I want to model amino acids in the active site of my amino acid oxidase flavoprotein and am going to try SwissDock and AutoDock Vina. Does anyone have experience with this type of modeling and know what is the best software for this? The main things I want to look at are how the active site residues and flavin interact with different amino acids, and match that with the reaction kinetics we have from the amino acid substrates. I want to be able to explain structurally why the Km or kcat of one amino acid is better than another based on how well they fit and interact with the active site. Thanks for any help!