On the decomposition of free energies

Journal of Molecular Biology

Volumn 263, Issue 2, 1996, Pages 123-125

  Brady, G Patrick ^a   Szabo, Attila ^b   Sharp, Kim A ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

Enthalpy decomposition; Entropy decomposition; Free energy components; Free energy separability

Indexed keywords

ARTICLE; DECOMPOSITION; ENERGY; MOLECULAR BIOLOGY; PRIORITY JOURNAL; THERMODYNAMICS;

EID: 0030601861     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0563     Document Type: Editorial

References (14)

1. Bash, P., Singh, C., Brown, F., Langridge, R. & Kollman, P. (1987). Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science, 235, 574-576.
2. Boresch, S. & Karplus, M. (1995). The meaning of component analysis: decomposition of the free energy in terms of specific interactions. J. Mol. Biol. 254, 801-807.
3. Boresch, S., Archontis, G. & Karplus, M. (1994). Free-energy simulations - the meaning of the individual contributions from a component analysis. Proteins: Struct. Funct. Genet. 20, 25-33.
4. Brady, G. P. & Sharp, K. A. (1995). Decomposition of interaction free energies in proteins and other complex systems. J. Mol. Biol. 254, 77-85.
5. Brooks, C. L. (1990). Molecular simulations of protein structure, dynamics and thermodynamics. In Computer Modelling of Fluids, Polymers and Solids (Catlow, C., Parker, S. & Allen, M., eds), pp. 289-334, Kluwer Academic Publishers, Dordrecht.
6. Gao, J., Kuczera, K., Tidor, B. & Karplus, M. (1989). Hidden thermodynamics of mutant proteins: a molecular dynamics analysis. Science, 244, 1069-1072.
7. Hirata, F., Redfern, P. & Levy, R. (1989). Viewing the Born model of ion hydration through a microscope. Int. J. Quant. Chem. 15, 179-190.
8. Mark, A. E. & van Gunsteren, W. F. (1994). Decomposition of the free energy of a system in terms of specific interactions. J. Mol. Biol. 240, 167-176.
9. Rashin, A. A. & Honig, B. (1985). Reevaluation of the Born model of ion hydration. J. Phys. Chem. 89, 5588-5593.
10. Roux, B., Yu, H. A. & Karplus, M. (1990). Molecular basis for the Born model of ion solvation. J. Phys. Chem. 94, 4683-4688.
11. Shi, Y., Mark, A. E., Wang, C., Huang, F., Berendsen, H. & van Gunsteren, W. (1993). Can the stability of protein mutants be predicted by free energy calculations? Protein Eng. 6, 289-295.
12. Smith, P. E. & van Gunsteren, W. F. (1994). When are free energy components meaningful? J. Phys. Chem. 98, 13735-13740.
13. Yu, H. A. & Karplus, M. (1988). A thermodynamic analysis of solvation. J. Chem. Phys. 89, 2366-2379.
14. Zwanzig, R. W. (1954). High-temperature equation of state by a perturbation method. I Nonpolar gases. J. Chem. Phys. 22, 1420-1426.