Figure 1.

HMM scores of immunoglobulin domains in the PDB. For each sequence in the PDB with a V-set domain, the scores of each of the eight HMMs covering antibody VH and VL domains and TCR V domains were compared. The highest and second highest scores are plotted and the assignments that are consistent with the highest score are shown for those with score above 90, a threshold chosen such that the highest scoring HMM and annotations in the PDB were fully consistent. Domains whose highest score is below 90 were uniformly not antibody structures and were classified as either constant domains if they were in the same chains as antibody VH or VL domains or NonAgR for non-antigen receptors, including shark IgNARs, CD8, the poliovirus receptor and the preB-cell receptor.