Permeability models and methods for creating the models are disclosed. The models include receiving as an input in vitro permeability and structure data for a particular compound. Then the data is mapped to at least one permeability. In some models the data is mapped to a plurality of permeabilities, each associated with a specific region in a mammalian GI tract. Some models may take into consideration solubility, permeability and at least one molecular descriptor associated with the compound of interest.