Homology Modeling - Loop Modeling

Loop Modeling

Regions of the target sequence that are not aligned to a template are modeled by loop modeling; they are the most susceptible to major modeling errors and occur with higher frequency when the target and template have low sequence identity. The coordinates of unmatched sections determined by loop modeling programs are generally much less accurate than those obtained from simply copying the coordinates of a known structure, particularly if the loop is longer than 10 residues. The first two sidechain dihedral angles (χ₁ and χ₂) can usually be estimated within 30° for an accurate backbone structure; however, the later dihedral angles found in longer side chains such as lysine and arginine are notoriously difficult to predict. Moreover, small errors in χ₁ (and, to a lesser extent, in χ₂) can cause relatively large errors in the positions of the atoms at the terminus of side chain; such atoms often have a functional importance, particularly when located near the active site.