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  Calculation of binding free energies.

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.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0027-79C1-2 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-002A-10EB-1
Genre: Book Chapter

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 Creators:
Gapsys, V.1, Author              
Michielssens, S.1, Author              
Peters, J. H.1, Author              
de Groot, B.1, Author              
Leonov, H.2, Author              
Affiliations:
1Research Group of Computational Biomolecular Dynamics, MPI for biophysical chemistry, Max Planck Society, ou_578573              
2Department of Theoretical and Computational Biophysics, MPI for biophysical chemistry, Max Planck Society, ou_578631              

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Free keywords: Free energy - Molecular dynamics - Alchemical transitions - Protein–ligand binding - Protein–protein interaction - Non-equilibrium methods - Hybrid topology - Crooks Fluctuation Theorem
 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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Language(s): eng - English
 Dates: 2015-01-01
 Publication Status: Published in print
 Pages: -
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 Rev. Method: Peer
 Identifiers: DOI: 10.1007/978-1-4939-1465-4_9
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Source 1

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Title: Molecular Modeling of Proteins
Source Genre: Book
 Creator(s):
Kukol, A., Editor
Affiliations:
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Publ. Info: New York, N.Y. : Humana Pr.; Springer
Pages: X, 474 Volume / Issue: - Sequence Number: - Start / End Page: 173 - 209 Identifier: ISBN: 978-1-4939-1464-7

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Title: Methods in Molecular Biology
Source Genre: Series
 Creator(s):
Walker, J. M., Editor
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Pages: - Volume / Issue: 1215 Sequence Number: - Start / End Page: - Identifier: -