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Table 3 Performance of QRNAS on RNA Puzzle #6 models in terms of model accuracy, as compared to RNAfitme and sander from the AMBER package

From: QRNAS: software tool for refinement of nucleic acid structures

RNA Puzzle #6 model RMSD [Å] INF_all INF_nWC Clashscore
Starting QRNAS RNAfitme sander Starting QRNAS RNAfitme sander Starting QRNAS RNAfitme sander Starting QRNAS RNAfitme sander
6_blanchet_1 21.39 22.29 22.34 22.30 0.761 0.754 0.742 0.761 0.462 0.462 0.405 0.462 0.74 0.00 1.28 0.55
6_blanchet_2 20.94 21.76 21.77 21.75 0.744 0.726 0.713 0.744 0.434 0.418 0.316 0.434 0.37 0.00 0.18 0.37
6_blanchet_3 20.57 21.32 21.32 21.31 0.745 0.754 0.696 0.745 0.405 0.452 0.337 0.405 0.55 0.00 1.10 0.74
6_blanchet_4 21.46 22.21 22.24 22.22 0.763 0.752 0.724 0.763 0.418 0.434 0.372 0.418 0.55 0.18 1.47 0.55
6_blanchet_5 23.54 24.19 24.18 24.18 0.724 0.728 0.706 0.724 0.337 0.372 0.337 0.337 0.74 0.55 0.92 0.74
6_bujnicki_1 36.50 37.00 36.98 36.96 0.720 0.721 0.729 0.720 0.300 0.224 0.194 0.300 0.55 0.00 0.55 0.55
6_bujnicki_2 30.47 30.93 30.90 30.89 0.701 0.692 0.699 0.701 0.254 0.337 0.323 0.254 1.29 0.18 1.10 1.29
6_bujnicki_3 31.79 32.14 32.11 32.09 0.637 0.638 0.651 0.637 0.258 0.258 0.270 0.258 1.11 0.37 0.92 1.11
6_bujnicki_4 31.64 32.07 32.05 32.04 0.657 0.652 0.646 0.657 0.135 0.135 0.115 0.135 1.84 0.18 1.28 1.84
6_chen_1 23.89 24.30 24.29 24.29 0.673 0.676 0.690 0.673 0.200 0.183 0.237 0.200 0.37 0.00 0.37 0.37
6_chen_2 21.73 22.13 22.17 22.15 0.656 0.662 0.663 0.656 0.200 0.283 0.254 0.200 0.18 0.18 0.55 0.18
6_chen_3 23.25 23.62 23.62 23.63 0.681 0.674 0.685 0.681 0.200 0.200 0.183 0.200 0.55 0.18 0.55 0.55
6_chen_4 21.71 22.15 22.11 22.12 0.669 0.688 0.699 0.669 0.224 0.298 0.316 0.224 1.84 0.18 1.65 1.84
6_chen_5 23.17 23.56 23.52 23.53 0.672 0.676 0.676 0.669 0.224 0.149 0.183 0.224 17.51 10.69 12.29 17.14
6_das_2 13.05 13.48 13.46 13.45 0.765 0.766 0.744 0.765 0.422 0.462 0.488 0.422 20.65 0.00 10.64 20.28
6_das_3 15.26 15.57 15.54 15.54 0.756 0.755 0.750 0.756 0.488 0.513 0.422 0.488 18.79 0.18 7.89 19.90
6_das_4 11.29 11.62 11.61 11.59 0.766 0.770 0.749 0.766 0.488 0.513 0.537 0.488 28.02 4.98 15.04 28.39
6_das_5 15.29 15.58 15.57 15.56 0.782 0.796 0.789 0.782 0.488 0.537 0.474 0.488 14.74 0.00 6.97 14.56
6_dokholyan_1 25.32 26.07 26.05 26.05 0.705 0.705 0.704 0.705 0.323 0.299 0.488 0.323 11.06 0.00 6.97 11.24
6_dokholyan_2 25.92 26.58 26.57 26.55 0.703 0.718 0.706 0.703 0.298 0.270 0.239 0.298 9.40 0.00 5.50 9.22
6_dokholyan_3 25.58 26.21 26.20 26.18 0.691 0.696 0.689 0.691 0.298 0.298 0.283 0.298 9.22 0.00 5.69 9.40
6_dokholyan_4 24.27 24.95 24.95 24.93 0.708 0.691 0.725 0.708 0.338 0.338 0.299 0.338 9.59 0.00 6.42 9.95
6_dokholyan_5 22.07 22.62 22.60 22.58 0.704 0.708 0.709 0.704 0.338 0.316 0.447 0.338 10.51 0.00 7.71 10.69
average 23.05 23.58 23.57 23.56 0.712 0.713 0.708 0.712 0.327 0.337 0.365 0.327 6.96 0.78 4.22 7.02