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Homology Modeling of Transporter Proteins

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Homology Modeling

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2627))

Abstract

Membrane transporter proteins are divided into channels/pores and carriers and constitute protein families of physiological and pharmacological importance. Several presently used therapeutic compounds elucidate their effects by targeting membrane transporter proteins, including anti-arrhythmic, anesthetic, antidepressant, anxiolytic and diuretic drugs. The lack of three-dimensional structures of human transporters hampers experimental studies and drug discovery. In this chapter, the use of homology modeling for generating structural models of membrane transporter proteins is reviewed. The increasing number of atomic resolution structures available as templates, together with improvements in methods and algorithms for sequence alignments, secondary structure predictions, and model generation, in addition to the increase in computational power have increased the applicability of homology modeling for generating structural models of transporter proteins. Different pitfalls and hints for template selection, multiple-sequence alignments, generation and optimization, validation of the models, and the use of transporter homology models for structure-based virtual ligand screening are discussed.

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  1. Molecular Pharmacology and Toxicology, Department of Medical Biology, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway

    Ingebrigt Sylte, Mari Gabrielsen & Kurt Kristiansen

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  1. Ingebrigt Sylte
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  2. Mari Gabrielsen
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  1. Faculty of Chemistry, University of Warsaw, Warsaw, Poland

    Sławomir Filipek

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Sylte, I., Gabrielsen, M., Kristiansen, K. (2023). Homology Modeling of Transporter Proteins. In: Filipek, S. (eds) Homology Modeling. Methods in Molecular Biology, vol 2627. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2974-1_14

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