Computer-assisted modeling of antibody variable domains.

Antibody modeling is an interesting option to gain structure-function insights and to allow rational engineering of these molecules in the absence of experimental data. Among a diversity of algorithms, software packages, and specialized Web servers, the protocol described here presents the following main features: (1) nonautomatic modeling process guided by direct application of antibody modeling principles; (2) local generation of molecular models using free software which can be used in most common operational systems; and (3) the resulting model quality is comparable to models generated by Web servers which represent the current standard of antibody modeling. Briefly, hybrid models of heavy- and light-chain variable domains are separately built by grafting segments from homologous templates (framework regions and complementarity-determining regions). Next, hybrid models are mutated to comply with the target's sequence and associated by fitting into a template structure that closely matches the predicted packing angle for the target variable domains. After a few cycles of energy minimization the model can be submitted to CDR-H3 optimization or its quality can be directly assessed.