2.1 Identification of antigen-binding CDRs
The structure of the EGFR DIII/Panitumumab complex (PDB entry 5SX4) was
used as the initial complex for extracting the affective CDRs in
interaction with the receptor. Two CDRs, H2 and H3, from the heavy chain
and L3 from the light chain were selected for grafting into three
scaffolds of Lipocalin (PDB entry 3dwt), Fn3 (1TTF), and VHH (3BX7). The
sequence of these CDRs defined by Parapred software [10], each with
two residues per site (residues on the upper and lower core of variable
domains affecting CDRs conformation) [9].