Computing tools for the sciences in the spotlight
Professor Michelle Kuttel, of the Computer Science Department at University of Cape Town, and her collaborators developed the CarbBuilder software application, which made it onto the cover of the Journal of Computational Chemistry thanks to its quality and capacity to create effective 3D models of complex carbohydrate molecules.
Carbohydrates are increasingly recognized as key factors in infectious disease mechanisms. The sophisticated algorithm that runs behinds the scenes to create the models enables scientists to explore the range of possible conformations, which is important for understanding the biological function of these molecules. The core algorithm and the software’s architecture were developed in-house, which consists of a recursive algorithm for exploring all the possibilities for a specified structure.
CarbBuilder is the first software application in the world to have this capability to build very large, branched polysaccharide structures. The cover image depicts a highly-branched repeating glycogen-like polysaccharide containing 740 glucose monomers, which was created with the CarbBuilder software based on just command-line (text-based) input of the primary structure of a carbohydrate.
This spotlight followed recognition of another tool developed by Kuttel and her students, which is aimed at the other end of the spectrum: health workers. They developed an eHealth application for Android mobile phones that enables a smartphone to act as an affordable and mobile alternative to an expensive microplate reader. This application is expected to support drug research in developing countries by enabling rapid, cheap drug assays in small laboratories and in fieldwork with a standard Android smartphone. Their contribution was honoured with a “Runner up” paper award at the IST-Africa 2016 conference.
The tools can be downloaded for free from Kuttel’s website