This talk presents basic principles of protein engineering aided by molecular
simulation techniques. We start with a brief introduction to proteins for their origins and their
functions as molecular motors and enzymes in terms of their structural components. We then
discuss about how protein structures hierarchy are defined into primary, secondary, and
tertiary structures so that certain patterns of protein folding can be understood in terms of
physical interactions. This understanding leads to a new research field, protein engineering, in
which evolution of proteins at the molecular level is mimicked and accelerated by altering a
few amino acids, which affecting both local physical properties and the global interaction
network. After that, we discussed about some basic principles and theoretical backgrounds of
molecular simulations and their applications in protein engineering in collaborations with
experimental labs. Finally, we discussed on the current advances and future trends of the
protein structure research involving new techniques, such as, machine learning and network
theory.