Antibody Design

IEDB method PIGS in B-cell epitope prediction http://tools.iedb.org/pigs/

The protein 3D structure prediction methods predicted helices at the places which were shown to be disordered regions by IUpred, ANCHOR and Disopred.

Use a module present in Biovia (Accelrys) Discovery studio software to design antibody (http://accelrys.com/products/collaborative-science/biovia-discovery-studio/antibody-modeling.html). You can also do a MHC Class I and II binding predictions with your antigen to check its affinity towards the HLA molecules if required.

PEP-FOLD3, Phyre, I-TASSER, Quark, CABS-fold, RaptorX, Rosetta