2.2 Identification of grafting loops
The initial coordinates of three selected graft acceptors were taken
from PDB accession codes 3BX7 (Scaf1), 1TTF (Scaf2), and 3dwt (Scaf3).
Three-dimensional models of 36 designed structures after immobilizing
CDR peptides into variable loops were generated by Modeller software
(Mod10.2). The best models with the lowest DOPE score from each 36
designed scaffolds were selected for further analysis. The scFv model of
the panitumumab antibody, also generated as the second reference
molecule beside the whole structure of the antibody, extracted from 5SX4
PDB entry, to be used for binding energy comparison. Then, the quality
of models was assessed by online web servers, including PDBSum
(http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/Generate.html )
and ProSA-web [11]. The model structures were evaluated by
Ramachandran Plot Assessment using the PDBSum server.