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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
  1. The first models from the NMR were used in this analysis. The PDBs that contains DNA/hybrid were not analyzed using RNAfitme and represented by ‘—‘in the table