Nucleic Acids: Difference between revisions
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===References=== | ===References=== | ||
* | * 3DNA | ||
** Lu, X.-J.; Olson, W. K. 3DNA: A Versatile, Integrated Software System for the Analysis, Rebuilding and Visualization of Three-Dimensional Nucleic-Acid Structures. ''Nature Protocols'' '''2008''', ''3 (7)'', 1213–1227. https://doi.org/10.1038/nprot.2008.104. | |||
** Lu, X.-J.; Olson, W. K. 3DNA: A Software Package for the Analysis, Rebuilding and Visualization of Three-Dimensional Nucleic Acid Structures. ''Nucl. Acids Res.'' '''2003''', ''31 (17)'', 5108–5121. https://doi.org/10.1093/nar/gkg680. | |||
* Gradients | |||
** Blanc, E.; Paciorek, W. On Planarity and Similarity Restraints. ''J. Appl. Crystallogr.'' '''2001''', ''34'', 480–483. https://doi.org/10.1107/S0021889801008470. | |||
Revision as of 17:59, 12 February 2019
Navigation: Documentation / Collective Variables / Nucleic Acids
Distance
Angle
Coordination
Shape
Special
Energy
Algebra
Collective Variables For Nucleic Acids
| Type | Description |
| NASBPP | simple base pair parameters |
| NASBO | simple base pair opening |
| NAPBO | primitive base pair opening |
| NABEND | nucleic acid bending |
Simple Base Pair Parameters
All simple base pair parameters (i.e., shear, stretch, stagger, buckle, propeller, opening) fully compatible with 3DNA are available via the NASBPP collective variable. The collective variable NASBO implements only the opening parameter and thus it should be a little bit computationally faster.
Reference coordinates for nucleobase rings are provided in the following table:
| Nucleobase | Ring Atoms | y-axis | File |
| A | @N9,C8,N7,C5,C6,N1,C2,N3,C4 | @C8 | A_ring_only.xyz |
| G | @N9,C8,N7,C5,C6,N1,C2,N3,C4 | @C8 | G_ring_only.xyz |
| C | @N1,C6,C5,C4,N3,C2 | @C6 | C_ring_only.xyz |
| T | @N1,C6,C5,C4,N3,C2 | @C6 | T_ring_only.xyz |
References
- 3DNA
- Lu, X.-J.; Olson, W. K. 3DNA: A Versatile, Integrated Software System for the Analysis, Rebuilding and Visualization of Three-Dimensional Nucleic-Acid Structures. Nature Protocols 2008, 3 (7), 1213–1227. https://doi.org/10.1038/nprot.2008.104.
- Lu, X.-J.; Olson, W. K. 3DNA: A Software Package for the Analysis, Rebuilding and Visualization of Three-Dimensional Nucleic Acid Structures. Nucl. Acids Res. 2003, 31 (17), 5108–5121. https://doi.org/10.1093/nar/gkg680.
- Gradients
- Blanc, E.; Paciorek, W. On Planarity and Similarity Restraints. J. Appl. Crystallogr. 2001, 34, 480–483. https://doi.org/10.1107/S0021889801008470.