Table 1 Performance of QRNAS on a selection of NMR structures in terms of optimization of MolProbity scores. QRNAS resolved nearly all steric clashes. It also improved backbone conformations and bond lengths in all studied cases at the price of small perturbations in the angle space. Quality scores of models optimized with RNAfitme and sander from the AMBER package are shown for comparison. In three cases, RNAfitme was unable to process the input file
From: QRNAS: software tool for refinement of nucleic acid structures
PDB ID | Clashscore | Bad backbone conf. [%] | Bad bonds [%] | Bad angles [%] | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Starting | QRNAS | RNAfitme | sander | starting | QRNAS | RNAfitme | sander | starting | QRNAS | RNAfitme | sander | starting | QRNAS | RNAfitme | sander | |
1A60 | 87.14 | 0.00 | 30.68 | 79.94 | 26.19 | 16.66 | 25.58 | 26.19 | 0.34 | 0.34 | 0.17 | 0.34 | 1.63 | 0.65 | 2.02 | 1.74 |
1B36 | 23.75 | 0.00 | 12.26 | 25.90 | 52.63 | 25.00 | 52.63 | 55.56 | 0.00 | 0.40 | 0.00 | 0.40 | 0.00 | 2.54 | 0.36 | 0.00 |
2L7D | 14.47 | 0.00 | – | 14.99 | 0.00 | 0.00 | – | 0.00 | 0.00 | 0.00 | – | 1.52 | 0.00 | 0.00 | – | 0.00 |
1P5M | 27.87 | 0.00 | 20.45 | 28.26 | 18.18 | 9.44 | 18.18 | 16.98 | 0.00 | 0.27 | 0.00 | 0.27 | 3.66 | 0.77 | 3.81 | 3.18 |
1YG3 | 85.46 | 0.00 | 30.94 | 91.22 | 64.29 | 53.85 | 64.29 | 69.23 | 2.58 | 0.55 | 2.56 | 3.29 | 4.44 | 4.40 | 4.58 | 4.75 |
2JYF | 66.93 | 0.00 | – | 64.75 | 9.30 | 12.20 | – | 9.76 | 0.00 | 0.35 | – | 0.35 | 0.00 | 1.00 | – | 0.35 |
2LC8 | 0.00 | 0.00 | 0.55 | 0.00 | 12.50 | 5.56 | 12.50 | 12.96 | 0.00 | 0.26 | 0.00 | 0.26 | 22.79 | 0.08 | 22.78 | 22.71 |
2 LU0 | 64.09 | 0.00 | 23.45 | 64.43 | 44.90 | 25.53 | 44.90 | 46.81 | 0.00 | 0.30 | 0.00 | 0.30 | 0.00 | 1.55 | 0.28 | 0.00 |
2M4Q | 23.09 | 0.00 | 16.13 | 21.38 | 7.41 | 0.00 | 7.41 | 8.00 | 0.00 | 0.57 | 0.00 | 0.57 | 0.00 | 0.73 | 4.07 | 4.21 |
2 M58 | 13.16 | 0.00 | 9.47 | 13.86 | 50.85 | 31.57 | 50.85 | 50.88 | 0.00 | 0.25 | 0.00 | 0.25 | 0.16 | 2.16 | 0.46 | 0.16 |
1BYX | 0.00 | 0.00 | – | 0.00 | 41.66 | 0.00 | – | 33.33 | 0.00 | 1.68 | – | 1.20 | 2.13 | 0.74 | – | 2.40 |
1DXN | 19.58 | 0.00 | 10.00 | 18.92 | 0.00 | 0.00 | 0.00 | 0.00 | 0.32 | 0.00 | 0.00 | 1.50 | 4.83 | 0.42 | 6.45 | 5.69 |