Biology Reference
In-Depth Information
20. Berendsen HJC, Postma JPM, van Gunsteren WF
et al
. (1984) Molecular
dynamics with coupling to an external bath
. J Chem Phys
81
: 3684.
21. Morishita T. (2000) Fluctuation formulas in molecular-dynamics simulations
with the weak coupling heat bath
. J Chem Phys
113
: 2976.
22. Kirkwood JG. (1935) Statistical mechanics of fluid mixture
. J Chem Phys
3
:
300-13.
23. Zwanzig RW. (1954) High-temperature equation of state by a perturbation
method. I. Nonpolar gases
. J Chem Phys
22
: 1420-6.
24. Tembe BL, McCammon JA. (1984) Ligand-receptor interactions
. Comput
Chem
8
: 281-3.
25. Bash PA, Singh UC, Brown FK
et al
. (1987) Calculation of the relative change
in binding free energy of a protein-inhibitor complex
. Science
235
: 574-6.
26. Frenkel D, Smit B. (2002)
Understanding Molecular Simulation: From Algorithms
to Applications.
San Diego, CA: Academic Press.
27. Bennett CH. (1976) Efficient estimation of free energy differences from Monte
Carlo data
. J Comput Phys
22
: 245-68.
28. Pitera JW, van Gunsteren WF. (2002) A comparison of non-bonded scaling
approaches for free energy calculations
. Mol Simul
28
: 45-65.
29. Beutler TC, Mark AE, van Schaik RC
et al
. (1994) Avoiding singularities and
numerical instabilities in free energy calculations based on molecular simulations
.
Chem Phys Lett
222
: 529-39.
30. Straatsma TP, McCammon JA. (1991) Multiconfiguration thermodynamic
integration
. J Chem Phys
95
: 1175-88.
31. van Gunsteren WF, Beutler TC, Fraternali F
et al
. (1993) Computation of free
energy in practice: choice of approximations and accuracy limiting factors.
In: van Gunsteren WF, Weiner PK, Wilkinson AJ (eds.).
Computer Simulation of
Biomolecular Systems: Theoretical and Experimental Applications
, Vol. 2. Leiden,
The Netherlands: Escom Science Publishers, pp. 315-48.
32. Fasnacht M, Swendsen RH, Rosenberg JM. (2004) Adaptive integration
method for Monte Carlo simulations
. Phys Rev E Stat Nonlin Soft Matter Phys
69
: 056704.
33. Ytreberg FM, Swendsen RH, Zuckerman DM. (2006) Comparison of free
energy methods for molecular systems
. J Chem Phys
125
: 184114.
34. Michielin O, Karplus M. (2002) Binding free energy differences in a TCR-peptide-
MHC complex induced by a peptide mutation: a simulation analysis
. J Mol Biol
324
: 547-69.
35. Oostenbrink C, van Gunsteren WF. (2005) Free energies of ligand binding for
structurally diverse compounds
. Proc Natl Acad Sci USA
102
: 6750-4.
36. Swanson JM, Henchman RH, McCammon JA. (2004) Revisiting free energy
calculations: a theoretical connection to MM/PBSA and direct calculation of the
association free energy
. Biophys J
86
: 67-74.