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.