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Book Chapter

Calculation of binding free energies.

MPS-Authors
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Gapsys,  V.
Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society;

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Michielssens,  S.
Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society;

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Peters,  J. H.
Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society;

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de Groot,  B.
Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society;

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Leonov,  H.
Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society;

Fulltext (public)

2157509.pdf
(Publisher version), 2MB

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Citation

Gapsys, V., Michielssens, S., Peters, J. H., de Groot, B., & Leonov, H. (2015). Calculation of binding free energies. In A. Kukol (Ed.), Molecular Modeling of Proteins (pp. 173-209). New York, N.Y.: Humana Pr.; Springer.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0027-79C1-2
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.