Nucleic Acids: Difference between revisions

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| [[CV:NASBPPOLD|NASBPPOLD]]
| [[CV:NASBPPOLD|NASBPPOLD]]
| simple base-pair parameters (OLD implementation)*
| simple base-pair parameters (OLD implementation)
|-
|-
| [[CV:NALSTP|NALSTP]]
| [[CV:NALSTP|NALSTP]]
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|-
|-
| [[CV:NASSTPOLD|NASSTPOLD]]
| [[CV:NASSTPOLD|NASSTPOLD]]
| simple base-pair step parameters (OLD implementation)*
| simple base-pair step parameters (OLD implementation)
|-
|-
| [[CV:NASBO|NASBO]]
| [[CV:NASBO|NASBO]]
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== Base-Pair Parameters ==   
== 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.  
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 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 CEPH procedure.  
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]].  
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:SF3.png|center|600px]]
[[File:Bpp.png|center|600px]]


== Base-Pair Step Parameters ==   
== Base-Pair Step Parameters ==   


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, 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 CEPH procedure.  
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 CEPH procedure.  
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===
* 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
* 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.

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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