Nucleic Acids: Difference between revisions
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The simple version is provided by [[CV:NASBPP|NASBPP]]. It uses an explicitly defined y-axis and Buckle, Propeller, Opening parameters are calculated as dihedral angles. | The simple version is provided by [[CV:NASBPP|NASBPP]]. It uses an explicitly defined y-axis and Buckle, Propeller, Opening parameters are calculated as dihedral angles. | ||
The local version is provided by [[CV:NALBPP|NALBPP]]. It uses a y-axis derived from the reference frames of two nucleobases and all parameters are calculated using the | The local version is provided by [[CV:NALBPP|NALBPP]]. It uses a y-axis derived from the superimposed reference frames of two nucleobases and all parameters are calculated using the CEHS scheme. | ||
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 than [[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 than [[CV:NASBPP|NASBPP]]. | ||
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PMFLib offers two variants of the base-pair step parameters: local and simple. They differ in the definition of the y-axes, ''i.e.'', Shift, Slide, Rise, Tilt, Roll, Twist. | PMFLib offers two variants of the base-pair step parameters: local and simple. They differ in the definition of the y-axes, ''i.e.'', Shift, Slide, Rise, Tilt, Roll, Twist. | ||
The simple version is provided by [[CV:NASSTP|NASSTP]]. It uses explicitly defined y-axes of two base pairs and all parameters are calculated using the | The simple version is provided by [[CV:NASSTP|NASSTP]]. It uses explicitly defined y-axes of two base pairs and all parameters are calculated using the CEHS scheme. | ||
The local version is provided by [[CV:NALSTP|NALSTP]]. It uses y-axes derived from the reference frames of four nucleobases and all parameters are calculated using the | The local version is provided by [[CV:NALSTP|NALSTP]]. It uses y-axes derived from the superimposed reference frames of four nucleobases and all parameters are calculated using the CEHS scheme. | ||
[[File:SF3.png|center|600px]] | [[File:SF3.png|center|600px]] | ||
== Reference Frames of Nucleobases == | |||
Reference coordinates for nucleobase rings are provided in the following table: | Reference coordinates for nucleobase rings are provided in the following table: | ||
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===References=== | ===References=== | ||
* CEHS Scheme | |||
** Lu, X. J.; ElHassan, M. A.; Hunter, C. A. Structure and Conformation of Helical Nucleic Acids: Analysis Program (SCHNAaP). ''J. Mol. Biol.'' '''1997''', ''273 (3)'', 668–680. https://doi.org/10.1006/jmbi.1997.1346. | |||
* 3DNA | * 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 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. | ||