Improved prediction of antibody VL–VH orientation

Antibodies are important immune molecules with high commercial value and therapeutic interest because of their ability to bind diverse antigens. Computational prediction of antibody structure can quickly reveal valuable information about the nature of these antigen-binding interactions, but only if the models are of sufficient quality. To achieve high model quality during complementarity-determining region (CDR) structural prediction, one must account for the V-L-V-H orientation. We developed a novel four-metric V-L-V-H orientation coordinate frame. Additionally, we extended the CDR grafting protocol in RosettaAntibody with a new method that diversifies V-L-V-H orientation by using 10 V-L-V-H orientation templates rather than a single one. We tested the multiple-template grafting protocol on two datasets of known antibody crystal structures. During the template-grafting phase, the new protocol improved the fraction of accurate V-L-V-H orientation predictions from only 26% (12/46) to 72% (33/46) of targets. After the full RosettaAntibody protocol, including CDR H3 remodeling and V-L-V-H re-orientation, the new protocol produced more candidate structures with accurate V-L-V-H orientation than the standard protocol in 43/46 targets (93%). The improved ability to predict V-L-V-H orientation will bolster predictions of other parts of the paratope, including the conformation of CDR H3, a grand challenge of antibody homology modeling.