AbDesigner3D is an integrated online application for identification of optimal immunizing peptides for antibody production using peptide-based strategy.

AbDesigner3D combines the features of AbDesigner (older  version) with the specialized display of 3D structural information from the Protein Data Bank (PDB) database allowing the most accurate determination of highly exposed regions on a protein. New features include the calculation of an accessible surface area (ASA) for each amino acid residue and the determination of protein-protein interacting residues (PPIRs). These features will help scientists to optimize their choice of immunogen peptides to assure that they are located at surface of the target protein, thus avoiding regions that may inaccessible to antibodies in applications that do not allow protein denaturation.

Interactive specialized viewer was implemented in the graphical results of AbDesigner3D to assist users to visualize output parameters that help in choosing an appropriate immunizing peptide(s) from the whole protein sequence.

When users click on any residue in the resulting heat map, the protein structure viewer will automatically re-center and highlight that selected residue and also its neighbouring residues.

The specialized protein structure display as well as interactive behaviour of AbDesigner3D outputs will greatly assist scientists to easily identify optimal immunizing peptide regions based on direct color rendering of the ASA and the PPIR values on both 3D structural surface and their corresponding heat maps.