FIGURE 1.

Specifics of the antibody structure in the context of modeling. (A) Variable region in the context of the entire antibody structure. The antibody binding site is located in the variable region composed of the variable heavy (Vh) and variable light (Vl) polypeptide chains associated with the constant portions (HC/LC). (B) Heavy/light chain orientation. The orientation of the Vh and Vl is not constant, and differing angles can affect the shape of the binding site. (C) Canonical structures of CDRs. Most of the binding residues (the paratope) are found in the complementarity-determining regions (CDRs). There are three CDRs on each of the heavy and light chains. All the CDRs except the CDR-H3 cluster into a set of “canonical shapes” depending on residues in key positions. (D) Heterogeneity of CDR-H3. CDR-H3 is not only the most variable of the regions but also usually the most important for antigen binding.