The Role of Jmol/JSmol in Teaching about Proteins

Jmol_logo13I teach a course devoted to one type of biomolecule: Proteins. The course is The Biology and Biochemistry of Proteins, Biol 443.  Biol 443 is a digital-rich course designed to use the wealth of information available on-line to study the structure, function and evolution of proteins. The digital visualization of models of protein structure has been an active area of interest since the 1960s. Over the past 20 years, researchers have developed several molecular graphics tools that use the raw structural data to display models of protein structures and empower the user to manipulate those models to study the molecular details of the protein’s structure. One of these molecular graphics tools is Jmol, a free, open source, cross-platform Java-based molecular viewer used to embed dynamic three-dimensional models of chemical structures and biomolecules into web pages. My next step in the development of digital communication in my classes is to incorporate the use of JSmol in all aspects of Biol 443: to incorporate JSmol driven models in lecture, to incorporate a series of lessons for students on how to use JSmol, and to require students to develop digital reports that incorporate, among other things, dynamic protein models displayed through the use of JSmol.  Read my full essay.