Modeling paratope and epitope interaction

Question

[Mac]

What bioinformatics programs can I use to model paratope and epitope interactions using protein sequences and known structure models of the antibody and antigen?

Answer 1

[mikhail.shugay]

Have you looked at the pipeline suggested at IEDB: http://tools.iedb.org/main/bcell/modeling-docking/? The Web servers for modeling 3D structure of antibody-protein complexes seems to be what you need, or at least can serve as a starting point.