomolecular simulation program package", J. Phys. Chem. A, 103, 3596.
-
(1999)
J. Phys. Chem. A
, vol.103
, pp. 3596
-
-
Scott, W.R.P.1
Hünenberger, P.H.2
Tironi, I.G.3
Mark, A.E.4
Billeter, S.R.5
Fennen, J.6
Torda, A.E.7
Huber, T.8
Krüger, P.9
Van Gunsteren, W.F.10
-
27
-
-
4544369164
-
A generalized reaction field method for molecular dynamics simulations
-
Tironi, I. G., Sperb, R., Smith, P. E. and van Gunsteren, W. F. (1995). "A generalized reaction field method for molecular dynamics simulations", J. Chem. Phys., 102, 5451.
-
(1995)
J. Chem. Phys.
, vol.102
, pp. 5451
-
-
Tironi, I.G.1
Sperb, R.2
Smith, P.E.3
Van Gunsteren, W.F.4
-
28
-
-
0000925957
-
Reaction field effects on the simulated properties of liquid water
-
Smith, P. E. and van Gunsteren, W. F. (1995). "Reaction field effects on the simulated properties of liquid water", Mol. Simulation, 15, 233.
-
(1995)
Mol. Simulation
, vol.15
, pp. 233
-
-
Smith, P.E.1
Van Gunsteren, W.F.2
-
29
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
Berendsen, H. J. C., Postma, J. P. M., van Gunsteren, W. F., DiNola, A. and Haak, J. R. (1984). "Molecular dynamics with coupling to an external bath", J. Chem. Phys., 81, 3684.
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
DiNola, A.4
Haak, J.R.5
-
30
-
-
0000249851
-
Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations
-
Beutler, T. C., Mark, A. E., van Schaik, R. C., Gerber, P. R. and van Gunsteren, W. F. (1994). "Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations", Chem. Phys. Letters, 22, 529.
-
(1994)
Chem. Phys. Letters
, vol.22
, pp. 529
-
-
Beutler, T.C.1
Mark, A.E.2
Van Schaik, R.C.3
Gerber, P.R.4
Van Gunsteren, W.F.5
|