De Novo Protein Design
De novo protein design seeks to determine the amino acid sequence or sequences that will fold into a given 3-dimensional template. One application of protein design is to discover novel peptide sequences that will bind with greater affinity than the native sequence to a target protein. Many computational tools are utilized to achieve this desired result. The image on the left depicts computational docking of small molecule inhibitors of Purine Nucleoside Phosphorylase (PNP) in order to determine a target binding site (shown in yellow). The image on the top-right shows clustering results, a useful tool to group together peptides with similar phi and psi angles. The two bottom-right images show design templates of an influenza virus peptide bound to Human Leukocyte Antigen (HLA), with the small peptide nestled in the binding groove of HLA.