Protein modelling Side chain modelling Antibody optimisation is to optimize the antibody-interacting surface of the antigen (epitope). Antigen optimisation is to optimize the antigen-interacting surface of the antibody (paratope). Antigen resurfacing is to resurface the antigen by varying the sequence of non-epitope regions. Rotamer likelihood prediction This includes rotamer likelihood prediction: the prediction of rotamer likelihoods for all 20 amino acid types at each position in a protein structure, where output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods. Methods might use a residue rotamer library. Protein modelling (side chains) Antibody optimisation beta12orEarlier Antigen resurfacing Antigen optimisation Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc.