PhD in Bioinformatics, Scientist in Antibody Development
Our research group went on a retreat (‘OPIGTREAT‘) comprised of presentations made by members of the group, on technical skills and latest research. In light of the booming of data in virtually all areas, my colleague and I decided to run a quick hands-on workshop on distributed computing, integrating the use of protein data.
In the published Protein Databank (PDB) entries, we recognise that, except for CDRH3, all other CDR loops adopt only a few structural conformations. It could be due to the preference of the original antibody’s germline – consider the fact that the PDB is heavily skewed towards humanised/engineered antibodies which attract pharmaceutical interest, where the CDR loops formed after the antigen exposure and maturation in other species are grafted onto the human antibody framework. Some frameworks may be predisposed to particular structural conformations in their acceptable CDR loops. The limited structural conformations are named “canonical forms” of the CDRs.
Epitope is the antibody-binding region on the cognate antigen. Predicting what kind of antigen surfaces bind to a known antibody is useful in reverse engineering the antibody to target specific antigen.