1. Adams P.L., Stahley M.R., Kosek A.B., Wang J. and Strobel S.A. (2004). Crystal structure of a self-splicing group I intron with both exons. Nature 430(6995): 45–50

    Article  Google Scholar 

  2. Babcock M.S., Pednaul T.E.P. and Olson W.K. (1994). Nucleic acid structure analysis. mathematics for local Cartesian and helical structure parameters that are truly comparable between structures. J. Mol. Biol. 237(1): 125–156

    Article  Google Scholar 

  3. Ban N., Nissen P., Hansen J., Moore P.B. and Steitz T.A. (2000). The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289(5481): 905–920

    Article  Google Scholar 

  4. Bayley M.J., Gardiner E.J., Willett P. and Artymiuk P.J. (2005). A fourier fingerprint-based method for protein surface representation. J. Chem. Inf. Model 45(3): 696–707

    Article  Google Scholar 

  5. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N. and Bourne P.E. (2000). The Protein Data Bank. Nucleic Acids Res. 28(1): 235–242

    Article  Google Scholar 

  6. Bourne P.E., Addess K.J., Bluhm W.F., Chen L., Deshpande N., Feng Z., Fleri W., Green R., Merino-Ott J.C., Townsend-Merino W., Weissig H., Westbrook J. and Berman H.M. (2004). The distribution and query systems of the RCSB Protein Data Bank. Nucleic Acids Res. 32(Database issue): D223–D225

    Article  Google Scholar 

  7. Deshpande N., Addess K.J., Bluhm W.F., Merino-Ott J.C., Townsend-Merino W., Zhang Q., Knezevich C., Xie L., Chen L., Feng Z., Green R.K., Flippen-Anderson J.L., Westbrook J., Berman H.M. and Bourne P.E. (2005). The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res. 33(Database issue): D233–D237

    Article  Google Scholar 

  8. Dror O., Nussinov R. and Wolfson H. (2005). alignment of RNA tertiary structures. Bioinformatics 21(Suppl 2): ii47–ii53

    Article  Google Scholar 

  9. Duarte C.M. and Pyle A.M. (1998). Stepping through an RNA structure: a novel approach to conformational analysis. J. Mol. Biol. 284(5): 1465–1478

    Article  Google Scholar 

  10. Duarte C.M., Wadley L.M. and Pyle A.M. (2003). RNA structure comparison, motif search and discovery using a reduced representation of RNA conformational space. Nucleic Acids Res. 31(16): 4755–4761

    Article  Google Scholar 

  11. Dutta S. and Berman H.M. (2005). Large macromolecular complexes in the Protein Data Bank: a status report. Structure 13(3): 381–388

    Article  Google Scholar 

  12. Francois B., Russell R.J., Murray J.B., Aboul-ela F., Masquida B., Vicens Q. and Westhof E. (2005). Crystal structures of complexes between aminoglycosides and decoding A site oligonucleotides: role of the number of rings and positive charges in the specific binding leading to miscoding. Nucleic. Acids Res. 33(17): 5677–5690

    Article  Google Scholar 

  13. Gendron P., Lemieux S. and Major F. (2001). Quantitative analysis of nucleic acid three-dimensional structures. J. Mol. Biol. 308(5): 919–936

    Article  Google Scholar 

  14. Golden B.L., Kim H. and Chase E. (2005). Crystal structure of a phage Twort group I ribozyme-product complex. Nat. Struct. Mol. Biol. 12(1): 82–89

    Article  Google Scholar 

  15. Golub G.H. and Van Loan C.F. (1996). Matrix computations, third edn Johns Hopkins Studies in the Mathematical Sciences. Johns Hopkins University Press, Baltimore

    Google Scholar 

  16. Harms J., Schluenzen F., Zarivach R., Bashan A., Gat S., Agmon I., Bartels H, Franceschi F. and Yonath A. (2001). High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell 107(5): 679–688

    Article  Google Scholar 

  17. Harrison A.M., South D.R., Willett P. and Artymiuk P.J. (2003). Representation, searching and discovery of patterns of bases in complex RNA structures. J. Comput. Aided. Mol. Des. 17(8): 537–549

    Article  Google Scholar 

  18. Hershkovitz E., Tannenbaum E., Howerton S.B., Sheth A., Tannenbaum A. and Williams L.D. (2003). Automated identification of RNA conformational motifs: theory and application to the HM LSU 23S rRNA. Nucleic. Acids. Res. 31(21): 6249–6257

    Article  Google Scholar 

  19. Hobza P. and Sponer J. (1999). Structure, energetics and dynamics of the nucleic acid base pairs: nonempirical ab initio calculations. Chem. Rev. 99(11): 3247–3276

    Article  Google Scholar 

  20. Hoffmann B., Mitchell G.T., Gendron P., Major F., Andersen A.A., Collins R.A. and Legault P. (2003). NMR Structure of the active conformation of the Varkud satellite ribozyme cleavage site. Proc. Natl. Acad. Sci. USA 100(12): 7003–8

    Article  Google Scholar 

  21. Holbrook S.R. (2005). Structure: the long and the short of it. Curr. Opin. Struct. Biol. 15(3): 302–308

    Article  Google Scholar 

  22. Horn B.K.P., Hilden H.M. and Nagahdaripour S. (1998). Closed-form solution of absolute orientation using orthonormal matrices. J. Opt. Soc. Am. A 5(7): 1127–1135

    Article  Google Scholar 

  23. Huang H.C., Nagaswamy U. and Fox G.E. (2005). The application of cluster analysis in the intercomparison of loop structures in RNA. RNA 11(4): 412–423

    Article  Google Scholar 

  24. Jossinet F. and Westhof E. (2005). Sequence to structure (S2S): display, manipulate and interconnect RNA data from sequence to structure. Bioinformatics 21(15): 3320–3321

    Article  Google Scholar 

  25. Kazantsev A.V., Krivenko A.A., Harrington D.J., Holbrook S.R., Adams P.D. and Pace N.R. (2005). Crystal structure of a bacterial ribonuclease P RNA. Proc. Natl. Acad. Sci. USA 102(38): 13392–13397

    Article  Google Scholar 

  26. Klein D.J., Schmeing T.M., Moore P.B. and Steitz T.A. (2001). The kink-turn: a new RNA secondary structure motif. Embo. J. 20(15): 4214–4221

    Article  Google Scholar 

  27. Klosterman P.S., Hendrix D.K., Tamura M., Holbrook S.R. and Brenner S.E. (2004). Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns. Nucleic. Acids. Res. 32(8): 2342–2352

    Article  Google Scholar 

  28. Leontis, N., Altman, R., Berman, H., Brenner, S.E., Brown, J., Engelke, D., Harvey, S.C., Holbrook, S.R., Jossinet, F., Lewis, S.E., Major, F., Mathews, D.H., Richardson, J.S., Williamson, J.R.E.W.: The RNA ontology consortium: An open invitation to the rna community. RNA 12 (2006)

  29. Leontis N., Lescoute A. and Westhof E. (2006). The building blocks and motifs of RNA architecture. Curr. Opin. Struct. Biol. 16(3): 274–287

    Article  Google Scholar 

  30. Leontis N.B., Stombaugh J. and Westhof E. (2002). The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic. Acids. Res. 30(16): 3497–3531

    Article  Google Scholar 

  31. Leontis N.B., Stombaugh J. and Westhof E. (2002). Motif prediction in ribosomal RNAs lessons and prospects for automated motif prediction in homologous RNA molecules. Biochimie 84(9): 961–973

    Article  Google Scholar 

  32. Leontis N.B. and Westhof E. (2001). Geometric nomenclature and classification of RNA base pairs. RNA 7(4): 499–512

    Article  Google Scholar 

  33. Leontis N.B. and Westhof E. (2003). Analysis of RNA motifs. Curr. Opin. Struct. Biol. 13(3): 300–308

    Article  Google Scholar 

  34. Lescoute A., Leontis N.B., Massire C. and Westhof E. (2005). Recurrent structural RNA motifs, isostericity matrices and sequence alignments. Nucleic. Acids. Res. 33(8): 2395–2409

    Article  Google Scholar 

  35. Major, F., Thibault, P.: In: T.~Lengauer (ed.) Bioinformatics: From Genomes to Therapies, pp. 491–539. Wiley, New York (2006)

  36. Major F., Turcotte M., Gautheret D., Lapalme G., Fillion E. and Cedergren R. (1991). The combination of symbolic and numerical computation for three-dimensional modeling of RNA. Science 253(5025): 1255–60

    Article  Google Scholar 

  37. Murray L.J., Arendall W.B., Richardson 3rd D.C. and Richardson J.S. (2003). RNA backbone is rotameric. Proc. Natl. Acad. Sci. USA 100(24): 13904–13909

    Article  Google Scholar 

  38. Murray L.J., Richardson J.S., Arendall W.B. and Richardson D.C. (2005). RNA backbone rotamers-finding your way in seven dimensions. Biochem. Soc. Trans. 33(Pt 3): 485–487

    Google Scholar 

  39. Olivier C., Poirier G., Gendron P., Boisgontier A., Major F. and Chartrand P. (2005). Identification of a conserved RNA motif essential for She2p recognition and mRNA localization to the yeast bud. Mol. Cell. Biol. 25(11): 4752–4766

    Article  Google Scholar 

  40. Olson W.K., Bansal M., Burley S.K., Dickerson R.E., Gerstein M., Harvey S.C., Heinemann U., Lu X.J., Neidle S., Shakked Z., Sklenar H., Suzuki M., Tung C.S., Westhof E., Wolberger C. and Berman H.M. (2001). A standard reference frame for the description of nucleic acid base-pair geometry. J. Mol. Biol. 313(1): 229–237

    Article  Google Scholar 

  41. Schneider B., Moravek Z. and Berman H.M. (2004). conformational classes. Nucleic. Acids. Res. 32(5): 1666–1677

    Article  Google Scholar 

  42. Schuwirth B.S., Borovinskaya M.A., Hau C.W., Zhang W., Vila-Sanjurjo A., Holton J.M. and Cate J.H. (2005). Structures of the bacterial ribosome at 3.5A resolution. Science 310(5749): 827–834

    Article  Google Scholar 

  43. Wadley L.M. and Pyle A.M. (2004). The identification of novel RNA structural motifs usingCOMPADRES: an automated approach to structural discovery. Nucleic. Acids. Res. 32(22): 6650–6659

    Article  Google Scholar 

  44. Wimberly B.T., Brodersen D.E., Morgan-Warren R.J., Carter A.P., Vonrhein C., Hartsch T., Ramakrishnan V. and Clemons W.M. (2000). Structure of the 30S ribosomal subunit.. Nature 407(6802): 327–339

    Article  Google Scholar 

  45. 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(13): 3450–3460

    Article  Google Scholar