Proteins possess many structural and functional characteristics that these features are not seen in any other biomolecules. So many biologists have been persuaded that using protein engineering design and build their desired proteins. These engineered proteins can act as new molecular tools for scientific, medical, industrial, etc. applications, so they can satisfy many human needs that are not met by natural proteins. Protein engineering based on calculations Strategy produces and screens the protein sequences with "in silico" (i.e. before its synthesis in the laboratory). Structure-based protein engineering calculations similarly use the calculations to discover the protein sequences. However, calculation-based protein engineering also emphasizes the new and useful protein engineering and investigating the relationship between structure and function of them. This study investigates the protein engineering tools in producing the recombinant and engineered proteins. For this purpose, bioinformatics studies, how to predict the second and third buildings based on homology and adaptive modeling, predicting protein performance for the production of recombinant proteins are investigated.