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Background: Glycine receptor (GlyR) is member of ligand-gated ion channels that are also referred to as the Cys-loop receptors due to conserved disulfide-bonded cysteines in the ligand binding domain (LBD).This receptor mediate signaling across synapses of the central and peripheral nervous systems and is an interesting therapeutic target.The homology model of GlyR can be used in structure based design of noval ligands.