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Volumn 5, Issue 1, 2010, Pages

Inverse folding of RNA pseudoknot structures

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EID: 77953712538     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-5-27     Document Type: Article
Times cited : (25)

References (44)
  • 2
    • 0029949699 scopus 로고    scopus 로고
    • Domain structure of the ribozyme from eubacterial ribonuclease P
    • 1369394, 8718684
    • Loria A, Pan T. Domain structure of the ribozyme from eubacterial ribonuclease P. RNA 1996, 2:551-563. 1369394, 8718684.
    • (1996) RNA , vol.2 , pp. 551-563
    • Loria, A.1    Pan, T.2
  • 3
    • 22744455135 scopus 로고    scopus 로고
    • Pseudoknots: RNA structures with diverse functions
    • 10.1371/journal.pbio.0030213, 1149493, 15941360
    • Staple DW, Butcher SE. Pseudoknots: RNA structures with diverse functions. PLoS Biol 2005, 3(6):e213. 10.1371/journal.pbio.0030213, 1149493, 15941360.
    • (2005) PLoS Biol , vol.3 , Issue.6
    • Staple, D.W.1    Butcher, S.E.2
  • 4
    • 0029348884 scopus 로고
    • A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs
    • 1369301, 7489516
    • Konings DA, Gutell RR. A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs. RNA 1995, 1:559-574. 1369301, 7489516.
    • (1995) RNA , vol.1 , pp. 559-574
    • Konings, D.A.1    Gutell, R.R.2
  • 5
    • 0026651981 scopus 로고
    • RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase
    • 10.1073/pnas.89.15.6988, 49630, 1379730
    • Tuerk C, MacDougal S, Gold L. RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase. Proc Natl Acad Sci USA 1992, 89(15):6988-6992. 10.1073/pnas.89.15.6988, 49630, 1379730.
    • (1992) Proc Natl Acad Sci USA , vol.89 , Issue.15 , pp. 6988-6992
    • Tuerk, C.1    MacDougal, S.2    Gold, L.3
  • 6
    • 0001652516 scopus 로고
    • New exact solution for the exterior gravitational field of a charged spinning mass
    • Chamorro A, Manko VS, Denisova TE. New exact solution for the exterior gravitational field of a charged spinning mass. Phys Rev D 1991, 44(10):3147-3151.
    • (1991) Phys Rev D , vol.44 , Issue.10 , pp. 3147-3151
    • Chamorro, A.1    Manko, V.S.2    Denisova, T.E.3
  • 7
    • 0033709625 scopus 로고    scopus 로고
    • RNA pseudoknot prediction in energy-based models
    • 10.1089/106652700750050862, 11108471
    • Lyngsø RB, Pedersen CNS. RNA pseudoknot prediction in energy-based models. J Comput Biol 2000, 7(3-4):409-427. 10.1089/106652700750050862, 11108471.
    • (2000) J Comput Biol , vol.7 , Issue.3-4 , pp. 409-427
    • Lyngsø, R.B.1    Pedersen, C.N.S.2
  • 8
    • 0018254569 scopus 로고
    • RNA secondary structure: A complete mathematical analysis
    • Smith TF, Waterman MS. RNA secondary structure: A complete mathematical analysis. Math Biol 1978, 42:257-266.
    • (1978) Math Biol , vol.42 , pp. 257-266
    • Smith, T.F.1    Waterman, M.S.2
  • 9
    • 0006572674 scopus 로고
    • Rapid dynamic programming methods for RNA secondary structure
    • Waterman MS, Smith TF. Rapid dynamic programming methods for RNA secondary structure. Adv Appl Math 1986, 7(4):455-464.
    • (1986) Adv Appl Math , vol.7 , Issue.4 , pp. 455-464
    • Waterman, M.S.1    Smith, T.F.2
  • 10
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
    • 10.1093/nar/9.1.133, 326673, 6163133
    • Zuker M, Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucl Acids Res 1981, 9:133-148. 10.1093/nar/9.1.133, 326673, 6163133.
    • (1981) Nucl Acids Res , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2
  • 11
    • 0019082587 scopus 로고
    • Fast algorithm for predicting the secondary structure of single-stranded RNA
    • 10.1073/pnas.77.11.6309, 350273, 6161375
    • Nussinov B, Jacobson AB. Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc Natl Acad Sci USA 1980, 77(11):6309-6313. 10.1073/pnas.77.11.6309, 350273, 6161375.
    • (1980) Proc Natl Acad Sci USA , vol.77 , Issue.11 , pp. 6309-6313
    • Nussinov, B.1    Jacobson, A.B.2
  • 12
    • 0002556146 scopus 로고
    • Some molecular details of the secondary structure of ribonucleic acid
    • 10.1038/188098a0, 13701785
    • Fresco JR, Alberts BM, Doty P. Some molecular details of the secondary structure of ribonucleic acid. Nature 1960, 188:98-101. 10.1038/188098a0, 13701785.
    • (1960) Nature , vol.188 , pp. 98-101
    • Fresco, J.R.1    Alberts, B.M.2    Doty, P.3
  • 13
    • 0015216137 scopus 로고
    • Estimation of Secondary Structure in Ribonucleic Acids
    • 10.1038/230362a0, 4927725
    • Jun IT, Uhlenbeck OC, Levine MD. Estimation of Secondary Structure in Ribonucleic Acids. Nature 1971, 230(5293):362-367. 10.1038/230362a0, 4927725.
    • (1971) Nature , vol.230 , Issue.5293 , pp. 362-367
    • Jun, I.T.1    Uhlenbeck, O.C.2    Levine, M.D.3
  • 14
    • 0015146785 scopus 로고
    • Prediction of RNA secondary structure
    • 10.1073/pnas.68.11.2682, 389500, 5288243
    • Delisi C, Crothers DM. Prediction of RNA secondary structure. Proc Natl Acad Sci USA 1971, 68(11):2682-2685. 10.1073/pnas.68.11.2682, 389500, 5288243.
    • (1971) Proc Natl Acad Sci USA , vol.68 , Issue.11 , pp. 2682-2685
    • Delisi, C.1    Crothers, D.M.2
  • 15
    • 0033524952 scopus 로고    scopus 로고
    • A dynamic programming algorithm for RNA structure prediction including pseudoknots
    • 10.1006/jmbi.1998.2436, 9925784
    • Rivas E, Eddy SR. A dynamic programming algorithm for RNA structure prediction including pseudoknots. J Mol Biol 1999, 285(5):2053-2068. 10.1006/jmbi.1998.2436, 9925784.
    • (1999) J Mol Biol , vol.285 , Issue.5 , pp. 2053-2068
    • Rivas, E.1    Eddy, S.R.2
  • 16
    • 2542514671 scopus 로고    scopus 로고
    • Paradigms for computational nucleic acid design
    • 10.1093/nar/gkh291, 390280, 14990744
    • Dirks RM, Lin M, Winfree E, Pierce NA. Paradigms for computational nucleic acid design. Nucleic Acids Res 2004, 32(4):1392-1403. 10.1093/nar/gkh291, 390280, 14990744.
    • (2004) Nucleic Acids Res , vol.32 , Issue.4 , pp. 1392-1403
    • Dirks, R.M.1    Lin, M.2    Winfree, E.3    Pierce, N.A.4
  • 17
    • 13244252326 scopus 로고    scopus 로고
    • Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics
    • Reeder J, Giegerich R. Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics. BMC Bioinformatics 2004, 5(104):2053-2068.
    • (2004) BMC Bioinformatics , vol.5 , Issue.104 , pp. 2053-2068
    • Reeder, J.1    Giegerich, R.2
  • 18
    • 25844447772 scopus 로고    scopus 로고
    • Hotkonts: Heuristic prediction of RNA secondary structures including pseudoknots
    • Ren J, Rastegari B, Condon A, Hoos H. Hotkonts: Heuristic prediction of RNA secondary structures including pseudoknots. RNA 2005, 15:1494-1504.
    • (2005) RNA , vol.15 , pp. 1494-1504
    • Ren, J.1    Rastegari, B.2    Condon, A.3    Hoos, H.4
  • 19
    • 77952299709 scopus 로고    scopus 로고
    • Folding 3-noncrossing RNA pseudoknot structures
    • Huang FWD, Peng WWJ, Reidys CM. Folding 3-noncrossing RNA pseudoknot structures. J Comp Biol 2009, 16(11):1549-75.
    • (2009) J Comp Biol , vol.16 , Issue.11 , pp. 1549-1575
    • Huang, F.W.D.1    Peng, W.W.J.2    Reidys, C.M.3
  • 20
    • 0016189342 scopus 로고
    • Stability of ribonucleic acid doublestranded helices
    • 10.1016/0022-2836(74)90357-X, 4427357
    • Borer PN, Dengler B, Tinoco JI, Uhlenbeck OC. Stability of ribonucleic acid doublestranded helices. J Mol Biol 1974, 86(4):843-853. 10.1016/0022-2836(74)90357-X, 4427357.
    • (1974) J Mol Biol , vol.86 , Issue.4 , pp. 843-853
    • Borer, P.N.1    Dengler, B.2    Tinoco, J.I.3    Uhlenbeck, O.C.4
  • 21
    • 0021760007 scopus 로고
    • An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules
    • 10.1093/nar/12.1Part1.31, 320981, 6694903
    • Papanicolaou C, Gouy M, Ninio J. An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules. Nucleic Acids Res 1984, 12:31-44. 10.1093/nar/12.1Part1.31, 320981, 6694903.
    • (1984) Nucleic Acids Res , vol.12 , pp. 31-44
    • Papanicolaou, C.1    Gouy, M.2    Ninio, J.3
  • 23
    • 0028000994 scopus 로고
    • Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding
    • 10.1073/pnas.91.20.9218, 44783, 7524072
    • Walter AE, Turner DH, Kim J, Lyttle MH, Muller P, Mathews DH, Zuker M. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci USA 1994, 91(20):9218-9222. 10.1073/pnas.91.20.9218, 44783, 7524072.
    • (1994) Proc Natl Acad Sci USA , vol.91 , Issue.20 , pp. 9218-9222
    • Walter, A.E.1    Turner, D.H.2    Kim, J.3    Lyttle, M.H.4    Muller, P.5    Mathews, D.H.6    Zuker, M.7
  • 24
    • 0032552882 scopus 로고    scopus 로고
    • Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs
    • 10.1021/bi9809425, 9778347
    • Xia T, SantaLucia JJ, 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(42):14719-13735. 10.1021/bi9809425, 9778347.
    • (1998) Biochemistry , vol.37 , Issue.42 , pp. 14719-113735
    • Xia, T.1    SantaLucia, J.J.2    Burkard, M.E.3    Kierzek, R.4    Schroeder, S.J.5    Jiao, X.6    Cox, C.7    Turner, D.H.8
  • 25
    • 0001947129 scopus 로고
    • Combinatorics of RNA hairpins and cloverleaves
    • Waterman MS. Combinatorics of RNA hairpins and cloverleaves. Stud Appl Math 1979, 60:91-96.
    • (1979) Stud Appl Math , vol.60 , pp. 91-96
    • Waterman, M.S.1
  • 26
    • 84968520263 scopus 로고
    • The number of finite topologies
    • D Kleitman BR. The number of finite topologies. Proc Amer Math Soc 1970, 25:276-282.
    • (1970) Proc Amer Math Soc , vol.25 , pp. 276-282
    • D Kleitman, B.R.1
  • 27
    • 38049010529 scopus 로고    scopus 로고
    • Combinatorics of RNA structures with pseudoknots
    • 10.1007/s11538-007-9240-y, 17896159
    • Jin EY, Qin J, Reidys CM. Combinatorics of RNA structures with pseudoknots. Bull Math Biol 2008, 70:45-67. 10.1007/s11538-007-9240-y, 17896159.
    • (2008) Bull Math Biol , vol.70 , pp. 45-67
    • Jin, E.Y.1    Qin, J.2    Reidys, C.M.3
  • 28
    • 58549116688 scopus 로고    scopus 로고
    • Combinatorial Design of Pseudoknot RNA
    • Jin EY, Reidys CM. Combinatorial Design of Pseudoknot RNA. Adv Appl Math 2009, 42(2):135-151.
    • (2009) Adv Appl Math , vol.42 , Issue.2 , pp. 135-151
    • Jin, E.Y.1    Reidys, C.M.2
  • 29
    • 76049085900 scopus 로고    scopus 로고
    • Random k-noncrossing RNA Structures
    • 10.1073/pnas.0907269106, 2799732, 20018731
    • Chen WYC, Han HSW, Reidys CM. Random k-noncrossing RNA Structures. Proc Natl Acad Sci USA 2009, 106(52):22061-22066. 10.1073/pnas.0907269106, 2799732, 20018731.
    • (2009) Proc Natl Acad Sci USA , vol.106 , Issue.52 , pp. 22061-22066
    • Chen, W.Y.C.1    Han, H.S.W.2    Reidys, C.M.3
  • 30
    • 0033032887 scopus 로고    scopus 로고
    • RNA Structures with Pseudo-Knots
    • 10.1006/bulm.1998.0085, 17883226
    • Stadler PF. RNA Structures with Pseudo-Knots. Bull Math Biol 1999, 61:437-467. 10.1006/bulm.1998.0085, 17883226.
    • (1999) Bull Math Biol , vol.61 , pp. 437-467
    • Stadler, P.F.1
  • 31
    • 57149114106 scopus 로고    scopus 로고
    • Canonical RNA Pseudoknot Structures
    • 10.1089/cmb.2008.0121, 19040363
    • Ma G, Reidys CM. Canonical RNA Pseudoknot Structures. J Comput Biol 2008, 15(10):1257-1273. 10.1089/cmb.2008.0121, 19040363.
    • (2008) J Comput Biol , vol.15 , Issue.10 , pp. 1257-1273
    • Ma, G.1    Reidys, C.M.2
  • 32
    • 46849100443 scopus 로고    scopus 로고
    • Statistics of canonical RNA pseudoknot structures
    • 10.1016/j.jtbi.2008.04.002, 18511081
    • Huang FWD, Reidys CM. Statistics of canonical RNA pseudoknot structures. J Theor Biol 2008, 253(3):570-578. 10.1016/j.jtbi.2008.04.002, 18511081.
    • (2008) J Theor Biol , vol.253 , Issue.3 , pp. 570-578
    • Huang, F.W.D.1    Reidys, C.M.2
  • 33
    • 0031105866 scopus 로고    scopus 로고
    • Generic properties of combinatory maps: neutral networks of RNA secondary structures
    • 10.1007/BF02462007, 9116604
    • Reidys CM, Stadler PF, Schuster P. Generic properties of combinatory maps: neutral networks of RNA secondary structures. Bull Math Biol 1997, 59(2):339-397. 10.1007/BF02462007, 9116604.
    • (1997) Bull Math Biol , vol.59 , Issue.2 , pp. 339-397
    • Reidys, C.M.1    Stadler, P.F.2    Schuster, P.3
  • 34
    • 58349085338 scopus 로고    scopus 로고
    • Local connectivity of neutral networks
    • 10.1007/s11538-008-9356-8, 19115073
    • Reidys CM. Local connectivity of neutral networks. Bull Math Biol 2008, 71(2):265-290. 10.1007/s11538-008-9356-8, 19115073.
    • (2008) Bull Math Biol , vol.71 , Issue.2 , pp. 265-290
    • Reidys, C.M.1
  • 36
    • 0842268067 scopus 로고    scopus 로고
    • A New Algorithm for RNA Secondary Structure Design
    • 10.1016/j.jmb.2003.12.041, 15095976
    • Andronescu M, Fejes AP, Hutter F, Hoos HH, A C. A New Algorithm for RNA Secondary Structure Design. J Mol Biol 2004, 336(2):607-624. 10.1016/j.jmb.2003.12.041, 15095976.
    • (2004) J Mol Biol , vol.336 , Issue.2 , pp. 607-624
    • Andronescu, M.1    Fejes, A.P.2    Hutter, F.3    Hoos, H.H.4    A, C.5
  • 37
    • 33747840719 scopus 로고    scopus 로고
    • INFO-RNA--a fast approach to inverse RNA folding
    • 10.1093/bioinformatics/btl194, 16709587
    • Busch A, Backofen R. INFO-RNA--a fast approach to inverse RNA folding. Bioinformatics 2006, 22(15):1823-1831. 10.1093/bioinformatics/btl194, 16709587.
    • (2006) Bioinformatics , vol.22 , Issue.15 , pp. 1823-1831
    • Busch, A.1    Backofen, R.2
  • 38
    • 38049046550 scopus 로고    scopus 로고
    • Central and local limit theorems for RNA structures
    • Jin EY, Reidys CM. Central and local limit theorems for RNA structures. J Theor Biol 2008, 253(3):547-559.
    • (2008) J Theor Biol , vol.253 , Issue.3 , pp. 547-559
    • Jin, E.Y.1    Reidys, C.M.2
  • 39
    • 77955170923 scopus 로고    scopus 로고
    • PseudoBase
    • PseudoBase. , http://www.ekevanbatenburg.nl/PKBASE/PKBGETCLS.HTML
  • 40
    • 77955172093 scopus 로고    scopus 로고
    • The pseudoknot structure of the glmS ribozyme pseudoknot P1.1
    • The pseudoknot structure of the glmS ribozyme pseudoknot P1.1. , http://www.ekevanbatenburg.nl/PKBASE/PKB00276.HTML
  • 41
    • 77955174856 scopus 로고    scopus 로고
    • Pseudoknot PKI of the internal ribosomal entry site (IRES) region
    • Pseudoknot PKI of the internal ribosomal entry site (IRES) region. , http://www.ekevanbatenburg.nl/PKBASE/PKB00221.HTML
  • 42
    • 77955176029 scopus 로고    scopus 로고
    • The pseudoknot of SELEX-isolated inhibitor (ligand 70.28) of HIV-1 reverse transcriptase
    • The pseudoknot of SELEX-isolated inhibitor (ligand 70.28) of HIV-1 reverse transcriptase. , http://www.ekevanbatenburg.nl/PKBASE/PKB00066.HTML
  • 43
    • 77955174494 scopus 로고    scopus 로고
    • Pseudoknot PK2 of E.coli tmRNA
    • Pseudoknot PK2 of E.coli tmRNA. , http://www.ekevanbatenburg.nl/PKBASE/PKB00050.HTML
  • 44
    • 77955176096 scopus 로고    scopus 로고
    • Pineapple mealybug wilt associated virus - 2
    • Pineapple mealybug wilt associated virus - 2. , http://www.ekevanbatenburg.nl/PKBASE/PKB00270.HTML


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