Nucleic Acids: Difference between revisions

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 {{CVS}}__NOEDITSECTION__
-Short Intro - overview of CVS
+= Collective Variables For Nucleic Acids =
 {|
-|
+| style="width: 5em;" | '''Type'''
-| NASBPP
+| '''Description'''
-| simple base pair parameters
+|-
-| NABEND
+| [[CV:NALBPP|NALBPP]]
-| nucleic acid bending
+| local base-pair parameters
-NAPBO 	primitive base opening
+|-
-NASBO 	simple base opening
+| [[CV:NASBPP|NASBPP]]
+| 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]]
+| simple base-pair opening
+|-
+| [[CV:NAPBO|NAPBO]]
+| primitive base-pair opening
+|-
+| [[CV:NABEND|NABEND]]
+| nucleic acid bending
+|}
+== Base-Pair Parameters ==
-Figure
+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.
-Legend
+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'''
+| '''Ring Atoms'''
+| '''y-axis (BPP)'''
+| '''y-axis (STP)'''
+| '''File'''
+|-
+| 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
+| @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
+| @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
+| @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===
-*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.