Researcher(s)
- Ava West, Computer Science, University of Delaware
Faculty Mentor(s)
- Jodi Hadden-Perilla, Chemistry and Biochemistry, University of Delaware
Abstract
Mechanical and biophysical characteristics of viral capsids have recently become a center of research interest. The increasing knowledge on the biological roles of these characteristics have fueled drug development intended to misdirect and disrupt viral capsid formation. Computational chemists contribute to this growing knowledge base by accurately simulating capsid dynamics, including in the presence of drug molecules. However, these are often large systems that include hundreds of thousands, if not millions, of atoms that can be challenging to visualize. Many of these capsids of interest have an icosahedral shape and are often organized according to Casper-Klug theory. Here, we present a tool for reducing the complexity of capsid visualization with geometric abstractions, which also allows measurement of the capsid’s geometrical properties, such as volume and sphericity. Using Tcl (a high-level programming language), we determine basic spatial information from a capsid’s PDB coordinate file and create a simplified polyhedral representation of it. Abstracted representations of viral capsids also aid in the development of educational resources tailored to the visually impaired. Drawing structurally complex capsids as simple geometric shapes allows them to be transformed into clear tactile graphics, accessible to users who are blind or have low vision.