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Linear Interaction Energy: Method and Applications in Drug Design

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Computational Drug Discovery and Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 819))

Abstract

A broad range of computational methods exist for the estimation of ligand–protein binding affinities. In this chapter we will provide a guide to the linear interaction energy (LIE) method for binding free energy calculations, focusing on the drug design problem. The method is implemented in combination with molecular dynamics (MD) sampling of relevant conformations of the ligands and complexes under consideration. The detailed procedure for MD sampling is followed by key notes in order to properly analyze such sampling and obtain sufficiently accurate estimations of ligand-binding affinities.

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Author information

Authors and Affiliations

  1. Fundación Pública Galega de Medicina Xenómica, Santiago University Hospital, Santiago de Compostela, Spain

    Hugo Gutiérrez-de-Terán

  2. Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden

    Johan Åqvist

Authors
  1. Hugo Gutiérrez-de-Terán
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  2. Johan Åqvist
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Corresponding author

Correspondence to Hugo Gutiérrez-de-Terán .

Editor information

Editors and Affiliations

  1. University of Utah, 30 South 2000 East Rm 307, Salt Lake City, 84112-5820, California, USA

    Riccardo Baron

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Gutiérrez-de-Terán, H., Åqvist, J. (2012). Linear Interaction Energy: Method and Applications in Drug Design. In: Baron, R. (eds) Computational Drug Discovery and Design. Methods in Molecular Biology, vol 819. Springer, New York, NY. https://doi.org/10.1007/978-1-61779-465-0_20

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  • DOI: https://doi.org/10.1007/978-1-61779-465-0_20

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  • Publisher Name: Springer, New York, NY

  • Print ISBN: 978-1-61779-464-3

  • Online ISBN: 978-1-61779-465-0

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