For the last few years, apart from minor revisions to the Protein Cycling Diet book, I have been playing around with the question of predicting how a polypeptide would fold if you knew only its amino acid sequence. This question is the holy grail of protein chemistry and has proven to be an exceedingly difficult problem and I hardly expect to solve it. I am now approaching it with a tool that I have not found others to have yet employed namely Jmol, an interactive viewer for three-dimensional chemical structures and a brilliant piece of work currently maintained by Bob Hanson of St. Olafs university.
I used to do my folding work in Java and then use Jmol to display the results. After Bob added the ability to edit polypeptides and in particular to rotate bonds, I was able to do all my work with the Jmol scripting language. My initial output was a library of Jmol scripts: a set of tools for generating and manipulating polypeptides (and polynucleotides) found here. Now I am attempting to write scripts for predictive folding and have decided to discuss my project in this blog. Accordingly I have changed the title to the more general topic, Protein folding. After all, the earlier diet topic was about how to help dispose of misfolded proteins, so I have only broadened the scope of the blog and will continue to speculate here on relevant developments in autophagy science as well.