Protein design seeks to identify novel amino acid sequences that will fold into a given template. Computational protein design minimizes the energy of the sequence in a given 3-dimensional template.
This picture shows a cartoon representation of the 3-dimensional template of a peptide (purple) bound to a Human leukocyte antigen (grey). The design template is used to find novel sequences of the peptide that will bind with greater affinity to the antigen.
The mesh in the image shows the surface of the antigen at a particular binding "pocket," allowing us to determine how well the yellow amino acid side chain of the peptide fits into that pocket. In the case of this particular pocket we can see that in order to bind more efficiently, the amino acid side chain should have more favorable energetic contacts than the template side chain offers.