title: Linear interaction energy: method and applications in drug design.
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.
authors.affiliation: Fundación Pública Galega de Medicina Xenómica, Santiago University Hospital, Santiago de Compostela, Spain. hugo.teran@usc.es
authors.forename: Hugo
authors.initials: H
authors.lastname: Gutiérrez-de-Terán
authors.forename: Johan
authors.initials: J
authors.lastname: Aqvist
mesh_terms: D019295:Computational Biology / Q000379:methods*; D015195:Drug Design; D004353:Drug Evaluation, Preclinical; D008024:Ligands; D056004:Molecular Dynamics Simulation; D011485:Protein Binding; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D008024:Ligands; D011506:Proteins; D014867:Water