This is a demo for running the protein design simulations described in "Removing T cell Epitopes with Computational Protein Design" (PNAS, in press). Just unzip and untar >> tar -xzf removing_tcell_epitopes_protein_design_demo.tar.gz And you sill see a directory structure that follows the computational results of the paper. Look in the README in the toplevel directory for instructions. Note: You need to have a current build of Rosetta (March 2014 or later) for this to work!