Nucleic Acid Analysis - Experimental vs MD Analysis
Helical Base Pair Steps
[Image courtesy of Neidle, S. (2007). Principles of nucleic acid structure.] |
[Image courtesy of Neidle, S. (2007). Principles of nucleic acid structure.] 
[Image courtesy of Neidle, S. (2007). Principles of nucleic acid structure.] |
MD BI/BII Population
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Experimental BI/BII Population
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MD Puckering
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Experimental Puckering
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CG 
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GC 
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CG 
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GC 
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CG 
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GC 
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CG 
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GC 
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CG 
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GC 
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CG 
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GC 
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CG 
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GC 
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CG 
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GC 
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CG 
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GC 
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CG 
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GC 
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CG 
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GC 
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CG 
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GC 
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CG 
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GC 
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CG 
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GC 
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| Mean | Stdev | |
| inclin-2-GC | 2.347 | 55.686 |
| Mean | Stdev | |
| tip-2-GC | -48.449 | 88.184 |
| Mean | Stdev | |
| xdisp-2-GC | -0.234 | 2.768 |
| Mean | Stdev | |
| ydisp-2-GC | 0.219 | 2.447 |
| Mean | Stdev | |
| inclin-3-CG | 0.669 | 49.894 |
| Mean | Stdev | |
| tip-3-CG | -50.103 | 89.779 |
| Mean | Stdev | |
| xdisp-3-CG | -0.233 | 2.413 |
| Mean | Stdev | |
| ydisp-3-CG | 0.047 | 2.078 |
| Mean | Stdev | |
| inclin-4-GC | 1.320 | 50.510 |
| Mean | Stdev | |
| tip-4-GC | -33.243 | 75.658 |
| Mean | Stdev | |
| xdisp-4-GC | -0.067 | 2.722 |
| Mean | Stdev | |
| ydisp-4-GC | -0.096 | 2.153 |
| Mean | Stdev | |
| inclin-5-CG | -1.542 | 50.045 |
| Mean | Stdev | |
| tip-5-CG | -44.072 | 87.754 |
| Mean | Stdev | |
| xdisp-5-CG | -0.021 | 2.565 |
| Mean | Stdev | |
| ydisp-5-CG | -0.236 | 2.366 |
| Mean | Stdev | |
| alpha-1-G | 0.000 | 0.000 |
| Mean | Stdev | |
| beta-1-G | 0.000 | 0.000 |
| Mean | Stdev | |
| chi-1-G | 106.702 | 79.462 |
| Mean | Stdev | |
| diff-1-G | -37.318 | 78.302 |
| Mean | Stdev | |
| epsil-1-G | 210.335 | 29.489 |
| Mean | Stdev | |
| gamma-1-G | 92.281 | 80.703 |
| Mean | Stdev | |
| phase-1-G | 160.140 | 25.790 |
| Mean | Stdev | |
| zeta-1-G | 247.653 | 66.166 |
| Mean | Stdev | |
| alpha-10-G | 247.032 | 79.907 |
| Mean | Stdev | |
| beta-10-G | 190.342 | 41.151 |
| Mean | Stdev | |
| chi-10-G | 226.831 | 52.078 |
| Mean | Stdev | |
| diff-10-G | -32.124 | 72.614 |
| Mean | Stdev | |
| epsil-10-G | 214.587 | 32.983 |
| Mean | Stdev | |
| gamma-10-G | 138.815 | 115.438 |
| Mean | Stdev | |
| phase-10-G | 159.007 | 38.994 |
| Mean | Stdev | |
| zeta-10-G | 246.711 | 60.514 |
| Mean | Stdev | |
| alpha-11-C | 234.454 | 85.851 |
| Mean | Stdev | |
| beta-11-C | 180.982 | 34.761 |
| Mean | Stdev | |
| chi-11-C | 227.439 | 20.751 |
| Mean | Stdev | |
| diff-11-C | -27.477 | 71.992 |
| Mean | Stdev | |
| epsil-11-C | 227.122 | 28.691 |
| Mean | Stdev | |
| gamma-11-C | 119.505 | 106.025 |
| Mean | Stdev | |
| phase-11-C | 153.014 | 31.726 |
| Mean | Stdev | |
| zeta-11-C | 254.599 | 67.398 |
| Mean | Stdev | |
| alpha-12-C | 232.247 | 87.100 |
| Mean | Stdev | |
| beta-12-C | 179.981 | 25.472 |
| Mean | Stdev | |
| chi-12-C | 225.094 | 20.800 |
| Mean | Stdev | |
| diff-12-C | 0.000 | 0.000 |
| Mean | Stdev | |
| epsil-12-C | 0.000 | 0.000 |
| Mean | Stdev | |
| gamma-12-C | 101.137 | 93.014 |
| Mean | Stdev | |
| phase-12-C | 156.967 | 31.621 |
| Mean | Stdev | |
| zeta-12-C | 0.000 | 0.000 |
| Mean | Stdev | |
| alpha-2-G | 259.751 | 68.446 |
| Mean | Stdev | |
| beta-2-G | 185.829 | 39.012 |
| Mean | Stdev | |
| chi-2-G | 213.965 | 69.208 |
| Mean | Stdev | |
| diff-2-G | -45.545 | 62.280 |
| Mean | Stdev | |
| epsil-2-G | 215.173 | 33.463 |
| Mean | Stdev | |
| gamma-2-G | 114.371 | 102.349 |
| Mean | Stdev | |
| phase-2-G | 161.268 | 47.890 |
| Mean | Stdev | |
| zeta-2-G | 260.718 | 51.138 |
| Mean | Stdev | |
| alpha-3-C | 251.694 | 67.857 |
| Mean | Stdev | |
| beta-3-C | 186.457 | 42.108 |
| Mean | Stdev | |
| chi-3-C | 230.910 | 22.544 |
| Mean | Stdev | |
| diff-3-C | -41.972 | 63.844 |
| Mean | Stdev | |
| epsil-3-C | 218.310 | 28.473 |
| Mean | Stdev | |
| gamma-3-C | 112.789 | 102.338 |
| Mean | Stdev | |
| phase-3-C | 148.129 | 40.133 |
| Mean | Stdev | |
| zeta-3-C | 260.282 | 53.766 |
| Mean | Stdev | |
| alpha-4-G | 247.755 | 76.860 |
| Mean | Stdev | |
| beta-4-G | 177.447 | 32.942 |
| Mean | Stdev | |
| chi-4-G | 222.825 | 48.647 |
| Mean | Stdev | |
| diff-4-G | -58.804 | 49.901 |
| Mean | Stdev | |
| epsil-4-G | 206.094 | 28.787 |
| Mean | Stdev | |
| gamma-4-G | 106.251 | 92.999 |
| Mean | Stdev | |
| phase-4-G | 160.174 | 41.172 |
| Mean | Stdev | |
| zeta-4-G | 264.897 | 36.160 |
| Mean | Stdev | |
| alpha-5-C | 261.916 | 52.471 |
| Mean | Stdev | |
| beta-5-C | 176.193 | 28.987 |
| Mean | Stdev | |
| chi-5-C | 227.810 | 20.604 |
| Mean | Stdev | |
| diff-5-C | -48.428 | 54.689 |
| Mean | Stdev | |
| epsil-5-C | 219.559 | 30.076 |
| Mean | Stdev | |
| gamma-5-C | 78.333 | 70.339 |
| Mean | Stdev | |
| phase-5-C | 153.212 | 38.351 |
| Mean | Stdev | |
| zeta-5-C | 267.987 | 48.057 |
| Mean | Stdev | |
| alpha-6-C | 258.839 | 68.717 |
| Mean | Stdev | |
| beta-6-C | 177.458 | 25.333 |
| Mean | Stdev | |
| chi-6-C | 228.686 | 19.531 |
| Mean | Stdev | |
| diff-6-C | 0.000 | 0.000 |
| Mean | Stdev | |
| epsil-6-C | 0.000 | 0.000 |
| Mean | Stdev | |
| gamma-6-C | 86.660 | 77.836 |
| Mean | Stdev | |
| phase-6-C | 153.154 | 33.443 |
| Mean | Stdev | |
| zeta-6-C | 0.000 | 0.000 |
| Mean | Stdev | |
| alpha-7-G | 0.000 | 0.000 |
| Mean | Stdev | |
| beta-7-G | 0.000 | 0.000 |
| Mean | Stdev | |
| chi-7-G | 175.382 | 85.335 |
| Mean | Stdev | |
| diff-7-G | -11.922 | 87.527 |
| Mean | Stdev | |
| epsil-7-G | 214.877 | 30.255 |
| Mean | Stdev | |
| gamma-7-G | 117.025 | 98.678 |
| Mean | Stdev | |
| phase-7-G | 157.257 | 39.502 |
| Mean | Stdev | |
| zeta-7-G | 226.799 | 76.548 |
| Mean | Stdev | |
| alpha-8-G | 233.788 | 88.939 |
| Mean | Stdev | |
| beta-8-G | 182.344 | 34.014 |
| Mean | Stdev | |
| chi-8-G | 227.992 | 52.625 |
| Mean | Stdev | |
| diff-8-G | -39.778 | 69.644 |
| Mean | Stdev | |
| epsil-8-G | 213.808 | 34.076 |
| Mean | Stdev | |
| gamma-8-G | 102.784 | 95.043 |
| Mean | Stdev | |
| phase-8-G | 160.169 | 38.226 |
| Mean | Stdev | |
| zeta-8-G | 253.586 | 59.767 |
| Mean | Stdev | |
| alpha-9-C | 255.609 | 64.576 |
| Mean | Stdev | |
| beta-9-C | 178.026 | 27.789 |
| Mean | Stdev | |
| chi-9-C | 230.006 | 22.266 |
| Mean | Stdev | |
| diff-9-C | -28.639 | 81.832 |
| Mean | Stdev | |
| epsil-9-C | 217.960 | 30.564 |
| Mean | Stdev | |
| gamma-9-C | 96.485 | 88.007 |
| Mean | Stdev | |
| phase-9-C | 147.384 | 42.234 |
| Mean | Stdev | |
| zeta-9-C | 246.599 | 74.375 |
| Mean | Stdev | |
| majd-2-GCGC | 0.064 | 1.288 |
| Mean | Stdev | |
| majw-2-GCGC | 7.471 | 5.679 |
| Mean | Stdev | |
| mind-2-GCGC | 0.037 | 1.495 |
| Mean | Stdev | |
| minw-2-GCGC | 10.281 | 4.035 |
| Mean | Stdev | |
| majd-3-CGCG | 0.212 | 2.134 |
| Mean | Stdev | |
| majw-3-CGCG | 8.367 | 4.595 |
| Mean | Stdev | |
| mind-3-CGCG | 1.870 | 2.143 |
| Mean | Stdev | |
| minw-3-CGCG | 7.337 | 4.109 |
| Mean | Stdev | |
| majd-4-GCGC | 0.782 | 1.954 |
| Mean | Stdev | |
| majw-4-GCGC | 7.311 | 5.844 |
| Mean | Stdev | |
| mind-4-GCGC | 2.288 | 2.215 |
| Mean | Stdev | |
| minw-4-GCGC | 6.256 | 3.874 |
| Mean | Stdev | |
| buckle-2-GC | -25.265 | 65.146 |
| Mean | Stdev | |
| opening-2-GC | -2.046 | 64.005 |
| Mean | Stdev | |
| propel-2-GC | -3.959 | 64.199 |
| Mean | Stdev | |
| shear-2-GC | 1.145 | 9.186 |
| Mean | Stdev | |
| stagger-2-GC | 0.554 | 9.199 |
| Mean | Stdev | |
| stretch-2-GC | -6.033 | 11.087 |
| Mean | Stdev | |
| buckle-3-CG | -14.040 | 59.900 |
| Mean | Stdev | |
| opening-3-CG | 0.167 | 60.111 |
| Mean | Stdev | |
| propel-3-CG | 4.099 | 63.143 |
| Mean | Stdev | |
| shear-3-CG | 0.154 | 7.335 |
| Mean | Stdev | |
| stagger-3-CG | -0.129 | 7.956 |
| Mean | Stdev | |
| stretch-3-CG | -4.082 | 9.073 |
| Mean | Stdev | |
| buckle-4-GC | -9.413 | 47.421 |
| Mean | Stdev | |
| opening-4-GC | 3.421 | 56.808 |
| Mean | Stdev | |
| propel-4-GC | -5.313 | 57.120 |
| Mean | Stdev | |
| shear-4-GC | 0.541 | 6.575 |
| Mean | Stdev | |
| stagger-4-GC | -0.260 | 7.022 |
| Mean | Stdev | |
| stretch-4-GC | -7.615 | 9.931 |
| Mean | Stdev | |
| buckle-5-CG | -18.448 | 63.477 |
| Mean | Stdev | |
| opening-5-CG | -0.348 | 62.891 |
| Mean | Stdev | |
| propel-5-CG | 1.143 | 63.062 |
| Mean | Stdev | |
| shear-5-CG | -0.039 | 7.858 |
| Mean | Stdev | |
| stagger-5-CG | -1.357 | 6.585 |
| Mean | Stdev | |
| stretch-5-CG | -5.394 | 9.732 |
| Mean | Stdev | |
| rise-2-GCGC | 2.804 | 3.595 |
| Mean | Stdev | |
| roll-2-GCGC | 12.908 | 63.826 |
| Mean | Stdev | |
| shift-2-GCGC | -0.228 | 4.022 |
| Mean | Stdev | |
| slide-2-GCGC | -0.372 | 3.717 |
| Mean | Stdev | |
| tilt-2-GCGC | -1.613 | 59.802 |
| Mean | Stdev | |
| twist-2-GCGC | 10.520 | 58.730 |
| Mean | Stdev | |
| rise-3-CGCG | 3.636 | 4.014 |
| Mean | Stdev | |
| roll-3-CGCG | -0.364 | 56.373 |
| Mean | Stdev | |
| shift-3-CGCG | 0.539 | 3.885 |
| Mean | Stdev | |
| slide-3-CGCG | -0.475 | 3.831 |
| Mean | Stdev | |
| tilt-3-CGCG | -5.098 | 55.570 |
| Mean | Stdev | |
| twist-3-CGCG | 22.406 | 55.835 |
| Mean | Stdev | |
| rise-4-GCGC | 3.433 | 3.263 |
| Mean | Stdev | |
| roll-4-GCGC | -1.155 | 60.935 |
| Mean | Stdev | |
| shift-4-GCGC | -0.462 | 3.478 |
| Mean | Stdev | |
| slide-4-GCGC | -1.001 | 3.070 |
| Mean | Stdev | |
| tilt-4-GCGC | 1.416 | 51.146 |
| Mean | Stdev | |
| twist-4-GCGC | 11.179 | 51.004 |
