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Volumn 11, Issue 2, 2013, Pages

RNAiFOLD: A constraint programming algorithm for rna inverse folding and molecular design

Author keywords

Computational biology; RNA inverse folding; RNA molecular design; synthetic biology

Indexed keywords

RNA; RIBOSWITCH;

EID: 84874358604     PISSN: 02197200     EISSN: 17576334     Source Type: Journal    
DOI: 10.1142/S0219720013500017     Document Type: Article
Times cited : (80)

References (67)
  • 1
    • 77952679687 scopus 로고    scopus 로고
    • Genetic control of mammalian T-cell proliferationwith synthetic RNA regulatory systems
    • Chen YY, Jensen MC, Smolke CD, Genetic control of mammalian T-cell proliferationwith synthetic RNA regulatory systems, Proc Natl Acad Sci USA 107(19):8531-8536, 2010.
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.19 , pp. 8531-8536
    • Chen, Y.Y.1    Jensen, M.C.2    Smolke, C.D.3
  • 2
    • 45149118469 scopus 로고    scopus 로고
    • Engineering BioBrick vectors from BioBrick parts
    • Shetty RP, Endy D, Knight TF, Jr. Engineering BioBrick vectors from BioBrick parts, J Biol Eng 2(1):5, 2008.
    • (2008) J Biol Eng , vol.2 , Issue.1 , pp. 5
    • Shetty, R.P.1    Endy, D.2    Knight Jr., T.F.3
  • 3
    • 84945709924 scopus 로고
    • On the approximation of curves by line segments using dynamic programming
    • Bellman R, On the approximation of curves by line segments using dynamic programming, Commun ACM 4(6):284, 1961.
    • (1961) Commun ACM , vol.4 , Issue.6 , pp. 284
    • Bellman, R.1
  • 5
    • 0032831634 scopus 로고    scopus 로고
    • Relationship between internucleotide linkage geometry and the stability of RNA
    • Soukup GA, Breaker RR, Relationship between internucleotide linkage geometry and the stability of RNA, RNA 5:1308-1325, 1999.
    • (1999) RNA , vol.5 , pp. 1308-1325
    • Soukup, G.A.1    Breaker, R.R.2
  • 8
    • 34249278470 scopus 로고    scopus 로고
    • Control of alternative RNA splicing and gene expression by eukaryotic riboswitches
    • Cheah MT, Wachter A, Sudarsan N, Breaker RR, Control of alternative RNA splicing and gene expression by eukaryotic riboswitches, Nature 447(7143):497-500, 2007.
    • (2007) Nature , vol.447 , Issue.7143 , pp. 497-500
    • Cheah, M.T.1    Wachter, A.2    Sudarsan, N.3    Breaker, R.R.4
  • 10
    • 0038210214 scopus 로고    scopus 로고
    • Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria
    • Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR, Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria, Cell 113(5):577-586, 2003.
    • (2003) Cell , vol.113 , Issue.5 , pp. 577-586
    • Mandal, M.1    Boese, B.2    Barrick, J.E.3    Winkler, W.C.4    Breaker, R.R.5
  • 11
    • 34548712632 scopus 로고    scopus 로고
    • Searching genomes for ribozymes and riboswitches
    • Hammann C, Westhof E, Searching genomes for ribozymes and riboswitches, Genome Biol 8:210, 2007.
    • (2007) Genome Biol , vol.8 , pp. 210
    • Hammann, C.1    Westhof, E.2
  • 12
    • 0037062949 scopus 로고    scopus 로고
    • The chemical repertoire of natural ribozymes
    • Doudna JA, Cech TR, The chemical repertoire of natural ribozymes, Nature 418(6894):222-228, 2002.
    • (2002) Nature , vol.418 , Issue.6894 , pp. 222-228
    • Doudna, J.A.1    Cech, T.R.2
  • 13
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • Hofacker IL, Vienna RNA secondary structure server, Nucleic Acid Res 31:3429-3431, 2003.
    • (2003) Nucleic Acid Res , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 14
    • 84934438960 scopus 로고    scopus 로고
    • UNAFold: Software for nucleic acid folding and hybridization
    • Markham NR, Zuker M, UNAFold: Software for nucleic acid folding and hybridization, Meth Mol Biol 453:3-31, 2008.
    • (2008) Meth Mol Biol , vol.453 , pp. 3-31
    • Markham, N.R.1    Zuker, M.2
  • 15
    • 2442626706 scopus 로고    scopus 로고
    • Incorporating chemical modication constraints into a dynamic programming algorithm forprediction of rna secondary structure
    • Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH, Incorporating chemical modication constraints into a dynamic programming algorithm forprediction of RNA secondary structure, Proc Natl Acad Sci USA 101:7287-7292, 2004.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 7287-7292
    • Mathews, D.H.1    Disney, M.D.2    Childs, J.L.3    Schroeder, S.J.4    Zuker, M.5    Turner, D.H.6
  • 17
    • 42749097747 scopus 로고    scopus 로고
    • Darn a weighted constraint solver for RNA motif localization
    • Zytnicki M, Gaspin C, Schiex T, Darn a weighted constraint solver for RNA motif localization, Constraints 13:91-109, 2008.
    • (2008) Constraints , vol.13 , pp. 91-109
    • Zytnicki, M.1    Gaspin, C.2    Schiex, T.3
  • 18
    • 0030812919 scopus 로고    scopus 로고
    • Finding the most signicant common sequence and structure motifs in a set of RNA sequences
    • Gorodkin J, Heyer LJ, Stormo GD, Finding the most signicant common sequence and structure motifs in a set of RNA sequences, Nucleic Acid Res 25(18):3724-3732, 1997.
    • (1997) Nucleic Acid Res , vol.25 , Issue.18 , pp. 3724-3732
    • Gorodkin, J.1    Heyer, L.J.2    Stormo, G.D.3
  • 19
    • 0036295198 scopus 로고    scopus 로고
    • Dynalign: An algorithm for nding the secondary structurecommon to two RNA sequences
    • Mathews DH, Turner DH, Dynalign: An algorithm for nding the secondary structurecommon to two RNA sequences, J Mol Biol 317:191-203, 2002.
    • (2002) J Mol Biol , vol.317 , pp. 191-203
    • Mathews, D.H.1    Turner, D.H.2
  • 20
    • 67649342878 scopus 로고    scopus 로고
    • Computational identi cation of riboswitches based on RNA conserved functional sequences and conformations
    • Chang T-H, Huang H-D, Wu L-C, Yeh C-T, Liu B-J, Horng J-T, Computational identi cation of riboswitches based on RNA conserved functional sequences and conformations, RNA 15(7), 2009.
    • (2009) RNA , vol.15 , Issue.7
    • Chang, T.-H.1    Huang, H.-D.2    Wu, L.-C.3    Yeh, C.-T.4    Liu, B.-J.5    Horng, J.-T.6
  • 21
    • 30344447264 scopus 로고    scopus 로고
    • Classication of real and pseudomicroRNA precursors using local structure-sequence features and support vector machine
    • Xue C, Li F, He T, Liu GP, Li Y, Zhang X, Classication of real and pseudomicroRNA precursors using local structure-sequence features and support vector machine, BMC Bioinformatics 6:310, 2005.
    • (2005) BMC Bioinformatics , vol.6 , pp. 310
    • Xue, C.1    Li, F.2    He, T.3    Liu, G.P.4    Li, Y.5    Zhang, X.6
  • 22
    • 43349108697 scopus 로고    scopus 로고
    • Identifying structural noncoding RNAs using RNAz
    • Washietl S, Hofacker IL, Identifying structural noncoding RNAs using RNAz, Curr Protoc Bioinformatics 19:12.7.1-12.7.18, 2007.
    • (2007) Curr Protoc Bioinformatics , vol.19 , pp. 1271-12718
    • Washietl, S.1    Hofacker, I.L.2
  • 23
    • 77952882024 scopus 로고    scopus 로고
    • Prediction and design of DNA and RNA structures
    • Andersen ES, Prediction and design of DNA and RNA structures, Nat Biotechnol 27(3):184-193, 2010.
    • (2010) Nat Biotechnol , vol.27 , Issue.3 , pp. 184-193
    • Andersen, E.S.1
  • 24
    • 78650488774 scopus 로고    scopus 로고
    • Nucleic acid sequence design via Effiient ensemble defect optimization
    • Zadeh JN, Wolfe BR, Pierce NA, Nucleic acid sequence design via Effiient ensemble defect optimization, J Comput Chem 32(3):439-452, 2011.
    • (2011) J Comput Chem , vol.32 , Issue.3 , pp. 439-452
    • Zadeh, J.N.1    Wolfe, B.R.2    Pierce, N.A.3
  • 25
    • 0015859467 scopus 로고
    • Principles that govern the folding of protein chains
    • Annsen CB, Principles that govern the folding of protein chains, Science 181:223-230, 1973.
    • (1973) Science , vol.181 , pp. 223-230
    • Annsen, C.B.1
  • 27
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker M, Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acid Res 31(13):3406-3415, 2003.
    • (2003) Nucleic Acid Res , vol.31 , Issue.13 , pp. 3406-3415
    • Zuker, M.1
  • 28
    • 0019876473 scopus 로고
    • Optimal computer folding of large RNA sequences usingthermodynamics and auxiliary information
    • Zuker M, Stiegler P, Optimal computer folding of large RNA sequences usingthermodynamics and auxiliary information, Nucleic Acids Res 9:133-148, 1981.
    • (1981) Nucleic Acids Res , vol.9 , pp. 133-148
    • Zuker, M.1    Stiegler, P.2
  • 29
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews DH, Sabina J, Zuker M, Turner DH, Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure, J Mol Biol 288:911-940, 1999.
    • (1999) J Mol Biol , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 30
    • 0032552882 scopus 로고    scopus 로고
    • Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs
    • Xia T, SantaLucia J, Jr., 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 37:14719-14735, 1999.
    • (1999) Biochemistry , vol.37 , pp. 14719-14735
    • Xia, T.1    SantaLucia Jr., J.2    Burkard, M.E.3    Kierzek, R.4    Schroeder, S.J.5    Jiao, X.6    Cox, C.7    Turner, D.H.8
  • 31
    • 0033709625 scopus 로고    scopus 로고
    • RNA pseudoknot prediction in energy-based models
    • Lyngso RB, Pedersen CN, RNA pseudoknot prediction in energy-based models, J Comput Biol 7(3-4):409-427, 2000.
    • (2000) J Comput Biol , vol.7 , Issue.3-4 , pp. 409-427
    • Lyngso, R.B.1    Pedersen, C.N.2
  • 32
    • 0027434244 scopus 로고
    • Thermal unfolding of a group i ribozyme: The lowtemperature transition is primarily disruption of tertiary structure
    • Banerjee AR, Jaeger JA, Turner DH, Thermal unfolding of a group I ribozyme: The lowtemperature transition is primarily disruption of tertiary structure Biochemistry 32:153-163, 1993.
    • (1993) Biochemistry , vol.32 , pp. 153-163
    • Banerjee, A.R.1    Jaeger, J.A.2    Turner, D.H.3
  • 33
    • 74249115345 scopus 로고    scopus 로고
    • Topology links RNA secondary structure with global conformation
    • Bailor MH, Sun X, Al-Hashimi HM, Topology links RNA secondary structure with global conformation, dynamics, and adaptation, Science 327(5962):202-206, 2010.
    • (2010) Dynamics, and Adaptation, Science , vol.327 , Issue.5962 , pp. 202-206
    • Bailor, M.H.1    Sun, X.2    Al-Hashimi, H.M.3
  • 34
    • 70350462752 scopus 로고    scopus 로고
    • Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures
    • Cho SS, Pincus DL, Thirumalai D, Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures, Proc Natl Acad Sci USA 106(41):17349-17354, 2009.
    • (2009) Proc Natl Acad Sci USA , vol.106 , Issue.41 , pp. 17349-17354
    • Cho, S.S.1    Pincus, D.L.2    Thirumalai, D.3
  • 35
    • 16344370497 scopus 로고    scopus 로고
    • RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNAAsp
    • Wilkinson KA, Merino EJ, Weeks KM, RNA SHAPE chemistry reveals nonhierarchical interactions dominate equilibrium structural transitions in tRNAAsp. J Am Chem Soc 127:4659-4667, 2005.
    • (2005) J Am Chem Soc , vol.127 , pp. 4659-4667
    • Wilkinson, K.A.1    Merino, E.J.2    Weeks, K.M.3
  • 36
    • 0032578472 scopus 로고    scopus 로고
    • RNA folding causes secondary structure rearrangement
    • Wu M, Tinoco I, Jr. RNA folding causes secondary structure rearrangement, PNAS 95(20):11555-11560, 1998.
    • (1998) PNAS , vol.95 , Issue.20 , pp. 11555-11560
    • Wu, M.1    Tinoco Jr., I.2
  • 39
    • 33747840719 scopus 로고    scopus 로고
    • Info-rna, a fast approach to inverse rna folding
    • Busch A, Backofen R, Info-rna, a fast approach to inverse RNA folding, Bioinformatics 22(15):1823-1831, 2006.
    • (2006) Bioinformatics , vol.22 , Issue.15 , pp. 1823-1831
    • Busch, A.1    Backofen, R.2
  • 40
    • 79961002039 scopus 로고    scopus 로고
    • MODENA: A multi-objective RNA inverse folding
    • Taneda A, MODENA: A multi-objective RNA inverse folding, Adv Appl Bioinform Chem 4:1-12, 2011.
    • (2011) Adv Appl Bioinform Chem , vol.4 , pp. 1-12
    • Taneda, A.1
  • 41
  • 44
    • 2542514671 scopus 로고    scopus 로고
    • Paradigms for computational nucleic acid design
    • Dirks RM, Lin M, Winfree E, Pierce NA, Paradigms for computational nucleic acid design, Nucleic Acid Res 32(4):1392-1403, 2004.
    • (2004) Nucleic Acid Res , vol.32 , Issue.4 , pp. 1392-1403
    • Dirks, R.M.1    Lin, M.2    Winfree, E.3    Pierce, N.A.4
  • 45
    • 77952299709 scopus 로고    scopus 로고
    • Folding 3-noncrossing RNA pseudoknot structures
    • Huang FW, Peng WW, Reidys CM, Folding 3-noncrossing RNA pseudoknot structures, J Comput Biol 16(11):1549-1575, 2009.
    • (2009) J Comput Biol , vol.16 , Issue.11 , pp. 1549-1575
    • Huang, F.W.1    Peng, W.W.2    Reidys, C.M.3
  • 46
    • 84944488447 scopus 로고
    • Intermodulation interference in radio systems/frequency of occurrence and control by channel selection
    • Babcock WC, Intermodulation interference in radio systems/frequency of occurrence and control by channel selection, Bell System Tech J 31:63-73, 1953.
    • (1953) Bell System Tech J , vol.31 , pp. 63-73
    • Babcock, W.C.1
  • 47
    • 34250956546 scopus 로고
    • Ein Satz über trigonometrische Polynome und seine Anwendungen in der Theorie der Fourier-Reihen
    • Sidon S, Ein Satz über trigonometrische Polynome und seine Anwendungen in der Theorie der Fourier-Reihen, Mathematische Annalen 106:536-539, 1932.
    • (1932) Mathematische Annalen , vol.106 , pp. 536-539
    • Sidon, S.1
  • 48
    • 67650727366 scopus 로고    scopus 로고
    • VARNA: Interactive drawing and editing of the RNA secondary structure
    • Darty K, Denise A, Ponty Y, VARNA: Interactive drawing and editing of the RNA secondary structure, Bioinformatics 25(15):1974-1975, 2009.
    • (2009) Bioinformatics , vol.25 , Issue.15 , pp. 1974-1975
    • Darty, K.1    Denise, A.2    Ponty, Y.3
  • 51
    • 0025264854 scopus 로고
    • The equilibrium partition function and base pair binding probabilities for RNA secondary structure
    • McCaskill JS, The equilibrium partition function and base pair binding probabilities for RNA secondary structure, Biopolymers 29:1105-1119, 1990.
    • (1990) Biopolymers , vol.29 , pp. 1105-1119
    • McCaskill, J.S.1
  • 52
    • 0024477261 scopus 로고
    • On nding all suboptimal foldings of an RNA molecule
    • Zuker M, On nding all suboptimal foldings of an RNA molecule, Science 244(4900):48-52, 1989.
    • (1989) Science , vol.244 , Issue.4900 , pp. 48-52
    • Zuker, M.1
  • 53
    • 0032502487 scopus 로고    scopus 로고
    • Barrier heights between ground states in a model of RNA secondary structure
    • Morgan SR, Higgs PG, Barrier heights between ground states in a model of RNA secondary structure, J Phys A: Math Gen 31:3153-3170, 1998.
    • (1998) J Phys A: Math Gen , vol.31 , pp. 3153-3170
    • Morgan, S.R.1    Higgs, P.G.2
  • 54
    • 79551535532 scopus 로고    scopus 로고
    • Computing the partition function for kinetically trapped RNA secondary structures
    • Lorenz WA, Clote P, Computing the partition function for kinetically trapped RNA secondary structures, PLoS One 6(1):e16178, 2011.
    • (2011) PLoS One , vol.6 , Issue.1
    • Lorenz, W.A.1    Clote, P.2
  • 55
    • 0031576996 scopus 로고    scopus 로고
    • Assessing the reliability of RNA folding using statistical mechanics
    • Huynen M, Gutell R, Konings D, Assessing the reliability of RNA folding using statistical mechanics, J Mol Biol 267:1104-1112, 1997.
    • (1997) J Mol Biol , vol.267 , pp. 1104-1112
    • Huynen, M.1    Gutell, R.2    Konings, D.3
  • 56
    • 34548454557 scopus 로고    scopus 로고
    • Structural features of metabolite-sensing riboswitches
    • Wakeman CA, Winkler WC, Dann CE, Structural features of metabolite-sensing riboswitches, Trends Biochem Sci 32(9):415-424, 2007.
    • (2007) Trends Biochem Sci , vol.32 , Issue.9 , pp. 415-424
    • Wakeman, C.A.1    Winkler, W.C.2    Dann, C.E.3
  • 57
    • 77950494855 scopus 로고    scopus 로고
    • Computing folding pathways between RNA secondary structures
    • Dotu I, Lorenz WA, Van Hentenryck P, Clote P, Computing folding pathways between RNA secondary structures, Nucleic Acid Res 38(5):1711-1722, 2010.
    • (2010) Nucleic Acid Res , vol.38 , Issue.5 , pp. 1711-1722
    • Dotu, I.1    Lorenz, W.A.2    Van Hentenryck, P.3    Clote, P.4
  • 58
    • 0034708334 scopus 로고    scopus 로고
    • Structure and function of the hairpin ribozyme
    • Fedor MJ, Structure and function of the hairpin ribozyme, J Mol Biol 297(2):269-291, 2000.
    • (2000) J Mol Biol , vol.297 , Issue.2 , pp. 269-291
    • Fedor, M.J.1
  • 61
    • 0035869008 scopus 로고    scopus 로고
    • Structure folding, and activity of the vs ribozyme: Importance of the 2-3-6 helical junction
    • Lafontaine D, Norman D, Lilley D, Structure, folding, and activity of the vs ribozyme: Importance of the 2-3-6 helical junction, EMBO J 20(6):1415-1424, 2001.
    • (2001) EMBO J , vol.20 , Issue.6 , pp. 1415-1424
    • Lafontaine, D.1    Norman, D.2    Lilley, D.3
  • 62
    • 0036015843 scopus 로고    scopus 로고
    • A selected ribozyme catalysing diverse dipeptide synthesis
    • Sun ZCL, Gottlieb R, Zhang B, A selected ribozyme catalysing diverse dipeptide synthesis, Chem Biol 9:619-628, 2002.
    • (2002) Chem Biol , vol.9 , pp. 619-628
    • Sun, Z.C.L.1    Gottlieb, R.2    Zhang, B.3
  • 63
    • 0033230172 scopus 로고    scopus 로고
    • Design and isolation of ribozyme-substrate pairs using RNase P-based ribozymes containing altered substrate binding sites
    • Mobley E, Pan T, Design and isolation of ribozyme-substrate pairs using RNase P-based ribozymes containing altered substrate binding sites, Nucleic Acids Res 27(21):4298-4304, 1999.
    • (1999) Nucleic Acids Res , vol.27 , Issue.21 , pp. 4298-4304
    • Mobley, E.1    Pan, T.2
  • 64
    • 0032527813 scopus 로고    scopus 로고
    • Comparative structure analysis of vertebrate ribonuclease P RNA
    • Pitulle C, Garcia-Paris M, Zamudio KR, Pace NR, Comparative structure analysis of vertebrate ribonuclease P RNA, Nucleic Acids Res 26(14):3333-3339, 1998.
    • (1998) Nucleic Acids Res , vol.26 , Issue.14 , pp. 3333-3339
    • Pitulle, C.1    Garcia-Paris, M.2    Zamudio, K.R.3    Pace, N.R.4
  • 65
    • 0026557264 scopus 로고
    • Secondary structure of the mRNA for ribosomal protein S20. Implications for cleavage by ribonuclease e
    • Mackie G, Secondary structure of the mRNA for ribosomal protein S20. Implications for cleavage by ribonuclease E, J Biol Chem 267:1054-1061, 1992.
    • (1992) J Biol Chem , vol.267 , pp. 1054-1061
    • MacKie, G.1
  • 66
    • 0029930931 scopus 로고    scopus 로고
    • Comparative analysis of ribonuclease P RNA structure in Archaea
    • Haas E, Armbruster D, Vucson B, Daniels C, Brown J, Comparative analysis of ribonuclease P RNA structure in Archaea, Nucleic Acids Res 24(7):1252-1259, 1996.
    • (1996) Nucleic Acids Res , vol.24 , Issue.7 , pp. 1252-1259
    • Haas, E.1    Armbruster, D.2    Vucson, B.3    Daniels, C.4    Brown, J.5
  • 67
    • 0035901549 scopus 로고    scopus 로고
    • Visualizing the solvent-inaccessible core of a group II intron ribozyme
    • Swisher J, Duartel C, Sul L, Pyle A, Visualizing the solvent-inaccessible core of a group II intron ribozyme, EMBO J 20(8):2051-2061, 2001.
    • (2001) EMBO J , vol.20 , Issue.8 , pp. 2051-2061
    • Swisher, J.1    Duartel, C.2    Sul, L.3    Pyle, A.4


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