The Protein Forge - Interactive Building of Polypeptides

Proteins carry out the algorithms of life. As such, they play an integral role in Systems biology. Given the rapid development of Systems biology, understanding biological processes at a molecular level has become more important to other disciplines, like medicine, as well. Yet, current didactic methods often fail to teach their students biochemistry effectively. We present the Protein Forge, a Virtual Reality application that aims to help primarily medical students to identify amino acids, the building blocks of proteins, and to teach them how those amino acids are chemically linked. The program follows a predefined workflow: its user identifies amino acids from a naturally occurring protein sequence one after the other. When choosing the right amino acid, the user is presented with an animation, showing the formation of a peptide bond, i.e., the bond between two amino acids. The program was implemented in scenery, an open-source framework for rendering VR scenes. To display amino acids, we developed a rudimentary molecular viewer for scenery, consisting of a data structure to store the molecule data and an algorithm to determine the atom positions in space for a given molecule. A video of the experience can be found here:https://cloudstore. zih.tu-dresden.de/index.php/s/JB898wJFgp2r6fT, the respective code here: https:// github.com/scenerygraphics/scenery/tree/peptide_chain.