Benchmark results of SCOP superfamily predictions by DBD-Threader.

The results are based on 110 DNA-binding domains from 84 predicted DNA-binding proteins that have official (True) SCOP assignments. The numbers of SCOP domain predictions are shown for four groups: Consistent (C) Un-annotated (U), Inconsistent (I), and Missed (M). Consistent predictions have the same SCOP superfamily assignments as the true assignments. If a DNA-binding domain is predicted based on a template without an official SCOP assignment, then the SCOP prediction is skipped and the domain belongs to the Un-annotated group. A target protein may contain multiple DNA-binding domains, and any domain not detected by DBD-Threader is a Missed domain. The remaining SCOP predictions, in which SCOP predictions are different from the official assignments, are considered Inconsistent. < > denotes mean. TM-scores and MCCs of DNA-binding residue predictions were calculated for all predicted domains per SCOP superfamily.