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.