Figure 2. CASP Targets superimposed using the Expanded FindCore approach for defining the set of “well defined” core atoms.

Superimpositions are shown for each target and labeled by their CASP10 Target ID. Coloration of the backbone traces indicates atom classification according to FindCore and subsequent expansion of the core atom set by iterative superimpostion. Saturated blue regions indicate the original FindCore atom set, regions added to the core in the iterated expansion process are sky blue and red regions are atoms that are not included in the well-defined atom set. Residues removed during the final editing process to ensure all core atoms belong to only those residues with a complete backbone set in the core are colored magenta. Note that the Expanded FindCore core (saturated and light blue) includes the well-packed, secondary structure rich geometric cores of the protein structures while most loops are excluded from the Expanded FindCore core. Residues excluded in the editing process typically are at the edges of well-defined structural elements. The circled (core) residue in T0655 is LYS 92, which is discussed in the main body of the text.