Nucleic Acids: Difference between revisions

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{{CVS}}__NOEDITSECTION__
{{CVS}}__NOEDITSECTION__


= Implemented Collective Variables =
= Collective Variables For Nucleic Acids =


{|
{|
| 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:NABEND|NABEND]]
| [[CV:NASSTPOLD|NASSTPOLD]]
| nucleic acid bending
| simple base-pair step parameters (OLD implementation)
|-
| [[CV:NASBO|NASBO]]
| simple base-pair opening
|-
|-
| [[CV:NAPBO|NAPBO]]
| [[CV:NAPBO|NAPBO]]
| primitive base opening
| primitive base-pair opening
|-
|-
| [[CV:NASBO|NASBO]]
| [[CV:NABEND|NABEND]]
| simple base opening
| nucleic acid bending
|}
|}


== Simple Base Pair Parameters ==   
== Base-Pair Parameters ==   


All simple base pair parameters fully compatible with 3DNA are available via [[CV:NASBPP|NASBPP]]. Reference coordinates for nucleobase rings are available here:
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.
 
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:Stp.png|center|600px]]
 
== Reference Frames of Nucleobases == 
 
Reference coordinates for nucleobase rings are provided in the following table:
{|
{|
| style="width: 5em;" | Nucleobase
| style="width: 5em;" | '''Nucleobase'''
| ''anti''  
| '''Ring Atoms'''
| ''syn''
| '''y-axis (BPP)'''
| '''y-axis (STP)'''
| '''File'''  
|-
|-
| A
| A
|
| @N9,C8,N7,C5,C6,N1,C2,N3,C4
|
| @C8
| @C1'
| [https://devel.ncbr.muni.cz/whitezone/pmflib/data/A_ring_only.xyz A_ring_only.xyz]
|-
|-
| G
| G
|
| @N9,C8,N7,C5,C6,N1,C2,N3,C4
|
| @C8
| @C1'
| [https://devel.ncbr.muni.cz/whitezone/pmflib/data/G_ring_only.xyz G_ring_only.xyz]
|-
|-
| C
| C
|
| @N1,C6,C5,C4,N3,C2
|
| @C6
| @C1'
| [https://devel.ncbr.muni.cz/whitezone/pmflib/data/C_ring_only.xyz C_ring_only.xyz]
|-
|-
| T
| T
|
| @N1,C6,C5,C4,N3,C2
|
| @C6
|-
| @C1'
|
| [https://devel.ncbr.muni.cz/whitezone/pmflib/data/T_ring_only.xyz T_ring_only.xyz]
|
|}  
|}  




===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.

Latest revision as of 15:13, 21 June 2021

Navigation: Documentation / Collective Variables / Nucleic Acids

Distance

Angle

Coordination

Shape

Nucleic Acids

Puckering

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, which both are fully compatible with 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 NASBPP. It uses an explicitly defined y-axis and Buckle, Propeller, Opening parameters are calculated as dihedral angles.

The local version is provided by 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 NASBO implements simple Opening only and thus it should be a little bit computationally faster than NASBPP.

Base-Pair Step Parameters

PMFLib offers two variants of the base-pair step parameters, local and simple, which both are fully compatible with 3DNA. They differ in the definition of the y-axes, i.e., Shift, Slide, Rise, Tilt, Roll, Twist.

The simple version is provided by 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 NALSTP. It uses y-axes derived from the superimposed reference frames of four nucleobases and all parameters are calculated using the CEHS scheme.

Reference Frames of Nucleobases

Reference coordinates for nucleobase rings are provided in the following table:

Nucleobase Ring Atoms y-axis (BPP) y-axis (STP) File
A @N9,C8,N7,C5,C6,N1,C2,N3,C4 @C8 @C1' A_ring_only.xyz
G @N9,C8,N7,C5,C6,N1,C2,N3,C4 @C8 @C1' G_ring_only.xyz
C @N1,C6,C5,C4,N3,C2 @C6 @C1' C_ring_only.xyz
T @N1,C6,C5,C4,N3,C2 @C6 @C1' T_ring_only.xyz


References

  • 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
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