A dynamic programming approach to generation of strong traces

In 2013 Gradišar et al. (National Institute of Chemistry, Slovenia) successfully designed a self-assembly tetrahedral polypeptide called TET12. It is a linear chain of twelve peptides, separated by flexible links, such that certain pairs of peptides “glued” together and formed coiled coil dimers. The end result was a stable tetrahedron in which each of its six edges was a coiled coil dimer.

In the following years mathematical models behind the self-assembly were studied by many researches and a number of theoretical results were obtained. Here, we are going to present the concept of strong traces and a dynamic programming algorithm for their generation.

This is joint work with Drago Bokal, Tomaž Pisanski and Jernej Rus.