Nucleic Acids: Difference between revisions
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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]] | ||
| Line 22: | Line 37: | ||
|} | |} | ||
== | == 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. | |||
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: | Reference coordinates for nucleobase rings are provided in the following table: | ||
{| | {| | ||
| style="width: 5em;" | Nucleobase | | style="width: 5em;" | '''Nucleobase''' | ||
| '' | | '''Ring Atoms''' | ||
| '''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=== | ||
* | * 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. | |||