The open-state homology model based on the structure of the β3ECD-α5TMD chimera (pdb: 5O8F) was loaded into Swissdock (http://www.swissdock.ch) and probed blindly by docking TETS using 5000–15,000 generated iterations. Swissdock uses the Chemistry at Harvard Macromolecular Mechanics force field (CHARMM) for estimating the chemical interactions and treats the protein as a grid. The accurate docking function was used with no flexibility allowed. The top results were examined visually, and only docking poses found in the TMD were further considered and are shown in Fig. 2.

Generation of a homology model of the α2β3γ2 GABAA receptor. (A) The X-ray structure of the β3ECD-α5TMD served as a template. (B) The Rosetta-generated homology model of the α2β3γ2 in the open state. The receptor is color-coded as follows: α2 (blue), β3 (red), γ2 (yellow). (C) Sequence alignment of α2, β3, and γ2 in the M2 segment. (D) Common numbering of pore-lining residues in GABAA receptors.

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