Abstract
Molecular dynamics simulations enable access to free energy differences governing the driving force underlying all biological processes. In the current chapter we describe alchemical methods allowing the calculation of relative free energy differences. We concentrate on the binding free energies that can be obtained using non-equilibrium approaches based on the Crooks Fluctuation Theorem. Together with the theoretical background, the chapter covers practical aspects of hybrid topology generation, simulation setup, and free energy estimation. An important aspect of the validation of a simulation setup is illustrated by means of calculating free energy differences along a full thermodynamic cycle. We provide a number of examples, including protein–ligand and protein–protein binding as well as ligand solvation free energy calculations.
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Notes
- 1.
Distance restraints on the P α , P γ and the Mg+2 will keep the atoms in their respective orientation in one of the two top clusters shown in Fig. 12b.
- 2.
A shorter transition time of 200 ps also gave a result that was fairly close to zero, but longer times were used to reduce the error.
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Gapsys, V., Michielssens, S., Peters, J.H., de Groot, B.L., Leonov, H. (2015). Calculation of Binding Free Energies. In: Kukol, A. (eds) Molecular Modeling of Proteins. Methods in Molecular Biology, vol 1215. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1465-4_9
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DOI: https://doi.org/10.1007/978-1-4939-1465-4_9
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