Calculations of relative hydration free energies: a comparative study using thermodynamic integration and an extrapolation method based on a single reference state

Article Abstract:

Issues concerning the use of molecular dynamics simulations to calculate the relative hydration free energies of organic molecules are presented.

Condensed matter, Benzene, Chemistry, Organic, Organic chemistry, Statistical mechanics

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Chromophore protonation states and the proton shuttle mechanism in green fluorescent protein: inferences drawn from ab initio theoretical studies of chemical structures and vibrational spectra

Article Abstract:

Inferences regarding the chromophore protonation states and the proton shuttle mechanism of green fluorescent protein are drawn on the basis of ab initio theoretical studies of chemical structure and vibrational spectra. The appearances of the corresponding features in the IR spectra could be affected due to the perturbing effects of protein solvation on the chromophores and residue vibrational modes.

Vibrational spectra, Chemical properties, Chromophores

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Computer simulation of protein-protein interactions

Article Abstract:

A broad overview of atomically detailed computer simulations methods that can be used for the examinations of protein-protein interactions is presented. Computer simulation methods can be used in combination with efficient search methods for determining the protein docking problem and weaker protein-protein interactions.

Proteins, Simulation methods, Simulation

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