The grey portion of this illustration is a spike, one of many that cover the outer shell of the coronavirus. My protein folding group, http://www.fold.it, has been working on the design of a protein that will bind with the spike. If this protein binds with coronavirus, it blocks the virus from attaching itself to human cells. This is one strategy used by hundreds of laboratories around the world racing to find a way to combat this deadly virus.
My task is to create the portion of the protein shown in the illustration in orange (hydrophobic; hates water) and blue (hydrophilic; loves water). The blue and white striped filaments represent hydrogen bonds. The red and blue dots represent bondable atoms. We use these cartoon elements to understand what is happening in its chemistry.
The best computer models are then grown in the wet lab at the University of Washington using a sequence of DNA produced according to the sequence generated by the computer model. If the newly created protein thrives, it is considered a viable candidate. The work so far this week uses a series of small computer programs to wiggle and shake the atoms of this long-chain molecule into a desired arrangement. My computer is running 24/7. In another four days, the programs finish running, and we’ll see if the result is useful.