Automated 3D structure composition for large RNAs

Nucleic Acids Research

Volumn 40, Issue 14, 2012, Pages

  Popenda, Mariusz ^a   Szachniuk, Marta ^b,c   Antczak, MacIej ^c   Purzycka, Katarzyna J ^a   Lukasiak, Piotr ^b,c   Bartol, Natalia ^c   Blazewicz, Jacek ^b,c   Adamiak, Ryszard W ^a  

^a Laboratory of Structural Chemistry of Nucleic Acids   (Poland)

^b INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

^c POZNAN UNIVERSITY OF TECHNOLOGY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

RNA 5S;

ARTICLE; AUTOMATION; COMPUTER INTERFACE; COMPUTER MODEL; COMPUTER PROGRAM; GENETIC ALGORITHM; HALOARCULA MARISMORTUI; INTERMETHOD COMPARISON; NONHUMAN; NUCLEIC ACID DATABASE; PREDICTION; PRIORITY JOURNAL; RETROPOSON; RNA ANALYSIS; RNA FRABASE DATABASE; RNA SECONDARY STRUCTURE; RNA SEQUENCE; RNA STRUCTURE; RNA TERTIARY STRUCTURE; RNA TRANSLATION; RNA TRANSPORT; STRUCTURE ACTIVITY RELATION; WEB BROWSER;

ALGORITHMS; DATABASES, NUCLEIC ACID; INTERNET; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; RETROELEMENTS; RNA; RNA, RIBOSOMAL, 5S; SOFTWARE;

EID: 84864953710     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks339     Document Type: Article

References (45)

1. Sashital, D.G. and Doudna, J.A. (2010) Structural insights into RNA interference. Curr. Opin. Struct. Biol., 20, 90-97.
2. Beezhold, K.J., Castranova, V. and Chen, F. (2010) Microprocessor of microRNAs: regulation and potential for therapeutic intervention. Mol. Cancer, 9, e134.
3. Rose, P.W., Beran, B., Bi, C., Bluhm, W.F., Dimitropoulos, D., Goodsell, D.S., Prlic, A., Quesada, M., Quinn, G.B., Westbrook, J.D. et al. (2011) The RCSB Protein Data Bank: redesigned web site and web services. Nucleic Acids Res., 39, D392-D401.
4. Leontis, N. and Westhof, E. (eds), (2012), "RNA 3D structure analysis and prediction", In: Series Nucleic Acids and Molecular Biology. Springer, Berlin and Heidelberg.
5. Mathews, D.H. and Turner, D.H. (2006) Prediction of RNA secondary structure by free energy minimization. Curr. Opin. Struct. Biol., 16, 270-278. (Pubitemid 43831654)
6. Xu, Z., Almudevar, A. and Mathews, D.H. (2012) Statistical evaluation of improvement in RNA secondary structure prediction. Nucleic Acids Res., 40, e26.
7. Mathews, D.H., Disney, M.D., Childs, J.L., Schroeder, S.J., Zuker, M. and Turner, D.H. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl Acad. Sci. USA, 101, 7287-7292. (Pubitemid 38638025)
8. Merino, E.J., Wilkinson, K.A., Coughlan, J.L. and Weeks, K.M. (2005) RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE). J. Am. Chem. Soc., 127, 4223-4231. (Pubitemid 40463047)
9. Wilkinson, K.A., Gorelick, R.J., Vasa, S.M., Guex, N., Rein, A., Mathews, D.H., Giddings, M.C. and Weeks, K.M. (2008) High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol., 6, e96.
10. Purzycka, K.J., Pachulska-Wieczorek, K. and Adamiak, R.W. (2011) The in vitro loose dimer structure and rearrangements of the HIV-2 leader RNA. Nucleic Acids Res., 39, 7234-7248.
11. Pang, P.S., Elazar, M., Pham, E.A. and Glenn, J.S. (2011) Simplified RNA secondary structure mapping by automation of SHAPE data analysis. Nucleic Acids Res., 39, e151.
12. Seetin, M.G. and Mathews, D.H. (2011) Automated RNA tertiary structure prediction from secondary structure and low-resolution restraints. J. Comput. Chem., April 21 (doi:10.1002/jcc.21806; epub ahead of print).
13. Martinez, H.M., Maizel, J.V. Jr and Shapiro, B.A. (2008) RNA2D3D: a program for generating, viewing, and comparing 3-dimensional models of RNA. J. Biomol. Struct. Dyn., 25, 669-683. (Pubitemid 351694136)
14. Jossinet, F., Ludwig, T.E. and Westhof, E. (2010) Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. Bioinformatics, 26, 2057-2059.
15. Sharma, S., Ding, F. and Dokholyan, N.V. (2008) iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinformatics, 24, 1951-1952.
16. Jonikas, M.A., Radmer, R.J., Laederach, A., Das, R., Pearlman, S., Herschlag, D. and Altman, R.B. (2009) Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters. RNA, 15, 189-199.
17. Jonikas, M.A., Radmer, R.J. and Altman, R.B. (2009) Knowledge-based instantiation of full atomic detail into coarse-grain RNA 3D structural models. Bioinformatics, 25, 3259-3266.
18. Flores, S.C. and Altman, R.B. (2010) Turning limited experimental information into 3D models of RNA. RNA, 16, 1769-1778.
19. Flores, S.C., Sherman, M.A., Bruns, C.M., Eastman, P. and Altman, R.B. (2011) Fast flexible modeling of RNA structure using internal coordinates. IEEE/ACM Trans. Comput. Biol. Bioinform., 8, 1247-1257.
20. Das, R., Karanicolas, J. and Baker, D. (2010) Atomic accuracy in predicting and designing noncanonical RNA structure. Nat. Methods, 7, 291-294.
21. Parisien, M. and Major, F. (2008) The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature, 452, 51-55. (Pubitemid 351355097)
22. Rother, M., Rother, K., Puton, T. and Bujnicki, J.M. (2011) ModeRNA: a tool for comparative modeling of RNA 3D structure. Nucleic Acids Res., 39, 4007-4022.
23. Wilks, Y. (2010) Machine Translation: Its Scope And Limits. Springer, New York.
24. Popenda, M., Blazewicz, M., Szachniuk, M. and Adamiak, R.W. (2008) RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures. Nucleic Acids Res., 36, D386-D391. (Pubitemid 351149754)
25. Popenda, M., Szachniuk, M., Blazewicz, M., Wasik, S., Burke, E.K., Blazewicz, J. and Adamiak, R.W. (2010) RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures. BMC Bioinformatics, 11, e231.
26. Schwieters, C.D., Kuszewski, J.J., Tjandra, N. and Clore, G.M. (2003) The Xplor-NIH NMR molecular structure determination package. J. Magn. Reson., 160, 65-73.
27. Macke, T. and Case, D.A. (1998) Modeling Unusual Nucleic Acid Structures. In: Leontes, N.B. and Santa Lucia, J. Jr (eds), Molecular Modeling of Nucleic Acids. American Chemical Society. Washington, DC, pp. 379-393. (Pubitemid 128436668)
28. Guntert, P., Mumenthaler, C. and Wuthrich, K. (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA. J. Mol. Biol., 273, 283-298. (Pubitemid 27460230)
29. Popenda, M., Bielecki, L. and Adamiak, R.W. (2006) High-throughput method for the prediction of low-resolution three-dimensional RNA structures. Nucleic Acids Symp. Ser. (Oxf), 50, 67-68.
30. Berman, H.M., Olson, W.K., Beveridge, D.L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.H., Srinivasan, A.R. and Schneider, B. (1992) The nucleic acid database: a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J., 63, 751-759.
31. Kabsch, W. (1976) Solution for best rotation to relate 2 sets of vectors. Acta Crystallogr. A, 32, 922-923.
32. Davis, I.M., Leaver-Fay, A., Chen, V.B., Block, J.N., Kapral, G.J., Wang, X., Murray, L.W., Arendall, W.B. III, Snoerink, J. and Richardson, J.S. (2007) MolProbity: all-atom contacts and structure validation for protein and nucleic acids. Nucleic Acids Res., 35, W375-W383.
33. Parisien, M., Cruz, J.A., Westhof, E. and Major, F. (2009) New metrics for comparing and assessing discrepancies between RNA 3D structures and models. RNA, 15, 1875-1885.
34. Yang, H., Jossinet, F., Leontis, N., Chen, L., Westbrook, J., Berman, H. and Westhof, E. (2003) Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res., 31, 3450-3460. (Pubitemid 37442176)
35. Gendron, P., Lemieux, S. and Major, F. (2001) Quantitative analysis of nucleic acid three-dimensional structures. J. Mol. Biol., 308, 919-936. (Pubitemid 32574369)
36. Reuter, J.S. and Mathews, D.H. (2010) RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics, 11, e129.
37. Wilkinson, K.A., Merino, E.J. and Weeks, K.M. (2006) Selective 20-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat. Protoc., 1, 1610-1616.
38. Das, R., Laederach, A., Pearlman, S.M., Herschlag, D. and Altman, R.B. (2005) SAFA: semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. RNA, 11, 344-354. (Pubitemid 40270826)
39. Gan, H.H., Pasquali, S. and Schlick, T. (2003) Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. Nucleic Acids Res., 31, 2926-2943. (Pubitemid 37442136)
40. Hofacker, I.L., Fontana, W., Stadler, P.F., Bonhoeffer, S., Tacker, M. and Schuster, P. (1994) Fast folding and comparison of RNA secondary structures. Monastch.. Chem., 125, 167-188.
41. Matthews, B.W. (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta, 405, 442-451.
42. Deigan, K.E., Li, T.W., Mathews, D.H. and Weeks, K.M. (2009) Accurate SHAPE-directed RNA structure determination. Proc. Natl Acad. Sci. USA, 106, 97-102.
43. Legiewicz, M., Zolotukhin, A.S., Pilkington, G.R., Purzycka, K.J., Mitchell, M., Uranishi, H., Bear, J., Pavlakis, G.N., Le Grice, S.F. and Felber, B.K. (2010) The RNA transport element of the murine musD retrotransposon requires long-range intramolecular interactions for function. J. Biol. Chem., 285, 42097-42104.
44. Byun, Y. and Han, K. (2009) PseudoViewer3: generating planar drawings of large-scale RNA structures with pseudoknots. Bioinformatics, 25, 1435-1437.
45. DeLano, W.L. (2002) The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos.