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Table 2 Performance of QRNAS on RNA Puzzle #1 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-Puzzles #1 models RMSD [Å] INF_all INF_nWC Clashscore
starting QRNAS RNAfitme sander starting QRNAS RNAfitme sander starting QRNAS RNAfitme sander starting QRNAS RNAfitme sander
1_bujnicki_1 5.70 5.63 5.60 5.63 0.825 0.778 0.522 0.787 0.750 0.750 0.866 0.750 0.00 0.00 0.00 0.00
1_bujnicki_2 6.13 5.98 5.93 5.97 0.776 0.774 0.496 0.736 0.289 0.671 0.500 0.289 61.25 1.40 18.91 60.88
1_bujnicki_3 5.28 5.24 5.22 5.23 0.796 0.761 0.483 0.750 0.707 0.408 0.866 0.707 48.21 2.10 10.81 48.32
1_bujnicki_4 4.94 4.87 4.84 4.84 0.703 0.654 0.357 0.652 0.250 0.378 0.354 0.250 69.06 0.70 14.86 70.22
1_bujnicki_5 5.11 4.91 4.95 5.01 0.701 0.664 0.376 0.656 0.378 0.333 0.378 0.378 66.30 2.10 23.65 68.12
1_chen_1 4.34 4.32 4.31 4.38 0.901 0.809 0.457 0.789 0.000 0.577 0.289 0.000 0.00 0.00 0.00 0.00
1_das_1 3.96 4.06 4.08 4.06 0.812 0.812 0.499 0.812 0.671 0.671 0.577 0.671 2.80 0.00 0.00 2.80
1_das_2 4.46 4.46 4.48 4.45 0.778 0.769 0.499 0.778 0.500 0.671 0.750 0.500 3.50 0.00 0.00 4.20
1_das_3 3.42 3.48 3.50 3.48 0.843 0.851 0.522 0.843 0.894 0.894 0.750 0.894 2.80 0.00 0.00 4.20
1_das_4 3.91 4.12 4.12 4.11 0.819 0.818 0.522 0.819 0.816 0.816 0.816 0.816 2.80 0.00 0.00 2.80
1_das_5 4.56 4.80 4.79 4.79 0.743 0.750 0.480 0.743 0.750 0.577 0.577 0.750 2.80 0.00 0.00 2.80
1_dokholyan_1 7.18 7.12 7.10 7.13 0.785 0.720 0.503 0.737 0.671 0.500 0.500 0.671 26.15 0.00 10.13 26.59
1_major_1 4.32 4.47 4.48 4.43 0.885 0.814 0.522 0.770 0.577 0.866 0.866 0.577 54.99 2.78 14.19 51.89
1_santalucia_1 5.75 5.46 5.41 5.43 0.864 0.776 0.510 0.755 0.577 0.577 0.577 0.577 25.07 0.00 8.78 21.71
average 4.93 4.92 4.92 4.92 0.802 0.768 0.482 0.759 0.559 0.621 0.619 0.559 26.12 0.65 7.24 26.04