Molecular dynamics simulation for rational protein engineering: Present and future prospectus

Recently protein engineering has been used as a pivotal tool for designing proteins with improved characteristics. While the experimental methods might be laborious and time-consuming, in silico protein design is a time and cost-effective approach. Moreover, in some cases, protein modeling might be the only way to obtain structural information where the experimental techniques are inapplicable. Molecular dynamics (MD) simulation is a method that allows the motion of protein to be simulated in defined conditions on the basis of classical molecular dynamics. MD simulation could widely be used when protein design needs accurate modeling of the target protein dynamics and also descriptions of the relation between conformational changes and function of protein at the atomic level. In this review, the effectiveness and the power of MD simulation in designing proteins with improved characteristics will be discussed.