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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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|}
|}


== Simple Base Pair Parameters ==   
== Base-Pair Parameters ==   
 
PMFLib offers two variants of the base-pair parameters, local and simple, which both are fully compatible with [https://x3dna.org/ 3DNA]. 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]]. 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 superimposed reference frames of two nucleobases and all parameters are calculated using the CEHS scheme.
 
The collective variable [[CV:NASBO|NASBO]] implements simple Opening only and thus it should be a little bit computationally faster than [[CV:NASBPP|NASBPP]].
 
[[File:Bpp.png|center|600px]]
 
== Base-Pair Step Parameters == 
 
PMFLib offers two variants of the base-pair step parameters, local and simple, which both are fully compatible with [https://x3dna.org/ 3DNA]. 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 CEHS scheme.


All simple base pair parameters (''i.e.'', shear, stretch, stagger, buckle, propeller, opening) fully compatible with 3DNA are available via the [[CV:NASBPP|NASBPP]] collective variable. The collective variable [[CV:NASBPP|NASBO]] implements only the opening parameter and thus it should be a little bit computationally faster.  
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:Stp.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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| style="width: 5em;" | '''Nucleobase'''  
| style="width: 5em;" | '''Nucleobase'''  
| '''Ring Atoms'''
| '''Ring Atoms'''
| '''y-axis'''
| '''y-axis (BPP)'''
| '''y-axis (STP)'''
| '''File'''  
| '''File'''  
|-
|-
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| @N9,C8,N7,C5,C6,N1,C2,N3,C4
| @N9,C8,N7,C5,C6,N1,C2,N3,C4
| @C8
| @C8
| @C1'
| [https://devel.ncbr.muni.cz/whitezone/pmflib/data/A_ring_only.xyz A_ring_only.xyz]
| [https://devel.ncbr.muni.cz/whitezone/pmflib/data/A_ring_only.xyz A_ring_only.xyz]
|-
|-
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| @N9,C8,N7,C5,C6,N1,C2,N3,C4
| @N9,C8,N7,C5,C6,N1,C2,N3,C4
| @C8
| @C8
| @C1'
| [https://devel.ncbr.muni.cz/whitezone/pmflib/data/G_ring_only.xyz G_ring_only.xyz]
| [https://devel.ncbr.muni.cz/whitezone/pmflib/data/G_ring_only.xyz G_ring_only.xyz]
|-
|-
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| @N1,C6,C5,C4,N3,C2
| @N1,C6,C5,C4,N3,C2
| @C6
| @C6
| @C1'
| [https://devel.ncbr.muni.cz/whitezone/pmflib/data/C_ring_only.xyz C_ring_only.xyz]
| [https://devel.ncbr.muni.cz/whitezone/pmflib/data/C_ring_only.xyz C_ring_only.xyz]
|-
|-
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| @N1,C6,C5,C4,N3,C2
| @N1,C6,C5,C4,N3,C2
| @C6
| @C6
| @C1'
| [https://devel.ncbr.muni.cz/whitezone/pmflib/data/T_ring_only.xyz T_ring_only.xyz]
| [https://devel.ncbr.muni.cz/whitezone/pmflib/data/T_ring_only.xyz T_ring_only.xyz]
|}  
|}  
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===References===
===References===
*cite the article
* Applications
** Bouchal, T.; Durník, I.; Illík, V.; Réblová, K.; Kulhánek, P. Importance of Base-Pair Opening for Mismatch Recognition. ''Nucleic Acids Res.'' '''2020''', ''48 (20)'', 11322–11334. https://doi.org/10.1093/nar/gkaa896.
** Ruzicka, M.; Soucek, R.; Kulhanek, P.; Radova, L.; Fajkusova, L.; Reblova, K. Bending of DNA Duplexes with Mutation Motifs. ''DNA Res.'' '''2019''', ''26 (4)'', 341–352. https://doi.org/10.1093/dnares/dsz013.
** Spackova, N.; Reblova, K. Role of Inosine-Uracil Base Pairs in the Canonical RNA Duplexes. ''Genes'' '''2018''', ''9 (7)'', 324. https://doi.org/10.3390/genes9070324.
** Ruzicka, M.; Kulhanek, P.; Radova, L.; Cechova, A.; Spackova, N.; Fajkusova, L.; Reblova, K. DNA Mutation Motifs in the Genes Associated with Inherited Diseases. ''PLOS ONE'' '''2017''', ''12 (8)'', e0182377. https://doi.org/10.1371/journal.pone.0182377.
* 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
** 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.
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