Foundations of Biomolecular Simulations: A Critical Introduction to Homology Modeling, Molecular Dynamics Simulations, and Free Energy Calculations of Membrane Proteins - Archive ouverte HAL Accéder directement au contenu
Chapitre D'ouvrage Année : 2014

Foundations of Biomolecular Simulations: A Critical Introduction to Homology Modeling, Molecular Dynamics Simulations, and Free Energy Calculations of Membrane Proteins

Résumé

We review foundations of biomolecular simulations that enable the study of membrane protein models with a particular focus on structure–function relationships and opportunities for drug design. A range of broadly used methods is presented comprising homology modeling, normal mode analysis, molecular dynamics simulations, and free energy calculations. These methods are illustrated with examples on several membrane protein systems, in particular ligand-gated ion channels such as the P2X receptors, the N-methyl-D-aspartate (NMDA) receptors, and the Cys-loop family of pentameric ion channels.
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Dates et versions

hal-01498051 , version 1 (29-03-2017)

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Jérôme Hénin, Marc Baaden, Antoine Taly. Foundations of Biomolecular Simulations: A Critical Introduction to Homology Modeling, Molecular Dynamics Simulations, and Free Energy Calculations of Membrane Proteins. Membrane Proteins Production for Structural Analysis, Springer New York, pp.347--392, 2014, 978-1-4939-0661-1. ⟨10.1007/978-1-4939-0662-8_13⟩. ⟨hal-01498051⟩
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