Русская версия English version   
Том 10   Выпуск 1   Год 2015
Баулин Е.Ф., Ройтберг М.А.

Стемовые мультиплеты: новый подход к описанию третичных мотивов РНК

Математическая биология и биоинформатика. 2015;10(1):54-59.

doi: 10.17537/2015.10.54.

Список литературы

  1. Zuker M, Mathews DH, Turner DH. Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In: RNA Biochemistry and Biotechnology. Eds. J. Barciszewski, B.F.C. Clark. Boston: Kluwer Academic Publishers; 1999. P. 11-43. (NATO ASI Series).
  2. Xia T, SantaLucia JJr, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, Turner DH. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry. 1998;37:4735. doi: 10.1021/bi9809425
  3. Darty K, Denise A, Ponty Y. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics. 2009;25(15):1974. doi: 10.1093/bioinformatics/btp250
  4. Lai D, Proctor JR, Zhu JYA, Meyer IM. R-CHIE: a web server and R package for visualizing RNA secondary structures. Nucleic Acids Research. 2012;40(12):e95. doi: 10.1093/nar/gks241
  5. Vanegas PL, Hudson GA, Davis AR, Kelly SC, Kirkpatrick CC, Znosko BM. RNA CoSSMos: Characterization of Secondary Structure Motifs-a searchable database of secondary structure motifs in RNA three-dimensional structures. Nucleic Acids Research. 2012;40:D439-D444. doi: 10.1093/nar/gkr943
  6. Popenda M, Szachniuk M, Blazewicz M, Wasik S, Burke EK, Blazewicz J, Adamiak RW. RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. BMC Bioinformatics. 2010;11(1):231. doi: 10.1186/1471-2105-11-231
  7. Han K, Lee Y, Kim W. PseudoViewer: automatic visualization of RNA pseudoknots. Bioinformatics. 2002;18(1):S321-S328. doi: 10.1093/bioinformatics/18.suppl_1.S321
  8. Haslinger C, Stadler PF. RNA structures with pseudo-knots: Graph-theoretical, combinatorial, and statistical properties. Bulletin of Mathematical Biology. 1999;61(3):437-467. doi: 10.1006/bulm.1998.0085
  9. Gan HH, Pasquali S, Schlick T. Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. Nucleic Acids Research. 2003;31(11):2926-2943. doi: 10.1093/nar/gkg365
  10. Rødland EA. Pseudoknots in RNA secondary structures: representation, enumeration, and prevalence. Journal of Computational Biology. 2006;13(6):1197-1213. doi: 10.1089/cmb.2006.13.1197
  11. Bon M, Vernizzi G, Orland H, Zee A. Topological classification of RNA structures. Journal of Molecular Biology. 2008;379(4):900-911. doi: 10.1016/j.jmb.2008.04.033
  12. Reidys CM, Huang FW, Andersen JE, Penner RC, Stadler PF, Nebel ME. Topology and prediction of RNA pseudoknots. Bioinformatics. 2011;27(8):1076-1085. doi: 10.1093/bioinformatics/btr090
  13. Leontis NB, Westhof E. Geometric nomenclature and classification of RNA base pairs. RNA. 2001;7(4):499-512. doi: 10.1017/S1355838201002515
  14. Chojnowski G, Waleń T, Bujnicki JM. RNA Bricks-a database of RNA 3D motifs and their interactions. Nucleic Acids Research. 2014;42(D1):D123-D131. doi: 10.1093/nar/gkt1084
  15. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Research. 2000;28(1):235-242. doi: 10.1093/nar/28.1.235
  16. Lu XJ, Olson WK. 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. doi: 10.1038/nprot.2008.104
  17. Hanson RM, Prilusky J, Renjian Z, Nakane T, Sussman JL. JSmol and the Next‐Generation Web‐Based Representation of 3D Molecular Structure as Applied to Proteopedia. Israel Journal of Chemistry. 2013;53(3-4):207-216. doi: 10.1002/ijch.201300024
Содержание Оригинальная статья
Мат. биол. и биоинф.
2015;10(1):54-59
doi: 10.17537/2015.10.54
опубликована на рус. яз.

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