Fig. 4

Quality of the final prediction for protein 1ctfA, 1iloA, and 1iieA. At each iteration step, a total of 1000 decoys were generated by Rosetta with corresponding weights of energy terms. We run clustering procedure for the 1000 decoys and finally selected the centroid of the largest cluster as the best decoy. The RMSD of the best decoys reduces as iteration proceeds, suggesting that the quality of prediction results increases