RosettaAntibodyDesign (RAbD): A general framework for computational antibody design
Fig 2
During the inner optimization cycle, a packing shell is created (cyan) around the chosen CDR (in this case, L1 in yellow), and its neighbors (in this case, L3 and the DE loop (L4) in blue). By default, 6 Å is used as the packing shell distance. During the inner loop, all side chains are optimized and amino acid changes are made to any CDRs or regions set to sequence. The chosen CDR and its neighbors additionally undergo backbone optimization during this stage according to the minimization type chosen.