Custom-designed or tailoring of proteins for specific applications is a highly active and growing area of research. A major part of this research is focused on protein engineering especially protein interfaces and interactions by employing biomolecular engineering tools. This research focus is partly due to the significance of protein interactions that are known to communicate critical information from the environment into cells to mobilize functional responses relevant to health and disease. Protein engineering can lead to custom-designed protein structures and biomaterials with the desired affinity, specificity, mechanism, or other properties that are of practical biomedical interests. Here, we describe a brief overview of protein engineering and some of the recent breakthroughs in biomedical applications of designer proteins. We discuss recent applications in new vaccine designs and advanced therapeutics for battling the challenges of complex diseases.