Protein engineering focuses on the design of new proteins or enzymes with new or desired functions. General targets of protein engineering are the modification of enzyme stability, activity, substrate specificity and enantioselectivity. The controlled manipulation of proteins allows a better understanding of functionality and enables further improvements in protein properties. 
The three main strategies of protein modification are: directed evolution, rational design, and a combination of both, semi-rational design. The directed evolution method uses a controlled environment to induce mutations and selection, while rational design manipulates amino acids directly.
A broad range of applications can be covered with modified proteins or enzymes, including biocatalysis for food as well as environmental, medical and nanobiotechnology applications.  Some examples of modified enzymes for use in the food, detergent and paper industries are proteases and amylases. Other enzymes like peroxidases and oxygenases are used in the environmental sector.
Because of the central role of proteins in biological functions, protein engineering is a crucial technology for new biological therapies. As a consequence, therapeutic proteins show great potential for the targeted treatment of diseases such as cancer, Alzheimer's, Parkinson's and HIV.
Advantages of protein/enzyme engineering in comparison to traditional chemical reactions:
- Efficiency (in enhancing the rate of chemical reactions)
- Substrate specificity (ability to discriminate between potential substrates)
- Environmental friendliness (no organic solvent or heavy metal toxic waste)
- Cheap and easy usage (many enzymes are commercially available)
- Possibility of enzyme combination (can be used together in sequence or cooperatively to catalyze multistep reactions)
- Regio- and stereospecific reactions (produce chiral pure products)
- Suitability for many different applications (medicine, chemical industry, food processing, agriculture)