Nicotinic acetylcholine receptors (nAChRs) are a diverse family of homo- or heteropentameric ligand-gated ion channels. Understanding the physiological role of each nAChR subtype and the key residues responsible for normal and pathological states is important. ${alpha}$-Conotoxin neuropeptides are highly selective probes capable of discriminating different subtypes of nAChRs. In this study, we performed homology modeling to generate the neuronal ${alpha}3$, ${eta}2$ and ${eta}4$ subunits using the x-ray structure of the ${alpha}1$ subunit as a template. The structures of the extracellular domains containing ligand binding sites in the ${alpha}3{eta}2$ and ${alpha}3{eta}4$ nAChR subtypes were constructed using MD simulations and ligand docking processes in their free and ligand-bound states using ${alpha}$-conotoxin GIC, which exhibited the highest ${alpha}3{eta}2$ vs. ${alpha}3{eta}4$ discrimination ratio. The results provide a reasonable structural basis for such a discriminatory ability, supporting the idea that the present strategy can be used for future investigations on nAChR-ligand complexes.