Figure 1.

Schematic representation of the MASTER search algorithm. (A) The search query, consisting of two disjoint segments, is shown on the left, and a database structure on the right. (B) A potential location of a match for the first segment (black dot designates the central residue). Given this alignment, possible locations for aligning the second segment are limited, as shown in (C), by the distance from the central residue of the first segment [see Eq. (10)]. Further, the individual RMSD of aligning the second fragment is also constrained given the error already incurred in aligning the first [see Eq. (6)]; so, an even smaller set of possibilities is available for the second segment. One of these is shown in (D).