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Absolute alchemical free energy calculations for ligand binding: a beginner’s guide

Abstract:

Many thermodynamic quantities can be extracted from computer simulations that generate an ensemble of microstates according to the principles of statistical mechanics. Among these quantities is the free energy of binding of a small molecule to a macromolecule, such as a protein. Here, we present an introductory overview of a protocol that allows for the estimation of ligand binding free energies via molecular dynamics simulations. While we focus on the binding of organic molecules to proteins...

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Publication status:
Published
Peer review status:
Peer reviewed

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Institution:
University of Oxford
Division:
MSD
Department:
Biochemistry
Oxford college:
Lady Margaret Hall
Role:
Author
Publisher:
Humana Press Publisher's website
Volume:
1762
Issue:
2018
Pages:
199-232
Series:
Methods in Molecular Biology
Host title:
Methods in Molecular Biology
Publication date:
2018-03-29
DOI:
EISSN:
1940-6029
ISSN:
1064-3745
Pmid:
29594774
Source identifiers:
834111
ISBN:
9781493977567
Language:
English
Keywords:
Pubs id:
pubs:834111
UUID:
uuid:b5ead25b-befe-4f1a-b318-257268758f5e
Local pid:
pubs:834111
Deposit date:
2018-04-18

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