Structural bioinformatics pipeline to build an antigen-autoantibody complex. (A) Antibody modeling of the Fv fragments of the II-1 and I-9 autoantibodies. Heavy chain (VH; shown in red) and light chain (VL; shown in green) built and orientated with each other. Complementary determining region 3 of VH (CDR-H3; shown in multiple colors) was grafted at different conformations to the Fv model. (B) Docking results of ADAMTS13 antigen-autoantibody complex following the protein-protein docking step. (C) Molecular dynamics simulations for each WT- and GoF-complex models were run. (D) A likely complex between ADAMTS13 antigen and autoantibody was selected by BFE calculations. Cys, cysteine.