Table 1.
A summary of the refinement results
| rmsd, Å | |||||||||||
| Target information | Feig | Seok | AWSEM-PCA | AWSEM-PCA, rmsd, Å | |||||||
| ID | Length | Initial rmsd, Å | Selected | Best | Selected | Best | Selected, top 1 | Selected, top 5 | PCA best | Selected, top 1 | Selected, top 5 |
| TR894 | 54 | 2.231 | 0.03 | 0.035 | -0.042 | 0.861 | 0.223 | 0.545 | 1.37 | 2.008 | 1.686 |
| TR884 | 71 | 3.749 | -0.05 | 0.095 | -0.031 | 0.639 | -1.679 | -1.043 | 3.11 (2.635) | 5.428 | 4.792 |
| TR922 | 74 | 2.45 | 0 | -0.29 | -0.535 | -0.04 | -1.237 | -0.836 | 2.49 | 3.687 | 3.286 |
| TR882 | 79 | 2.357 | 0.09 | 0.358 | -0.008 | 0.957 | -0.396 | 0.069 | 1.4 | 2.753 | 2.288 |
| TR896 | 86 | 8.161 | -0.06 | 0.028 | -0.043 | 0.571 | -0.469 | 0.15 | 7.59 | 8.63 | 8.011 |
| TR872 | 88 | 5.589 | -0.04 | 1.697 | 0.05 | 2.989 | 2.43 | 2.43 | 2.6 (2.659) | 3.159 | 3.159 |
| TR594 | 89 | 4.66 | -0.05 | 0.302 | -0.786 | 0 | -1.058 | -1.058 | 4.66 | 5.718 | 5.718 |
| TR862 | 101 (93) | 5.553 | 0.06 | 0.18 | 0.008 | 1.043 | -0.661 | -0.361 | 4.51 | 6.214 | 5.914 |
| TR869 | 104 | 12.362 | -0.12 | 0.011 | -0.024 | 2.102 | 0.053 | 0.053 | 10.26 | 12.309 | 12.309 |
| TR898 | 106 | 13.944 | -0.05 | 0.39 | 0.025 | 2.074 | 0.483 | 0.483 | 11.87 | 13.461 | 13.461 |
| TR885 | 114 | 2.404 | 0.05 | 0.118 | -0.47 | 0.804 | -0.78 | -0.002 | 1.6 | 3.184 | 2.406 |
| TR866 | 115 (104) | 3.268 | 0.18 | 0.497 | 0.101 | 1.878 | 1.617 | 1.745 | 1.39 | 1.651 | 1.523 |
| TR868 | 130 (106) | 1.964 | -0.02 | 0.123 | 0.123 | 0.674 | -0.59 | 0.022 | 1.29 | 2.554 | 1.942 |
| TR891 | 119 (112) | 1.549 | 0.08 | -0.006 | -0.024 | 0.159 | -0.363 | -0.363 | 1.39 | 1.912 | 1.912 |
| TR895 | 120 | 4.408 | 0.01 | 0.471 | 0.292 | 0.628 | -0.464 | -0.464 | 3.78 | 4.872 | 4.872 |
| TR870 | 123 (110) | 7.625 | -0.1 | 0.584 | 0.273 | -0.025 | -1.486 | -1.191 | 7.65 | 9.111 | 8.816 |
| TR921 | 138 | 3.505 | -0.04 | 0.116 | -0.253 | 0.545 | 0.256 | 0.333 | 2.96 | 3.249 | 3.172 |
| TR877 | 142 | 3.008 | 0.02 | 0.156 | 0.07 | 0.178 | 0.001 | 0.001 | 2.83 | 3.007 | 3.007 |
| TR948 | 161 | 6.737 | -0.07 | 1.642 | 1.263 | 1.687 | 0.316 | 1.173 | 5.05 (4.340) | 6.421 | 5.564 |
| TR947 | 175 | 13.035 | 0.03 | 0.329 | 0.329 | 5.415 | 3.466 | 3.466 | 7.62 | 9.569 | 9.569 |
The proteins are ordered by their sequence length. All of the reported rmsd values are calculated over the CA atoms only. “Initial rmsd” refers to the rmsd of the given initial structure downloaded from the CASP12 official website from the experimentally determined reference structure, which was also obtained from the CASP12 website. The “Feig” and “Seok” columns refer to the results published by the top two best-performing teams in the CASP12 competition (refs. 30 and 29, respectively). “AWSEM-PCA” refers to the performance of the PC-guided refinement protocol. “Best” refers to the structure with the lowest rmsd, and “selected” refers to the rmsd of the structures that were blindly selected. Additional “PCA Best” rmsds are provided in parentheses for three of the targets that were singled out for further detailed study: TR884, TR872, and TR948. The values in parentheses refer to the results of the simulations where the strengths of the side-chain dihedral barriers were halved. Since the lowest rmsd structures are not available in the publication from the team “Feig,” we do not report those values.