Antibody Modeling
Homology modeling of antibodies used in this study was generated by using BLAST algorithm (National Center for Biotechnology Information) to compare our sequence against the non-redundant protein data bank (PDB) for Fab and Fc structures that have a high level of sequence similarity with the target molecule. High similarity structures were found for the framework region and CDR loop regions separately. Once pdb files are identified that best represent the molecule of interest, MOE software was used to graft the structures together and mutated to the new targeted sequence. The final structure was energy minimized. The final structure phi and psi angles were plotted to ensure that they fall within what is allowed for proteins (reference Ramachandran plot) (Ramachandran, Ramakrishnan, & Sasisekharan, 1963). The final Fab and Fc structure were superimposed on a full antibody structure, the linker sequence was connected, and disulfide bonds were formed. The overall structure is energy minimized to reduce backbone and side chain strain using steepest decent algorithm.