Designing a Peptide Ligand with Dead End Elimination

In protein redesign one of the main challenges is the ability to evaluate many different conformations of the redesigned protein in order to determine the best structure. One approach to this problem is to provably get rid of bad protein conformations using dead-end elimination (DEE). DEE was first developed for application to protein structure evaluation by Desmet et al. [1]. Since then there have been many advances in both the pruning criteria and its applications. My project aim is to extend Donald Lab DEE algorithm implementation in order to design peptide ligands. Specifically, I apply my extension to the cystic fibrosis transmembrane conductance regulator (CFTR) and cystic fibrosis associated ligand (CAL) system.