Comparison of an antibody model with an X-ray structure: the variable fragment of BR96

A model of the BR96 antibody variable regions is compared to two X-ray structures of a BR96-carbohydrate complex, independently determined after the model was built and analyzed. The comparison illustrates the opportunities and limitations of antibody modeling. Encouraging results were obtained for the prediction of single CDR loop conformations and for the outline of the BR96 antigen binding site. The comparison of CDR loop conformations in the two X-ray structures provides a realistic reference frame for the CDR loop predictions. CDR loop prediction accuracy is lower when not only conformational, but also positional criteria are taken into account.