Monoclonal antibodies are produced in vivo by injection of a target protein (the "antigen") into mice. However, the outcome of immunization and subsequent antibody production depends largely on complex biological conditions. An alternate approach, called "phage display," offers clear advantages, such as cost and speed, and suggests the further capability of genetically engineering specific peptides with high affinity to any target protein. To date, attention has focused on selecting short, unique, surface-accessible peptides on the target protein for injection into mice. However, it is conceivable that antibodies could be produced that recognize closely spaced but discontinuous peptides or surface-exposed residues contained within protein secondary structural units, such as alpha-helices. We are not aware of any publicly available software that can automate the selection of suitable discontinuous peptides or residues on the target protein for improved antibody production, or that can assist in the engineering of protein-based ligands.
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