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Volumn 11, Issue 7, 2014, Pages 891-905

Re-analysis of cryoEM data on HCV IRES bound to 40S subunit of human ribosome integrated with recent structural information suggests new contact regions between ribosomal proteins and HCV RNA

Author keywords

Cryo electron microscopy; Hepatitis C; Protein modeling; RNA Protein interactions

Indexed keywords

40S RIBOSOME PROTEIN; RIBOSOME PROTEIN; RIBOSOME PROTEIN S26; RIBOSOME PROTEIN S27; RIBOSOME PROTEIN S28; RIBOSOME PROTEIN S5; UNCLASSIFIED DRUG; VIRUS RNA;

EID: 84907512377     PISSN: 15476286     EISSN: 15558584     Source Type: Journal    
DOI: 10.4161/rna.29545     Document Type: Article
Times cited : (13)

References (98)
  • 1
    • 0033600934 scopus 로고    scopus 로고
    • The hepatitis C virus internal ribosome entry site adopts an ion-dependent tertiary fold
    • PMID:10497018
    • KieftJS, ZhouK, JubinR, MurrayMG, LauJY, DoudnaJA.The hepatitis C virus internal ribosome entry site adopts an ion-dependent tertiary fold.J MolBiol1999; 292:513-29; PMID:10497018; http://dx.doi.org/10.1006/jmbi.1999.3095
    • (1999) J MolBiol , vol.292 , pp. 513-529
    • Kieft, J.S.1    Zhou, K.2    Jubin, R.3    Murray, M.G.4    Lau, J.Y.5    Doudna, J.A.6
  • 2
    • 33646186734 scopus 로고    scopus 로고
    • Initiation factor-independent translation mediated by the hepatitis C virus internal ribosome entry site
    • PMID:16556939
    • LancasterAM, JanE, SarnowP. Initiation factor-independent translation mediated by the hepatitis C virus internal ribosome entry site.RNA2006; 12:894-902; PMID:16556939; http://dx.doi.org/10.1261/rna.2342306
    • (2006) RNA , vol.12 , pp. 894-902
    • Lancaster, A.M.1    Jan, E.2    Sarnow, P.3
  • 3
    • 0031905698 scopus 로고    scopus 로고
    • A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal translation initiation of hepatitis C and classical swine fever virus RNAs
    • PMID:9420332
    • PestovaTV, ShatskyIN, FletcherSP, JacksonRJ, HellenCU. A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal translation initiation of hepatitis C and classical swine fever virus RNAs.Genes Dev1998; 12:67-83; PMID:9420332; http://dx.doi.org/10.1101/gad.12.1.67
    • (1998) Genes Dev , vol.12 , pp. 67-83
    • Pestova, T.V.1    Shatsky, I.N.2    Fletcher, S.P.3    Jackson, R.J.4    Hellen, C.U.5
  • 4
    • 0035831269 scopus 로고    scopus 로고
    • Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit
    • PMID:11239155
    • SpahnCM, KieftJS, GrassucciRA, PenczekPA, ZhouK, DoudnaJA, FrankJ. Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit.Science2001; 291:1959-62; PMID:11239155; http://dx.doi.org/10.1126/science.1058409
    • (2001) Science , vol.291 , pp. 1959-1962
    • Spahn, C.M.1    Kieft, J.S.2    Grassucci, R.A.3    Penczek, P.A.4    Zhou, K.5    Doudna, J.A.6    Frank, J.7
  • 5
    • 7044228006 scopus 로고    scopus 로고
    • The pathway of HCV IRES-mediated translation initiation
    • PMID:15507208
    • OttoGA, PuglisiJD. The pathway of HCV IRES-mediated translation initiation.Cell2004; 119:369-80; PMID:15507208; http://dx.doi.org/10.1016/j.cell.2004.09.038
    • (2004) Cell , vol.119 , pp. 369-380
    • Otto, G.A.1    Puglisi, J.D.2
  • 6
    • 33845623845 scopus 로고    scopus 로고
    • Structural and mechanistic insights into hepatitis C viral translation initiation
    • PMID:17128284
    • FraserCS, DoudnaJA. Structural and mechanistic insights into hepatitis C viral translation initiation. Nat Rev Microbiol2007; 5:29-38; PMID:17128284; http://dx.doi.org/10.1038/nrmicro1558
    • (2007) Nat Rev Microbiol , vol.5 , pp. 29-38
    • Fraser, C.S.1    Doudna, J.A.2
  • 7
    • 84866001193 scopus 로고    scopus 로고
    • Eukaryotic initiation factor 5B: A new player for the anti-hepatitis C virus effect of ribavirin?
    • PMID:22824093
    • GalmozziE, AghemoA, ColomboM. Eukaryotic initiation factor 5B: a new player for the anti-hepatitis C virus effect of ribavirin?Med Hypotheses2012; 79:471-3; PMID:22824093; http://dx.doi.org/10.1016/j.mehy.2012.06.026
    • (2012) Med Hypotheses , vol.79 , pp. 471-473
    • Galmozzi, E.1    Aghemo, A.2    Colombo, M.3
  • 8
    • 49449093122 scopus 로고    scopus 로고
    • Eukaryotic translation initiation machinery can operate in a bacterial-like mode without eIF2
    • PMID:18604219
    • TereninIM, DmitrievSE, AndreevDE, ShatskyIN. Eukaryotic translation initiation machinery can operate in a bacterial-like mode without eIF2.Nat StructMolBiol2008; 15:836-41; PMID:18604219; http://dx.doi.org/10.1038/nsmb.1445
    • (2008) Nat StructMolBiol , vol.15 , pp. 836-841
    • Terenin, I.M.1    Dmitriev, S.E.2    Andreev, D.E.3    Shatsky, I.N.4
  • 9
    • 84855863141 scopus 로고    scopus 로고
    • IRES-mediated translation of cellular messenger RNA operates in eIF2α-independent manner during stress
    • PMID:21917851
    • ThakorN, HolcikM. IRES-mediated translation of cellular messenger RNA operates in eIF2α-independent manner during stress.Nucleic Acids Res2012; 40:541-52; PMID:21917851; http://dx.doi.org/10.1093/nar/gkr701
    • (2012) Nucleic Acids Res , vol.40 , pp. 541-552
    • Thakor, N.1    Holcik, M.2
  • 10
    • 13944271964 scopus 로고    scopus 로고
    • Position of the CrPV IRES on the 40S subunit and factor dependence of IRES/80S ribosome assembly
    • PMID:15332113
    • PestovaTV, LomakinIB, HellenCU. Position of the CrPV IRES on the 40S subunit and factor dependence of IRES/80S ribosome assembly.EMBO Rep2004; 5:906-13; PMID:15332113; http://dx.doi.org/10.1038/sj.embor.7400240
    • (2004) EMBO Rep , vol.5 , pp. 906-913
    • Pestova, T.V.1    Lomakin, I.B.2    Hellen, C.U.3
  • 12
    • 0037369073 scopus 로고    scopus 로고
    • Viral internal ribosome entry site elements: Novel ribosome-RNA complexes and roles in viral pathogenesis
    • PMID:12584303
    • SarnowP. Viral internal ribosome entry site elements: novel ribosome-RNA complexes and roles in viral pathogenesis.J Virol2003; 77:2801-6; PMID:12584303; http://dx.doi.org/10.1128/JVI.77.5.2801-2806.2003
    • (2003) J Virol , vol.77 , pp. 2801-2806
    • Sarnow, P.1
  • 14
    • 3042666265 scopus 로고    scopus 로고
    • Inhibition of hepatitis C virus IRES-mediated translation by small RNAs analogous to stem-loop structures of the 5′-untranslated region
    • PMID:15020704
    • RayPS, DasS. Inhibition of hepatitis C virus IRES-mediated translation by small RNAs analogous to stem-loop structures of the 5′-untranslated region.Nucleic Acids Res2004; 32:1678-87; PMID:15020704; http://dx.doi.org/10.1093/nar/gkh328
    • (2004) Nucleic Acids Res , vol.32 , pp. 1678-1687
    • Ray, P.S.1    Das, S.2
  • 15
    • 0031779191 scopus 로고    scopus 로고
    • A small yeast RNA blocks hepatitis C virus internal ribosome entry site (HCV IRES)-mediated translation and inhibits replication of a chimeric poliovirus under translational control of the HCV IRES element
    • PMID:9621022
    • DasS, OttM, YamaneA, TsaiW, GromeierM, LahserF, GuptaS, DasguptaA. A small yeast RNA blocks hepatitis C virus internal ribosome entry site (HCV IRES)-mediated translation and inhibits replication of a chimeric poliovirus under translational control of the HCV IRES element.J Virol1998; 72:5638-47; PMID:9621022
    • (1998) J Virol , vol.72 , pp. 5638-5647
    • Das, S.1    Ott, M.2    Yamane, A.3    Tsai, W.4    Gromeier, M.5    Lahser, F.6    Gupta, S.7    Dasgupta, A.8
  • 16
    • 69449093055 scopus 로고    scopus 로고
    • Targeted delivery of hepatitis C virus-specific short hairpin RNA in mouse liver using Sendai virosomes
    • PMID:19297606
    • SubramanianN, ManiP, RoyS, GnanasundramSV, SarkarDP, DasS. Targeted delivery of hepatitis C virus-specific short hairpin RNA in mouse liver using Sendai virosomes.J Gen Virol2009; 90:1812-9; PMID:19297606; http://dx.doi.org/10.1099/vir.0.010579-0
    • (2009) J Gen Virol , vol.90 , pp. 1812-1819
    • Subramanian, N.1    Mani, P.2    Roy, S.3    Gnanasundram, S.V.4    Sarkar, D.P.5    Das, S.6
  • 17
    • 0029972264 scopus 로고    scopus 로고
    • A potential therapeutic application of hairpin ribozymes: In vitro and in vivo studies of gene therapy for hepatitis C virus infection
    • PMID:9044745
    • WelchPJ, TritzR, YeiS, LeavittM, YuM, BarberJ. A potential therapeutic application of hairpin ribozymes: in vitro and in vivo studies of gene therapy for hepatitis C virus infection.Gene Ther1996; 3:994-1001; PMID:9044745
    • (1996) Gene Ther , vol.3 , pp. 994-1001
    • Welch, P.J.1    Tritz, R.2    Yei, S.3    Leavitt, M.4    Yu, M.5    Barber, J.6
  • 18
    • 80054080846 scopus 로고    scopus 로고
    • Crystal structure of the HCV IRES central domain reveals strategy for start-codon positioning
    • PMID:22000514
    • BerryKE, WaghrayS, MortimerSA, BaiY, DoudnaJA. Crystal structure of the HCV IRES central domain reveals strategy for start-codon positioning. Structure2011; 19:1456-66; PMID:22000514; http://dx.doi.org/10.1016/j.str.2011.08.002
    • (2011) Structure , vol.19 , pp. 1456-1466
    • Berry, K.E.1    Waghray, S.2    Mortimer, S.A.3    Bai, Y.4    Doudna, J.A.5
  • 19
    • 0026674719 scopus 로고
    • Secondary structure of the 5′nontranslated regions of hepatitis C virus and pestivirus genomic RNAs
    • PMID:1329037
    • BrownEA, ZhangH, PingLH, LemonSM. Secondary structure of the 5′nontranslated regions of hepatitis C virus and pestivirus genomic RNAs.Nucleic Acids Res1992; 20:5041-5; PMID:1329037; http://dx.doi.org/10.1093/nar/20.19.5041
    • (1992) Nucleic Acids Res , vol.20 , pp. 5041-5045
    • Brown, E.A.1    Zhang, H.2    Ping, L.H.3    Lemon, S.M.4
  • 20
    • 0029949695 scopus 로고    scopus 로고
    • Stability of a stemloop involving the initiator AUG controls the efficiency of internal initiation of translation on hepatitis C virus RNA
    • PMID:8849773
    • HondaM, BrownEA, LemonSM. Stability of a stemloop involving the initiator AUG controls the efficiency of internal initiation of translation on hepatitis C virus RNA.RNA1996; 2:955-68; PMID:8849773
    • (1996) RNA , vol.2 , pp. 955-968
    • Honda, M.1    Brown, E.A.2    Lemon, S.M.3
  • 22
    • 27644484907 scopus 로고    scopus 로고
    • Structure of the hepatitis C virus IRES bound to the human 80S ribosome: Remodeling of the HCV IRES
    • PMID:16271893
    • BoehringerD, ThermannR, Ostareck-LedererA, LewisJD, StarkH. Structure of the hepatitis C virus IRES bound to the human 80S ribosome: remodeling of the HCV IRES.Structure2005; 13:1695-706; PMID:16271893; http://dx.doi.org/10.1016/j.str.2005.08.008
    • (2005) Structure , vol.13 , pp. 1695-1706
    • Boehringer, D.1    Thermann, R.2    Ostareck-Lederer, A.3    Lewis, J.D.4    Stark, H.5
  • 23
    • 0035260658 scopus 로고    scopus 로고
    • Mechanism of ribosome recruitment by hepatitis C IRES RNA
    • PMID:11233977
    • KieftJS, ZhouK, JubinR, DoudnaJA. Mechanism of ribosome recruitment by hepatitis C IRES RNA. RNA2001; 7:194-206; PMID:11233977; http://dx.doi.org/10.1017/S1355838201001790
    • (2001) RNA , vol.7 , pp. 194-206
    • Kieft, J.S.1    Zhou, K.2    Jubin, R.3    Doudna, J.A.4
  • 24
    • 0033673387 scopus 로고    scopus 로고
    • Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function
    • PMID:11101890
    • LukavskyPJ, OttoGA, LancasterAM, SarnowP, PuglisiJD. Structures of two RNA domains essential for hepatitis C virus internal ribosome entry site function.Nat StructBiol2000; 7:1105-10; PMID:11101890; http://dx.doi.org/10.1038/81951
    • (2000) Nat StructBiol , vol.7 , pp. 1105-1110
    • Lukavsky, P.J.1    Otto, G.A.2    Lancaster, A.M.3    Sarnow, P.4    Puglisi, J.D.5
  • 25
    • 0036677165 scopus 로고    scopus 로고
    • Domains on the hepatitis C virus internal ribosome entry site for 40s subunit binding
    • PMID:12212848
    • LytleJR, WuL, RobertsonHD. Domains on the hepatitis C virus internal ribosome entry site for 40s subunit binding.RNA2002; 8:1045-55; PMID:12212848; http://dx.doi.org/10.1017/S1355838202029965
    • (2002) RNA , vol.8 , pp. 1045-1055
    • Lytle, J.R.1    Wu, L.2    Robertson, H.D.3
  • 26
    • 0035834686 scopus 로고    scopus 로고
    • Mutational analysis of the different bulge regions of hepatitis C virus domain II and their influence on internal ribosome entry site translational ability
    • PMID:11498532
    • Odreman-MacchioliF, BaralleFE, BurattiE. Mutational analysis of the different bulge regions of hepatitis C virus domain II and their influence on internal ribosome entry site translational ability.J BiolChem2001; 276:41648-55; PMID:11498532; http://dx.doi.org/10.1074/jbc.M104128200
    • (2001) J BiolChem , vol.276 , pp. 41648-41655
    • Odreman-Macchioli, F.1    Baralle, F.E.2    Buratti, E.3
  • 27
    • 0032782434 scopus 로고    scopus 로고
    • Mutational analysis of a conserved tetraloop in the 5′ untranslated region of hepatitis C virus identifies a novel RNA element essential for the internal ribosome entry site function
    • PMID:10403373
    • PsaridiL, GeorgopoulouU, VarakliotiA, MavromaraP. Mutational analysis of a conserved tetraloop in the 5′ untranslated region of hepatitis C virus identifies a novel RNA element essential for the internal ribosome entry site function.FEBS Lett1999; 453:49-53; PMID:10403373; http://dx.doi.org/10.1016/S0014-5793(99)00662-6
    • (1999) FEBS Lett , vol.453 , pp. 49-53
    • Psaridi, L.1    Georgopoulou, U.2    Varaklioti, A.3    Mavromara, P.4
  • 28
    • 84873570263 scopus 로고    scopus 로고
    • HCV IRES manipulates the ribosome to promote the switch from translation initiation to elongation
    • PMID:23262488
    • FilbinME, VollmarBS, ShiD, GonenT, KieftJS. HCV IRES manipulates the ribosome to promote the switch from translation initiation to elongation.Nat StructMolBiol2013; 20:150-8; PMID:23262488; http://dx.doi.org/10.1038/nsmb.2465
    • (2013) Nat StructMolBiol , vol.20 , pp. 150-158
    • Filbin, M.E.1    Vollmar, B.S.2    Shi, D.3    Gonen, T.4    Kieft, J.S.5
  • 29
    • 0032881293 scopus 로고    scopus 로고
    • Specific interaction of a 25-kilo-dalton cellular protein, a 40S ribosomal subunit protein, with the internal ribosome entry site of hepatitis C virus genome
    • PMID:10541019
    • FukushiS, OkadaM, KageyamaT, HoshinoFB, KatayamaK. Specific interaction of a 25-kilo-dalton cellular protein, a 40S ribosomal subunit protein, with the internal ribosome entry site of hepatitis C virus genome.Virus Genes1999; 19:153-61; PMID:10541019; http://dx.doi.org/10.1023/A:1008131325056
    • (1999) Virus Genes , vol.19 , pp. 153-161
    • Fukushi, S.1    Okada, M.2    Kageyama, T.3    Hoshino, F.B.4    Katayama, K.5
  • 30
    • 0035877795 scopus 로고    scopus 로고
    • Ribosomal protein S5 interacts with the internal ribosomal entry site of hepatitis C virus
    • PMID:11331271
    • FukushiS, OkadaM, StahlJ, KageyamaT, HoshinoFB, KatayamaK. Ribosomal protein S5 interacts with the internal ribosomal entry site of hepatitis C virus.J BiolChem2001; 276:20824-6; PMID:11331271; http://dx.doi.org/10.1074/jbc.C100206200
    • (2001) J BiolChem , vol.276 , pp. 20824-20826
    • Fukushi, S.1    Okada, M.2    Stahl, J.3    Kageyama, T.4    Hoshino, F.B.5    Katayama, K.6
  • 31
    • 0036077344 scopus 로고    scopus 로고
    • Ribosomal proteins mediate the hepatitis C virus IRES-HeLa 40S interaction
    • PMID:12166646
    • OttoGA, LukavskyPJ, LancasterAM, SarnowP, PuglisiJD. Ribosomal proteins mediate the hepatitis C virus IRES-HeLa 40S interaction.RNA2002; 8:913-23; PMID:12166646; http://dx.doi.org/10.1017/S1355838202022057
    • (2002) RNA , vol.8 , pp. 913-923
    • Otto, G.A.1    Lukavsky, P.J.2    Lancaster, A.M.3    Sarnow, P.4    Puglisi, J.D.5
  • 32
    • 7044232145 scopus 로고    scopus 로고
    • Riboproteomics of the hepatitis C virus internal ribosomal entry site
    • PMID:15473682
    • LuH, LiW, NobleWS, PayanD, AndersonDC. Riboproteomics of the hepatitis C virus internal ribosomal entry site.J Proteome Res2004; 3:949-57; PMID:15473682; http://dx.doi.org/10.1021/pr0499592
    • (2004) J Proteome Res , vol.3 , pp. 949-957
    • Lu, H.1    Li, W.2    Noble, W.S.3    Payan, D.4    Anderson, D.C.5
  • 33
    • 79951510534 scopus 로고    scopus 로고
    • Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1
    • PMID:21205638
    • RablJ, LeibundgutM, AtaideSF, HaagA, BanN. Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1.Science2011; 331:730-6; PMID:21205638; http://dx.doi.org/10.1126/science.1198308
    • (2011) Science , vol.331 , pp. 730-736
    • Rabl, J.1    Leibundgut, M.2    Ataide, S.F.3    Haag, A.4    Ban, N.5
  • 34
    • 78649426085 scopus 로고    scopus 로고
    • Crystal structure of the eukaryotic ribosome
    • PMID:21109664
    • Ben-ShemA, JennerL, YusupovaG, YusupovM. Crystal structure of the eukaryotic ribosome. Science2010; 330:1203-9; PMID:21109664; http://dx.doi.org/10.1126/science.1194294
    • (2010) Science , vol.330 , pp. 1203-1209
    • Ben-Shem, A.1    Jenner, L.2    Yusupova, G.3    Yusupov, M.4
  • 36
    • 84885932370 scopus 로고    scopus 로고
    • HCV IRES interacts with the 18S rRNA to activate the 40S ribosome for subsequent steps of translation initiation
    • PMID:23873958
    • MalyginAA, KossinovaOA, ShatskyIN, KarpovaGG. HCV IRES interacts with the 18S rRNA to activate the 40S ribosome for subsequent steps of translation initiation.Nucleic Acids Res2013; 41:8706-14; PMID:23873958; http://dx.doi.org/10.1093/nar/gkt632
    • (2013) Nucleic Acids Res , vol.41 , pp. 8706-8714
    • Malygin, A.A.1    Kossinova, O.A.2    Shatsky, I.N.3    Karpova, G.G.4
  • 38
    • 33846959081 scopus 로고    scopus 로고
    • HCV and CSFV IRES domain II mediate eIF2 release during 80S ribosome assembly
    • PMID:17255934
    • LockerN, EastonLE, LukavskyPJ. HCV and CSFV IRES domain II mediate eIF2 release during 80S ribosome assembly.EMBO J2007; 26:795-805; PMID:17255934; http://dx.doi.org/10.1038/sj.emboj.7601549
    • (2007) EMBO J , vol.26 , pp. 795-805
    • Locker, N.1    Easton, L.E.2    Lukavsky, P.J.3
  • 39
    • 64049105338 scopus 로고    scopus 로고
    • The pathway of hepatitis C virus mRNA recruitment to the human ribosome
    • PMID:19287397
    • FraserCS, HersheyJW, DoudnaJA. The pathway of hepatitis C virus mRNA recruitment to the human ribosome.Nat StructMolBiol2009; 16:397-404; PMID:19287397; http://dx.doi.org/10.1038/nsmb.1572
    • (2009) Nat StructMolBiol , vol.16 , pp. 397-404
    • Fraser, C.S.1    Hershey, J.W.2    Doudna, J.A.3
  • 40
    • 79959320660 scopus 로고    scopus 로고
    • HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit's decoding groove
    • PMID:21606179
    • FilbinME, KieftJS. HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit's decoding groove.RNA2011; 17:1258-73; PMID:21606179; http://dx.doi.org/10.1261/rna.2594011
    • (2011) RNA , vol.17 , pp. 1258-1273
    • Filbin, M.E.1    Kieft, J.S.2
  • 41
    • 84875903667 scopus 로고    scopus 로고
    • Structure of the full-length HCV IRES in solution
    • PMID:23511476
    • PérardJ, LeyratC, BaudinF, DrouetE, JaminM. Structure of the full-length HCV IRES in solution. Nat Commun2013; 4:1612; PMID:23511476; http://dx.doi.org/10.1038/ncomms2611
    • (2013) Nat Commun , vol.4 , pp. 1612
    • Pérard, J.1    Leyrat, C.2    Baudin, F.3    Drouet, E.4    Jamin, M.5
  • 43
    • 77952581453 scopus 로고    scopus 로고
    • Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions
    • PintilieGD, ZhangJ, GoddardTD, ChiuW, GossardDC. Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions. J StructBiol2010; 170:427-38.
    • (2010) J StructBiol , vol.170 , pp. 427-438
    • Pintilie, G.D.1    Zhang, J.2    Goddard, T.D.3    Chiu, W.4    Gossard, D.C.5
  • 44
    • 0032475963 scopus 로고    scopus 로고
    • Supersites within superfolds.Binding site similarity in the absence of homology
    • PMID:9743635
    • RussellRB, SasieniPD, SternbergMJ. Supersites within superfolds.Binding site similarity in the absence of homology.J MolBiol1998; 282:903-18; PMID:9743635; http://dx.doi.org/10.1006/jmbi.1998.2043
    • (1998) J MolBiol , vol.282 , pp. 903-918
    • Russell, R.B.1    Sasieni, P.D.2    Sternberg, M.J.3
  • 45
    • 1842454912 scopus 로고    scopus 로고
    • Prediction of functional sites by analysis of sequence and structure conservation
    • PMID:15010543
    • PanchenkoAR, KondrashovF, BryantS. Prediction of functional sites by analysis of sequence and structure conservation.Protein Sci2004; 13:884-92; PMID:15010543; http://dx.doi.org/10.1110/ps.03465504
    • (2004) Protein Sci , vol.13 , pp. 884-892
    • Panchenko, A.R.1    Kondrashov, F.2    Bryant, S.3
  • 46
    • 84896701134 scopus 로고    scopus 로고
    • Identifying RNA-binding residues based on evolutionary conserved structural and energetic features
    • PMID:24343026
    • ChenYC, SargsyanK, WrightJD, HuangYS, LimC. Identifying RNA-binding residues based on evolutionary conserved structural and energetic features. Nucleic Acids Res2014; 42:e15; PMID:24343026; http://dx.doi.org/10.1093/nar/gkt1299
    • (2014) Nucleic Acids Res , vol.42 , pp. e15
    • Chen, Y.C.1    Sargsyan, K.2    Wright, J.D.3    Huang, Y.S.4    Lim, C.5
  • 47
    • 0033556127 scopus 로고    scopus 로고
    • RNA binding strategies of ribosomal proteins
    • PMID:9862955
    • DraperDE, ReynaldoLP. RNA binding strategies of ribosomal proteins.Nucleic Acids Res1999; 27:381-8; PMID:9862955; http://dx.doi.org/10.1093/nar/27.2.381
    • (1999) Nucleic Acids Res , vol.27 , pp. 381-388
    • Draper, D.E.1    Reynaldo, L.P.2
  • 48
    • 34249316905 scopus 로고    scopus 로고
    • RNA-binding proteins: Modular design for efficient function
    • PMID:17473849
    • LundeBM, MooreC, VaraniG. RNA-binding proteins: modular design for efficient function.Nat Rev Mol Cell Biol2007; 8:479-90; PMID:17473849; http://dx.doi.org/10.1038/nrm2178
    • (2007) Nat Rev Mol Cell Biol , vol.8 , pp. 479-490
    • Lunde, B.M.1    Moore, C.2    Varani, G.3
  • 49
    • 84870276089 scopus 로고    scopus 로고
    • Identification of nucleotide-binding sites in protein structures: A novel approach based on nucleotide modularity
    • PMID:23209685
    • ParcaL, GherardiniPF, TruglioM, MangoneI, FerrèF, Helmer-CitterichM, AusielloG. Identification of nucleotide-binding sites in protein structures: a novel approach based on nucleotide modularity. PLoS One2012; 7:e50240; PMID:23209685; http://dx.doi.org/10.1371/journal.pone.0050240
    • (2012) PLoS One , vol.7 , pp. e50240
    • Parca, L.1    Gherardini, P.F.2    Truglio, M.3    Mangone, I.4    Ferrè, F.5    Helmer-Citterich, M.6    Ausiello, G.7
  • 50
    • 56649103902 scopus 로고    scopus 로고
    • Searching protein structure databases with DaliLite v.3
    • PMID:18818215
    • HolmL, KääriäinenS, RosenströmP, SchenkelA. Searching protein structure databases with DaliLite v.3.Bioinformatics2008; 24:2780-1; PMID:18818215; http://dx.doi.org/10.1093/bioinformatics/btn507
    • (2008) Bioinformatics , vol.24 , pp. 2780-2781
    • Holm, L.1    Kääriäinen, S.2    Rosenström, P.3    Schenkel, A.4
  • 52
    • 84884837017 scopus 로고    scopus 로고
    • Computational prediction of associations between long non-coding RNAs and proteins
    • PMID:24063787
    • LuQ, RenS, LuM, ZhangY, ZhuD, ZhangX, LiT. Computational prediction of associations between long non-coding RNAs and proteins.BMC Genomics2013; 14:651; PMID:24063787; http://dx.doi.org/10.1186/1471-2164-14-651
    • (2013) BMC Genomics , vol.14 , pp. 651
    • Lu, Q.1    Ren, S.2    Lu, M.3    Zhang, Y.4    Zhu, D.5    Zhang, X.6    Li, T.7
  • 54
    • 77953886400 scopus 로고    scopus 로고
    • BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features
    • PMID:20522253
    • WangL, HuangC, YangMQ, YangJY. BindN+ for accurate prediction of DNA and RNA-binding residues from protein sequence features.BMC SystBiol2010; 4(Suppl 1):S3; PMID:20522253; http://dx.doi.org/10.1186/1752-0509-4-S1-S3
    • (2010) BMC SystBiol , vol.4 , pp. S3
    • Wang, L.1    Huang, C.2    Yang, M.Q.3    Yang, J.Y.4
  • 55
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
    • PMID:12580598
    • DominguezC, BoelensR, BonvinAM. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information.J Am ChemSoc2003; 125:1731-7; PMID:12580598; http://dx.doi.org/10.1021/ja026939x
    • (2003) J Am ChemSoc , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.3
  • 56
    • 77955371384 scopus 로고    scopus 로고
    • Building macromolecular assemblies by information-driven docking: Introducing the HADDOCK multibody docking server
    • PMID:20305088
    • KaracaE, MelquiondAS, de VriesSJ, KastritisPL, BonvinAM. Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server.Mol Cell Proteomics2010; 9:1784-94; PMID:20305088; http://dx.doi.org/10.1074/mcp.M000051-MCP201
    • (2010) Mol Cell Proteomics , vol.9 , pp. 1784-1794
    • Karaca, E.1    Melquiond, A.S.2    De Vries, S.J.3    Kastritis, P.L.4    Bonvin, A.M.5
  • 57
    • 49249118038 scopus 로고    scopus 로고
    • A protein-DNA docking benchmark
    • PMID:18583363
    • van DijkM, BonvinAM. A protein-DNA docking benchmark.Nucleic Acids Res2008; 36:e88; PMID:18583363; http://dx.doi.org/10.1093/nar/gkn386
    • (2008) Nucleic Acids Res , vol.36 , pp. e88
    • Van Dijk, M.1    Bonvin, A.M.2
  • 58
    • 0344628782 scopus 로고    scopus 로고
    • Structure of HCV IRES domain II determined by NMR
    • PMID:14578934
    • LukavskyPJ, KimI, OttoGA, PuglisiJD. Structure of HCV IRES domain II determined by NMR. Nat StructBiol2003; 10:1033-8; PMID:14578934; http://dx.doi.org/10.1038/nsb1004
    • (2003) Nat StructBiol , vol.10 , pp. 1033-1038
    • Lukavsky, P.J.1    Kim, I.2    Otto, G.A.3    Puglisi, J.D.4
  • 61
    • 66149157000 scopus 로고    scopus 로고
    • Insights into substrate stabilization from snapshots of the peptidyltransferase center of the intact 70S ribosome
    • PMID:19363482
    • VoorheesRM, WeixlbaumerA, LoakesD, KelleyAC, RamakrishnanV. Insights into substrate stabilization from snapshots of the peptidyltransferase center of the intact 70S ribosome.Nat StructMolBiol2009; 16:528-33; PMID:19363482; http://dx.doi.org/10.1038/nsmb.1577
    • (2009) Nat StructMolBiol , vol.16 , pp. 528-533
    • Voorhees, R.M.1    Weixlbaumer, A.2    Loakes, D.3    Kelley, A.C.4    Ramakrishnan, V.5
  • 62
    • 79953780968 scopus 로고    scopus 로고
    • How mutations in tRNA distant from the anticodon affect the fidelity of decoding
    • PMID:21378964
    • SchmeingTM, VoorheesRM, KelleyAC, RamakrishnanV. How mutations in tRNA distant from the anticodon affect the fidelity of decoding.Nat StructMolBiol2011; 18:432-6; PMID:21378964; http://dx.doi.org/10.1038/nsmb.2003
    • (2011) Nat StructMolBiol , vol.18 , pp. 432-436
    • Schmeing, T.M.1    Voorhees, R.M.2    Kelley, A.C.3    Ramakrishnan, V.4
  • 63
    • 84881666192 scopus 로고    scopus 로고
    • The initiation of mammalian protein synthesis and mRNA scanning mechanism
    • PMID:23873042
    • LomakinIB, SteitzTA. The initiation of mammalian protein synthesis and mRNA scanning mechanism. Nature2013; 500:307-11; PMID:23873042; http://dx.doi.org/10.1038/nature12355
    • (2013) Nature , vol.500 , pp. 307-311
    • Lomakin, I.B.1    Steitz, T.A.2
  • 64
    • 78049250815 scopus 로고    scopus 로고
    • Revisiting the structures of several antibiotics bound to the bacterial ribosome
    • PMID:20876130
    • BulkleyD, InnisCA, BlahaG, SteitzTA. Revisiting the structures of several antibiotics bound to the bacterial ribosome.ProcNatlAcadSci U S A2010; 107:17158-63; PMID:20876130; http://dx.doi.org/10.1073/pnas.1008685107
    • (2010) ProcNatlAcadSci U S A , vol.107 , pp. 17158-17163
    • Bulkley, D.1    Innis, C.A.2    Blaha, G.3    Steitz, T.A.4
  • 65
    • 0032232180 scopus 로고    scopus 로고
    • MANIP: An interactive tool for modelling RNA
    • PMID:10522239
    • MassireC, WesthofE. MANIP: an interactive tool for modelling RNA.J Mol Graph Model1998; 16:197-205, 255-7; PMID:10522239; http://dx.doi.org/10.1016/S1093-3263(98)80004-1
    • (1998) J Mol Graph Model , vol.16
    • Massire, C.1    Westhof, E.2
  • 66
    • 0030801742 scopus 로고    scopus 로고
    • A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. I. Fitting the RNA to a 3D electron microscopic map at 20 A
    • PMID:9281424
    • MuellerF, BrimacombeR. A new model for the three-dimensional folding of Escherichia coli 16 S ribosomal RNA. I. Fitting the RNA to a 3D electron microscopic map at 20 A.J MolBiol1997; 271:524-44; PMID:9281424; http://dx.doi.org/10.1006/jmbi.1997.1210
    • (1997) J MolBiol , vol.271 , pp. 524-544
    • Mueller, F.1    Brimacombe, R.2
  • 67
    • 42949089487 scopus 로고    scopus 로고
    • Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics
    • PMID:18462672
    • TrabucoLG, VillaE, MitraK, FrankJ, SchultenK. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure2008; 16:673-83; PMID:18462672; http://dx.doi.org/10.1016/j.str.2008.03.005
    • (2008) Structure , vol.16 , pp. 673-683
    • Trabuco, L.G.1    Villa, E.2    Mitra, K.3    Frank, J.4    Schulten, K.5
  • 68
    • 70349267547 scopus 로고    scopus 로고
    • Molecular dynamics flexible fitting: A practical guide to combine cryo-electron microscopy and X-ray crystallography
    • PMID:19398010
    • TrabucoLG, VillaE, SchreinerE, HarrisonCB, SchultenK. Molecular dynamics flexible fitting: a practical guide to combine cryo-electron microscopy and X-ray crystallography.Methods2009; 49:174-80; PMID:19398010; http://dx.doi.org/10.1016/j.ymeth.2009.04.005
    • (2009) Methods , vol.49 , pp. 174-180
    • Trabuco, L.G.1    Villa, E.2    Schreiner, E.3    Harrison, C.B.4    Schulten, K.5
  • 69
    • 30044446378 scopus 로고    scopus 로고
    • An mRNA-rRNA base-pairing mechanism for translation initiation in eukaryotes
    • PMID:16341227
    • DresiosJ, ChappellSA, ZhouW, MauroVP. An mRNA-rRNA base-pairing mechanism for translation initiation in eukaryotes.Nat StructMolBiol2006; 13:30-4; PMID:16341227; http://dx.doi.org/10.1038/nsmb1031
    • (2006) Nat StructMolBiol , vol.13 , pp. 30-34
    • Dresios, J.1    Chappell, S.A.2    Zhou, W.3    Mauro, V.P.4
  • 70
    • 34247105689 scopus 로고    scopus 로고
    • Eukaryotic ribosomal protein RPS25 interacts with the conserved loop region in a dicistroviralintergenic internal ribosome entry site
    • PMID:17287295
    • NishiyamaT, YamamotoH, UchiumiT, NakashimaN. Eukaryotic ribosomal protein RPS25 interacts with the conserved loop region in a dicistroviralintergenic internal ribosome entry site.Nucleic Acids Res2007; 35:1514-21; PMID:17287295; http://dx.doi.org/10.1093/nar/gkl1121
    • (2007) Nucleic Acids Res , vol.35 , pp. 1514-1521
    • Nishiyama, T.1    Yamamoto, H.2    Uchiumi, T.3    Nakashima, N.4
  • 72
    • 72549101167 scopus 로고    scopus 로고
    • RPS25 is essential for translation initiation by the Dicistroviridae and hepatitis C viral IRESs
    • PMID:19952110
    • LandryDM, HertzMI, ThompsonSR. RPS25 is essential for translation initiation by the Dicistroviridae and hepatitis C viral IRESs.Genes Dev2009; 23:2753-64; PMID:19952110; http://dx.doi.org/10.1101/gad.1832209
    • (2009) Genes Dev , vol.23 , pp. 2753-2764
    • Landry, D.M.1    Hertz, M.I.2    Thompson, S.R.3
  • 73
    • 0035901537 scopus 로고    scopus 로고
    • The structural basis of acyl coenzyme A-dependent regulation of the transcription factor FadR
    • PMID:11296236
    • van AaltenDM, DiRussoCC, KnudsenJ. The structural basis of acyl coenzyme A-dependent regulation of the transcription factor FadR.EMBO J2001; 20:2041-50; PMID:11296236; http://dx.doi.org/10.1093/emboj/20.8.2041
    • (2001) EMBO J , vol.20 , pp. 2041-2050
    • Van Aalten, D.M.1    DiRusso, C.C.2    Knudsen, J.3
  • 74
    • 33747148179 scopus 로고    scopus 로고
    • Molecular environment of the subdomain IIIe loop of the RNA IRES element of hepatitis C virus on the human 40S ribosomal subunit
    • PMID:16808174
    • LaletinaES, GraiferDM, MalyginAA, ShatskiiIN, KarpovaGG. [Molecular environment of the subdomain IIIe loop of the RNA IRES element of hepatitis C virus on the human 40S ribosomal subunit]. BioorgKhim2006; 32:311-9; PMID:16808174
    • (2006) BioorgKhim , vol.32 , pp. 311-319
    • Laletina, E.S.1    Graifer, D.M.2    Malygin, A.A.3    Shatskii, I.N.4    Karpova, G.G.5
  • 75
    • 70449717470 scopus 로고    scopus 로고
    • Conserved functional domains and a novel tertiary interaction near the pseudoknot drive translational activity of hepatitis C virus and hepatitis C virus-like internal ribosome entry sites
    • PMID:19596815
    • EastonLE, LockerN, LukavskyPJ. Conserved functional domains and a novel tertiary interaction near the pseudoknot drive translational activity of hepatitis C virus and hepatitis C virus-like internal ribosome entry sites.Nucleic Acids Res2009; 37:5537-49; PMID:19596815; http://dx.doi.org/10.1093/nar/gkp588
    • (2009) Nucleic Acids Res , vol.37 , pp. 5537-5549
    • Easton, L.E.1    Locker, N.2    Lukavsky, P.J.3
  • 76
    • 84872856529 scopus 로고    scopus 로고
    • Proteins of the human 40S ribosomal subunit involved in hepatitis C IRES binding as revealed from fluorescent labeling
    • PMID:23379559
    • MalyginAA, ShatskyIN, KarpovaGG. Proteins of the human 40S ribosomal subunit involved in hepatitis C IRES binding as revealed from fluorescent labeling.Biochemistry (Mosc)2013; 78:53-9; PMID:23379559; http://dx.doi.org/10.1134/S0006297913010069
    • (2013) Biochemistry (Mosc) , vol.78 , pp. 53-59
    • Malygin, A.A.1    Shatsky, I.N.2    Karpova, G.G.3
  • 77
    • 0029331431 scopus 로고
    • An RNA pseudoknot is an essential structural element of the internal ribosome entry site located within the hepatitis C virus 5′ noncoding region
    • PMID:7489514
    • WangC, LeSY, AliN, SiddiquiA. An RNA pseudoknot is an essential structural element of the internal ribosome entry site located within the hepatitis C virus 5′ noncoding region.RNA1995; 1:526-37; PMID:7489514
    • (1995) RNA , vol.1 , pp. 526-537
    • Wang, C.1    Le, S.Y.2    Ali, N.3    Siddiqui, A.4
  • 78
    • 84866624397 scopus 로고    scopus 로고
    • Targeting ribosome assembly on the HCV RNA using a small RNA molecule
    • PMID:22858675
    • BhatP, GnanasundramSV, ManiP, RayPS, SarkarDP, DasS. Targeting ribosome assembly on the HCV RNA using a small RNA molecule.RNA Biol2012; 9:1110-9; PMID:22858675; http://dx.doi.org/10.4161/rna.21208
    • (2012) RNA Biol , vol.9 , pp. 1110-1119
    • Bhat, P.1    Gnanasundram, S.V.2    Mani, P.3    Ray, P.S.4    Sarkar, D.P.5    Das, S.6
  • 79
    • 0038029925 scopus 로고    scopus 로고
    • Positioning of mRNA codons with respect to 18S rRNA at the P and E sites of human ribosome
    • PMID:12759190
    • DemeshkinaN, LaletinaE, MeschaninovaM, Ven'yaminovaA, GraiferD, KarpovaG. Positioning of mRNA codons with respect to 18S rRNA at the P and E sites of human ribosome.BiochimBiophysActa2003; 1627:39-46; PMID:12759190; http://dx.doi.org/10.1016/S0167-4781(03)00072-1
    • (2003) BiochimBiophysActa , vol.1627 , pp. 39-46
    • Demeshkina, N.1    Laletina, E.2    Meschaninova, M.3    Ven'yaminova, A.4    Graifer, D.5    Karpova, G.6
  • 80
    • 44649095899 scopus 로고    scopus 로고
    • Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes
    • PMID:18464793
    • PisarevAV, KolupaevaVG, YusupovMM, HellenCU, PestovaTV. Ribosomal position and contacts of mRNA in eukaryotic translation initiation complexes. EMBO J2008; 27:1609-21; PMID:18464793; http://dx.doi.org/10.1038/emboj.2008.90
    • (2008) EMBO J , vol.27 , pp. 1609-1621
    • Pisarev, A.V.1    Kolupaeva, V.G.2    Yusupov, M.M.3    Hellen, C.U.4    Pestova, T.V.5
  • 81
    • 23344431785 scopus 로고    scopus 로고
    • Ribosomal proteins cross-linked to the initiator AUG codon of a mRNA in the translation initiation complex by UV-irradiation
    • PMID:16046447
    • TakahashiY, HirayamaS, OdaniS. Ribosomal proteins cross-linked to the initiator AUG codon of a mRNA in the translation initiation complex by UV-irradiation.J Biochem2005; 138:41-6; PMID:16046447; http://dx.doi.org/10.1093/jb/mvi096
    • (2005) J Biochem , vol.138 , pp. 41-46
    • Takahashi, Y.1    Hirayama, S.2    Odani, S.3
  • 82
    • 84860151944 scopus 로고    scopus 로고
    • A central fragment of ribosomal protein S26 containing the eukaryote-specific motif YxxPKxYxK is a key component of the ribosomal binding site of mRNA region 5′ of the E site codon
    • PMID:22167470
    • SharifulinD, KhairulinaY, IvanovA, MeschaninovaM, Ven'yaminovaA, GraiferD, KarpovaG. A central fragment of ribosomal protein S26 containing the eukaryote-specific motif YxxPKxYxK is a key component of the ribosomal binding site of mRNA region 5′ of the E site codon.Nucleic Acids Res2012; 40:3056-65; PMID:22167470; http://dx.doi.org/10.1093/nar/gkr1212
    • (2012) Nucleic Acids Res , vol.40 , pp. 3056-3065
    • Sharifulin, D.1    Khairulina, Y.2    Ivanov, A.3    Meschaninova, M.4    Ven'yaminova, A.5    Graifer, D.6    Karpova, G.7
  • 83
    • 22444444478 scopus 로고    scopus 로고
    • Mass spectrometric analysis of the human 40S ribosomal subunit: Native and HCV IRES-bound complexes
    • PMID:15883184
    • YuY, JiH, DoudnaJA, LearyJA. Mass spectrometric analysis of the human 40S ribosomal subunit: native and HCV IRES-bound complexes.Protein Sci2005; 14:1438-46; PMID:15883184; http://dx.doi.org/10.1110/ps.041293005
    • (2005) Protein Sci , vol.14 , pp. 1438-1446
    • Yu, Y.1    Ji, H.2    Doudna, J.A.3    Leary, J.A.4
  • 84
    • 33645804973 scopus 로고    scopus 로고
    • Proteins surrounding hairpin IIIe of the hepatitis C virus internal ribosome entry site on the human 40S ribosomal subunit
    • PMID:16614452
    • LaletinaE, GraiferD, MalyginA, IvanovA, ShatskyI, KarpovaG. Proteins surrounding hairpin IIIe of the hepatitis C virus internal ribosome entry site on the human 40S ribosomal subunit.Nucleic Acids Res2006; 34:2027-36; PMID:16614452; http://dx.doi.org/10.1093/nar/gkl155
    • (2006) Nucleic Acids Res , vol.34 , pp. 2027-2036
    • Laletina, E.1    Graifer, D.2    Malygin, A.3    Ivanov, A.4    Shatsky, I.5    Karpova, G.6
  • 85
    • 62549152278 scopus 로고    scopus 로고
    • Positioning of subdomain IIId and apical loop of domain II of the hepatitis C IRES on the human 40S ribosome
    • PMID:19129232
    • BabaylovaE, GraiferD, MalyginA, StahlJ, ShatskyI, KarpovaG. Positioning of subdomain IIId and apical loop of domain II of the hepatitis C IRES on the human 40S ribosome.Nucleic Acids Res2009; 37:1141-51; PMID:19129232; http://dx.doi.org/10.1093/nar/gkn1026
    • (2009) Nucleic Acids Res , vol.37 , pp. 1141-1151
    • Babaylova, E.1    Graifer, D.2    Malygin, A.3    Stahl, J.4    Shatsky, I.5    Karpova, G.6
  • 86
    • 67849119062 scopus 로고    scopus 로고
    • Inhibition of hepatitis C virus replication and internal ribosome entry site-dependent translation by an RNA molecule
    • PMID:19264618
    • Romero-LópezC, Díaz-GonzálezR, BarrosodelJesusA, Berzal-HerranzA. Inhibition of hepatitis C virus replication and internal ribosome entry site-dependent translation by an RNA molecule.J Gen Virol2009; 90:1659-69; PMID:19264618; http://dx.doi.org/10.1099/vir.0.008821-0
    • (2009) J Gen Virol , vol.90 , pp. 1659-1669
    • Romero-López, C.1    Díaz-González, R.2    Barroso-delJesus, A.3    Berzal-Herranz, A.4
  • 87
    • 0030498233 scopus 로고    scopus 로고
    • xdlMAPMAN and xdlDATAMAN - Programs for reformatting, analysis and manipulation of biomacromolecular electrondensity maps and reflection data sets
    • PMID:15299647
    • KleywegtGJ, JonesTA. xdlMAPMAN and xdlDATAMAN - programs for reformatting, analysis and manipulation of biomacromolecular electrondensity maps and reflection data sets.ActaCrystallogr D BiolCrystallogr1996; 52:826-8; PMID:15299647; http://dx.doi.org/10.1107/S0907444995014983
    • (1996) ActaCrystallogr D BiolCrystallogr , vol.52 , pp. 826-828
    • Kleywegt, G.J.1    Jones, T.A.2
  • 88
    • 0032780181 scopus 로고    scopus 로고
    • Situs: A package for docking crystal structures into low-resolution maps from electron microscopy
    • PMID:10222274
    • WriggersW, MilliganRA, McCammonJA. Situs: A package for docking crystal structures into low-resolution maps from electron microscopy.J StructBiol1999; 125:185-95; PMID:10222274; http://dx.doi.org/10.1006/jsbi.1998.4080
    • (1999) J StructBiol , vol.125 , pp. 185-195
    • Wriggers, W.1    Milligan, R.A.2    McCammon, J.A.3
  • 89
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • PMID:8254673
    • SaliA, BlundellTL. Comparative protein modelling by satisfaction of spatial restraints.J MolBiol1993; 234:779-815; PMID:8254673; http://dx.doi.org/10.1006/jmbi.1993.1626
    • (1993) J MolBiol , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 90
    • 33749578940 scopus 로고    scopus 로고
    • Statistical potential for assessment and prediction of protein structures
    • PMID:17075131
    • ShenMY, SaliA. Statistical potential for assessment and prediction of protein structures.Protein Sci2006; 15:2507-24; PMID:17075131; http://dx.doi.org/10.1110/ps.062416606
    • (2006) Protein Sci , vol.15 , pp. 2507-2524
    • Shen, M.Y.1    Sali, A.2
  • 91
    • 85047692291 scopus 로고    scopus 로고
    • Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling
    • PMID:15754305
    • SorinEJ, PandeVS. Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling.J ComputChem2005; 26:682-90; PMID:15754305; http://dx.doi.org/10.1002/jcc.20208
    • (2005) J ComputChem , vol.26 , pp. 682-690
    • Sorin, E.J.1    Pande, V.S.2
  • 93
    • 0036237981 scopus 로고    scopus 로고
    • Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation
    • PMID:11927953
    • KieftJS, ZhouK, GrechA, JubinR, DoudnaJA. Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation. Nat StructBiol2002; 9:370-4; PMID:11927953
    • (2002) Nat StructBiol , vol.9 , pp. 370-374
    • Kieft, J.S.1    Zhou, K.2    Grech, A.3    Jubin, R.4    Doudna, J.A.5
  • 94
    • 40449139010 scopus 로고    scopus 로고
    • The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
    • PMID:18322526
    • ParisienM, MajorF. The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature2008; 452:51-5; PMID:18322526; http://dx.doi.org/10.1038/nature06684
    • (2008) Nature , vol.452 , pp. 51-55
    • Parisien, M.1    Major, F.2
  • 95
    • 79959292152 scopus 로고    scopus 로고
    • ModeRNA: A tool for comparative modeling of RNA 3D structure
    • PMID:21300639
    • RotherM, RotherK, PutonT, BujnickiJM. ModeRNA: a tool for comparative modeling of RNA 3D structure.Nucleic Acids Res2011; 39:4007-22; PMID:21300639; http://dx.doi.org/10.1093/nar/gkq1320
    • (2011) Nucleic Acids Res , vol.39 , pp. 4007-4022
    • Rother, M.1    Rother, K.2    Puton, T.3    Bujnicki, J.M.4
  • 96
    • 77958470166 scopus 로고    scopus 로고
    • R3D Align: Global pairwise alignment of RNA 3D structures using local superpositions
    • PMID:20929913
    • RahrigRR, LeontisNB, ZirbelCL. R3D Align: global pairwise alignment of RNA 3D structures using local superpositions.Bioinformatics2010; 26:2689-97; PMID:20929913; http://dx.doi.org/10.1093/bioinformatics/btq506
    • (2010) Bioinformatics , vol.26 , pp. 2689-2697
    • Rahrig, R.R.1    Leontis, N.B.2    Zirbel, C.L.3
  • 97
    • 77954269050 scopus 로고    scopus 로고
    • Freiburg RNA Tools: A web server integrating INTARNA, EXPARNA and LOCARNA
    • PMID:20444875
    • SmithC, HeyneS, RichterAS, WillS, BackofenR. Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LOCARNA.Nucleic Acids Res2010; 38:W373-7; PMID:20444875; http://dx.doi.org/10.1093/nar/gkq316
    • (2010) Nucleic Acids Res , vol.38 , pp. W373-W377
    • Smith, C.1    Heyne, S.2    Richter, A.S.3    Will, S.4    Backofen, R.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.