Fig. 2

Circularly-permuted protein structure models constructed by CirPred and conventional modeling methods. The CPM55 of DHFR has been reported viable (CP site on the native DHFR: Pro55) [15]. Several comparative structure modeling methods were applied to construct the model of this CPM. Conventional methods failed to model part of the CPM (panel c and d) or produced incorrect domain orientations (panel e). The proposed CirPred method correctly constructed the full-length model (panel b). Structures shown in this figure include a the native DHFR (PDB 1rx4A), and the model of CPM55 constructed by b CirPred c SWISS-MODEL [18], d RaptorX [19], and e Robetta [20]. Structures are drawn in the same orientation and scale. The blue and red colors indicate the N- and C-terminal proportions, respectively, of the protein. The α-carbon atoms of termini residues are shown as spheres