Carbohydrates are important molecules in energy storage and cellular recognition. New methods are used and discussed to capture important structural details of created by the protein/carbohydrate interactions. In particular, the thermodynamics of carbohydrate binding are explored, and a new model to accurately calculate the free energy of binding is developed. Additionally, a new method of describing the pucker of carbohydrate ring with three coordinates is discussed. These methods are then applied to Family 1 Glycoside Hydrolases.