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) | ||
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| [[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) | ||
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| [[CV:NASBO|NASBO]] | | [[CV:NASBO|NASBO]] | ||
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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: | [[File:Bpp.png|center|600px]] | ||
== Base-Pair Step Parameters == | == Base-Pair Step Parameters == | ||
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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. | 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: | [[File:Stp.png|center|600px]] | ||
== Reference Frames of Nucleobases == | == Reference Frames of Nucleobases == | ||
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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 | * 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. | ** 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. | ||