Technical Abstract: Glucoamylase is an enzyme that hydrolyzes starch to glucose. The enzyme is an important component of the corn fructose sweeteners industry. Extensive efforts are underway to find variants of this enzyme with different catalytic properties, including modified thermal stability and pH activity. Several studies have been undertaken to define the substrate specificity of the enzyme, and classical screening and genetic manipulation experiments have also been reported to isolate mutants with different catalytic properties. In this work we report on efforts to simulate the binding of small substrates into the active site of this enzyme. Several monosaccharides, disaccharides, and known inhibitors have been docked using Monte Carlo-based AutoDock 2.1 (Scripps Research Institute, La Jolla, CA). The computational results compared favorably with published crystallography results and kinetically-determined binding constant for several of the docked molecules. This information should lead to a more detailed understanding of the catalytic functions of this enzyme and should help direct future mutagenesis studies.