Amino acids free energy calculations

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. 

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. 

It is possible to calculate whether a particular sequence of amino acids present in a protein is consistent with a transmembrane location. This can be done by consulting a table that hsts the hydrophobicities of each of the 20 common amino acids and the free energy val-... 

Sayano, K. Kono, H. Gromiha, M. M. Sarai, A., Multicanonical Monte Carlo calculation of the free-energy map of the base-amino acid interaction, J. Comput. Chem. 2000, 21, 954-962... 

Archontis, G. Simonson, T. Karplus, M., Binding free energies and free energy components from molecular dynamics and Poisson-Boltzmann calculations. Application to amino acid recognition by aspartyl-tRNA synthetase, J. Mol. Biol. 2001, 306, 307-327... 

Villa, A. Mark, A. E., Calculation of the free energy of solvation for neutral analogs of amino acid side chains, J. Comput. Chem. 2002, 23, 548-553. 

Maccallum, J. L. Tieleman, D. P., Calculation of the water-cyclohexane transfer free energies of neutral amino acid side-chain analogs using the OPLS all-atom force held, J. Comput. Chem. 2003, 24, 1930-1935. 

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