FIGURE 1.
(A) Crystal structure representation of the P4P6 subdomain of the T. thermophila group I intron (PDB ID 1GID). In this study we used the secondary structure derived from the crystal structure as a reference as determined by NDB (Berman et al. 2002) excluding all tertiary contacts. (B) Secondary structure derived from the P4P6 crystal structure used as a reference. The PPV and sensitivity of the structure are 1 and it has a Manhattan distance of 0 since it is the reference structure. (C) sFold decoy with lowest Manhattan distance and greatest sum of PPV and sensitivity found in the 106 decoys that we generated for this analysis. (D) sFold decoy with the largest Manhattan distance and low PPV and sensitivity.