Nucleic Acids: Difference between revisions
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| style="width: 5em;" | '''Type''' | | style="width: 5em;" | '''Type''' | ||
| '''Description''' | | '''Description''' | ||
|- | |||
| [[CV:NALBPP|NALBPP]] | |||
| local base-pair parameters | |||
|- | |- | ||
| [[CV:NASBPP|NASBPP]] | | [[CV:NASBPP|NASBPP]] | ||
| simple base pair parameters | | simple base-pair parameters | ||
|- | |||
| [[CV:NASBPPOLD|NASBPPOLD]] | |||
| simple base-pair parameters (OLD implementation)* | |||
|- | |||
| [[CV:NALSTP|NALSTP]] | |||
| local base-pair step parameters | |||
|- | |||
| [[CV:NASSTP|NASSTP]] | |||
| simple base-pair step parameters | |||
|- | |||
| [[CV:NASSTPOLD|NASSTPOLD]] | |||
| simple base-pair step parameters (OLD implementation)* | |||
|- | |- | ||
| [[CV:NASBO|NASBO]] | | [[CV:NASBO|NASBO]] | ||
| simple base pair opening | | simple base-pair opening | ||
|- | |- | ||
| [[CV:NAPBO|NAPBO]] | | [[CV:NAPBO|NAPBO]] | ||
| primitive base pair opening | | primitive base-pair opening | ||
|- | |- | ||
| [[CV:NABEND|NABEND]] | | [[CV:NABEND|NABEND]] | ||
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|} | |} | ||
== | == Base-Pair Parameters == | ||
PMFLib offers two variants of the base-pair parameters: local and simple. They differ in the definition of the y-axis and the procedure to calculate six base-pair parameters (''i.e.'', Shear, Stretch, Stagger, Buckle, Propeller, Opening). The simple version is provided by [[CV:NASBPP|NASBPP]], while the local version is provided [[CV:NASBPP|NASBPP]]. Both implementations are fully compatible with [https://x3dna.org/ 3DNA]. The collective variable [[CV:NASBO|NASBO]] implements simple Opening only and thus it should be a little bit computationally faster. | |||
[[File:SF3.png|center|600px]] | [[File:SF3.png|center|600px]] | ||
== Base-Pair Step Parameters == | |||
Revision as of 11:49, 21 June 2021
Navigation: Documentation / Collective Variables / Nucleic Acids
Distance
Angle
Coordination
Shape
Special
Energy
Algebra
Collective Variables For Nucleic Acids
| Type | Description |
| NALBPP | local base-pair parameters |
| NASBPP | simple base-pair parameters |
| NASBPPOLD | simple base-pair parameters (OLD implementation)* |
| NALSTP | local base-pair step parameters |
| NASSTP | simple base-pair step parameters |
| NASSTPOLD | simple base-pair step parameters (OLD implementation)* |
| NASBO | simple base-pair opening |
| NAPBO | primitive base-pair opening |
| NABEND | nucleic acid bending |
Base-Pair Parameters
PMFLib offers two variants of the base-pair parameters: local and simple. They differ in the definition of the y-axis and the procedure to calculate six base-pair parameters (i.e., Shear, Stretch, Stagger, Buckle, Propeller, Opening). The simple version is provided by NASBPP, while the local version is provided NASBPP. Both implementations are fully compatible with 3DNA. The collective variable NASBO implements simple Opening only and thus it should be a little bit computationally faster.
Base-Pair Step Parameters
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.