Use of Molecular Dynamics Data in Biochemistry Courses

The aim of this manuscript is to explain the application of an amphipathy scale obtained from molecular dynamics simulations and to demonstrate how it can be useful in the protein structure field. It is shown that this scale is easy to be used with the advantage of revealing domains of transmembrane a-helix of proteins without the need of knowing anything besides the protein primary structure. In addition, it allows the students to correlate concepts of protein structure and function, energy minimization, molecular dynamics simulations, and protein location.