4.3. Epitope Prediction and CDR Annotations

Conformational epitopes were predicted with the Epipred tool of the SAbPred web server [49,50]. Based on combined conformational matching of the antibody–antigen structures via geometric fitting and knowledge-based asymmetrical antibody–antigen scoring, epitopes of the antigen are listed rank-wise. The score of an epitope is given by:

where T_ab and T_ag are the amino acid types of the antibody and antigen residues, respectively, that belong to node n. The stereochemistry and geometry of selected epitopes was verified by Ramachandran plot via MOE’s inbuilt utility.

CDRs of antibodies retrieved from the PDB database are annotated according to the numbering scheme of Chothia and Lesk [51,52]. Instead of whole Fab regions, CDRs of the mAbs were considered ligand sites in the docking and simulation.