Figure 4. Two (one easy and one medium) cases in Testing Set II successfully predicted by our protocol (RPDOCK & DECKRP).

The dark color represents native structures and the light color represents predicted ones. Proteins of predicted structures are superimposed onto native structures. (a) Complex of tRNA delta(2)-isopentenylpyrophosphate transferase (PDB code 2ZM5, easy case). Our protocol predicted the first near-native structure (RMSD = 8.2Å) at N_P = 1. (b) Complex of L-seryl-tRNA(Sec) kinase and selenocysteine tRNA (3ADD, medium case). Our protocol predicted the first near-native structure (RMSD = 6.8 Å) at N_P = 3.