Proteins free energy calculations

S. Miyamoto and P. A. Kollman. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches. Proteins, 16 226-245, 1993. 

Y-Y Shi, AE Mark, C Wang, F Fluang, FIJC Berendsen, WF Van Gunsteren. Can the stability of protein mutants be predicted by free energy calculations Protein Eng 6 289-295,... 

Pearlman, D. A. Charifson, P. S., Are free energy calculations useful in practice A comparison with rapid scoring functions for the p38 MAP kinase protein system, J. Med. Chem. 2001, 44, 3417-3423... 

Simonson, T. Archontis, G. Karplus, M., Continuum treatment of long-range interactions in free energy calculations. Application to protein-ligand binding, J. Phys. Chem. B 1997, 101, 8349-8362... 

So far we have discussed various techniques for computing the PMF. The other type of free energy calculation commonly performed is alchemical transformation where two different systems are compared. Such calculations have many applications such as Lennard-Jones fluid with and without dipoles for each particles, comparison of ethanol (CH3CH2OH) and ethane thiol (CH3CH2SH), replacing one amino acid by another in a protein, changing the formula for a compound in drug discovery, etc. 

Free energy calculations rely on a well-known thermodynamic perturbation theory [6, 21, 22], which is recalled in Chap. 2. We consider a molecular system, described by the potential energy function U(rN), which depends on the coordinates of the N atoms rN = (n, r2,..., r/v). The system could be a biomolecule in solution, for example. We limit ourselves to a classical mechanical description, for simplicity. Practical calculations always consider differences between two or more similar systems, such as a protein complexed with two different ligands. Therefore, we consider a change in the system, such that the potential energy function becomes ... 

Simonson, T. Brimger, A. T., Thermodynamics of protein-peptide binding in the ribonuclease S system studied by molecular dynamics and free energy calculations.,... 

Rozanska, X. Chipot, C., Modeling ion-ion interaction in proteins a molecular dynamics free energy calculation of the guanidinium-acetate association, J. Chem. Phys. 2000, 112, 9691-9694. 

Shirts, M. Pitera, J. Swope, W. Pande, V., Extremely precise free energy calculations of amino acid chain analogs comparison of common molecular mechanical force fields for proteins, J. Chem. Phys. 2003,119, 5740-5761. 

Dang, L. X. Merz, K. M. Kollman, P. A., Free-energy calculations on protein stability - Thr1B7-Val157 Mutation of T4 lysozyme, J. Am. Chem. Soc. 1989, 111, 8505-8508. 

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