Figure 12. Domain division.

(a) A target protein covered (aligned with) five templates is divided into two domains because the two regions do not share any common templates. (b) Template combination. The template T1 with the highest template weight is selected first. T2 is selected because the TM-score between T1 and T2 is >0.7. T3 is chosen because it covers at least 10 continuous uncovered target residues. (c) Template superposition. T1 is the center template. T2, T3, and T4 are superposed with T1 because they share common residues with T1. T5 does not share common residues with T1, so it is superposed with T4. (d) Sampling points for gaps. The radius of the outside circle is 4.5 Å, and the radius of the inner circle is 3.5 Å. The sampling algorithm randomly samples point between the two circles. In the region circled by red, the gap is at the N-terminal. The distance d₁ between an accepted sampled point and the first covered residue is between 3.5 Å and 4.5 Å. In the region circled by blue, the three-residue gap is in the middle, and the distance between the two ends of the gap (d_AB) is 8.2 Å. The distance d₂ between an accepted sampled point and the last covered residue before the gap is between 3.5 Å and 4.5 Å. The distance d₃ between an accepted sampled point and the first covered residue after the gap is between 4.1 Å and 11.4 Å.