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Ion channels, as part of natures’ solution for regulating biological environments, are particularly interesting to device engineers seeking to understand how nanoscale molecular systems realize device-like functions, such as bio-sensing of organic analytes. What’s more, attaching molecular adaptors in desired orientations inside genetically engineered ion channels enhances the system functionality as a biosensor. In general, a hierarchy of simulation methodologies is needed to study different aspects of a biological system like ion channels. Biology Monte Carlo (BioMOCA), a three-dimensional coarse-grained ion channel simulator, offers a powerful and general approach to study ion channel permeation. In this paper, we have employed BioMOCA to study genetically engineered mutations of α-Hemolysin, with covalently attached β-Cyclodextrin. While the wild type α-Hemolysin is known to be slightly anion selective, the mutations introduce a slightly different charge distribution in the protein, resulting in stronger selectivity towards anions.