In the developing world, managing animal disease is a demanding endeavor. Research and development for new drugs are greatly aided by computational developments in the medical sciences. Drug discovery is a challenging process requiring interdisciplinary collaboration to create effective and affordable veterinary medications. The use of bioinformatics for veterinary drug discovery was not often applied to the study of molecular interactions. Veterinarians in academia and industry need to accelerate attention to understand and harness the tremendous potential of computational approaches to decode the complex molecular machinery of livestock systems for drug discovery. One of the earliest methods in drug design to be employed is structure-based design. Investigating and predicting the 3D structure of a drug target, such as a receptor protein, validation, and binding site analysis, specifically falls under “structure-based design.” This chapter’s goal is to provide an overview of studies in the area of drug target structure modeling that have aided in the search for novel medications. In particular, protein structure prediction, visualization and validation, binding site prediction, characterization, and their limitations and recent advances will be emphasized.