Protein engineering is the process of developing useful or valuable proteins. It is a young discipline, with much research taking place into the understanding of protein folding and recognition for protein design principles.

There are two general strategies for protein engineering, rational design and directed evolution. These techniques are not mutually exclusive; researchers will often apply both. In the future, more detailed knowledge of protein structure and function, as well as advancements in high-throughput technology, may greatly expand the capabilities of protein engineering. Eventually, even unnatural amino acids may be incorporated thanks to a new method that allows the inclusion of novel amino acids in the genetic code.

In rational protein design, the scientist uses detailed knowledge of the structure and function of the protein to make desired changes. This generally has the advantage of being inexpensive and technically easy, since site-directed mutagenesis techniques are well-developed. However, its major drawback is that detailed structural knowledge of a protein is often unavailable, and even when it is available, it can be extremely difficult to predict the effects of various mutations.