메뉴 건너뛰기




Volumn 9, Issue 9, 2014, Pages

Vfold: A web server for RNA structure and folding thermodynamics prediction

Author keywords

[No Author keywords available]

Indexed keywords

DNA STRUCTURE; ENTROPY; EXPERIMENTAL MODEL; HEAT; MELTING POINT; MODEL; NUCLEOTIDE SEQUENCE; PHYSICS; PREDICTION; RNA FOLDING; RNA STRUCTURE; THERMODYNAMICS; UNITED STATES; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; HUMAN; INTERNET; PROTEIN DATABASE; RNA STABILITY;

EID: 84923602610     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0107504     Document Type: Article
Times cited : (137)

References (45)
  • 1
    • 0037062949 scopus 로고    scopus 로고
    • The chemical repertoire of natural ribozymes
    • Doudna JA, Cech TR (2002). The chemical repertoire of natural ribozymes. Nature, 418: 222-228.
    • (2002) Nature , vol.418 , pp. 222-228
    • Doudna, J.A.1    Cech, T.R.2
  • 3
    • 79951495822 scopus 로고    scopus 로고
    • LncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 39 UTRs via Alu elements
    • Gong C, Maquat LE (2011). lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 39 UTRs via Alu elements. Nature, 470: 284-288.
    • (2011) Nature , vol.470 , pp. 284-288
    • Gong, C.1    Maquat, L.E.2
  • 4
    • 58249088751 scopus 로고    scopus 로고
    • MicroRNAs: Target recognition and regulatory functions
    • Bartel DP (2009). MicroRNAs: target recognition and regulatory functions. Cell, 136: 215-233.
    • (2009) Cell , vol.136 , pp. 215-233
    • Bartel, D.P.1
  • 5
    • 34748821761 scopus 로고    scopus 로고
    • The role of site accessibility in microRNA target recognition
    • Kertesz M, Iovino N, Unnerstall U, Gaul U, Segal E (2007). The role of site accessibility in microRNA target recognition. Nat. Genet., 39: 1278-1284.
    • (2007) Nat. Genet. , vol.39 , pp. 1278-1284
    • Kertesz, M.1    Iovino, N.2    Unnerstall, U.3    Gaul, U.4    Segal, E.5
  • 8
    • 77953648210 scopus 로고    scopus 로고
    • On the significance of an RNA tertiary structure prediction
    • Hajdin CE, Ding F, Dokholyan NV, Weeks KM (2010). On the significance of an RNA tertiary structure prediction. RNA, 16, 1340-1349.
    • (2010) RNA , vol.16 , pp. 1340-1349
    • Hajdin, C.E.1    Ding, F.2    Dokholyan, N.V.3    Weeks, K.M.4
  • 9
    • 84875471554 scopus 로고    scopus 로고
    • RNA 3D structure prediction by using a coarse-grained model and experimental data
    • Xia Z, Bell DR, Shi Y, Ren P (2013). RNA 3D structure prediction by using a coarse-grained model and experimental data. J Phys Chem B, 117, 3135-3144.
    • (2013) J Phys Chem B , vol.117 , pp. 3135-3144
    • Xia, Z.1    Bell, D.R.2    Shi, Y.3    Ren, P.4
  • 10
    • 84864438963 scopus 로고    scopus 로고
    • Kinetic mechanism of conformational switch between bistable RNA hairpins
    • Xu X, Chen S-J (2012). Kinetic mechanism of conformational switch between bistable RNA hairpins. J Am Chem Soc, 134, 12499-12507.
    • (2012) J Am Chem Soc , vol.134 , pp. 12499-12507
    • Xu, X.1    Chen, S.-J.2
  • 11
    • 33750040264 scopus 로고    scopus 로고
    • Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics
    • Bussi G, Gervasio FL, Laio A, Parrinello M (2006). Free-energy landscape for beta hairpin folding from combined parallel tempering and metadynamics. J Am Chem Soc, 128, 13435-13441.
    • (2006) J Am Chem Soc , vol.128 , pp. 13435-13441
    • Bussi, G.1    Gervasio, F.L.2    Laio, A.3    Parrinello, M.4
  • 12
    • 84960165652 scopus 로고    scopus 로고
    • Efficiently computing the 2D energy landscape of RNA
    • In Press
    • Senter E, Dotu I, Clote P (2014). Efficiently computing the 2D energy landscape of RNA. J Math Biol, In Press.
    • (2014) J Math Biol
    • Senter, E.1    Dotu, I.2    Clote, P.3
  • 13
    • 54849437727 scopus 로고    scopus 로고
    • Relative stability of helices determines the folding landscape of adenine riboswitch aptamers
    • Lin JC, Thirumalai D (2008). Relative stability of helices determines the folding landscape of adenine riboswitch aptamers. J Am Chem Soc, 130, 14080-14081.
    • (2008) J Am Chem Soc , vol.130 , pp. 14080-14081
    • Lin, J.C.1    Thirumalai, D.2
  • 15
    • 23144449520 scopus 로고    scopus 로고
    • The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search
    • Havgaard JH, Lyngso RB, Gorodkin J (2005). The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search. Nucleic Acids Res, 33: W650-W653.
    • (2005) Nucleic Acids Res , vol.33 , pp. W650-W653
    • Havgaard, J.H.1    Lyngso, R.B.2    Gorodkin, J.3
  • 17
    • 67849086863 scopus 로고    scopus 로고
    • CENTROIDFOLD: A web server for RNA secondary structure prediction
    • Sato K, Hamada M, Asai K, Mituyama T (2009). CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res, 37, W277-W280.
    • (2009) Nucleic Acids Res , vol.37 , pp. W277-W280
    • Sato, K.1    Hamada, M.2    Asai, K.3    Mituyama, T.4
  • 18
    • 0036295198 scopus 로고    scopus 로고
    • Dynalign: An algorithm for finding the secondary structure common to two RNA sequences
    • Mathews DH, Turner DH (2002). Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. J Mol Biol, 317, 191-203.
    • (2002) J Mol Biol , vol.317 , pp. 191-203
    • Mathews, D.H.1    Turner, D.H.2
  • 19
    • 33744790273 scopus 로고    scopus 로고
    • Prediction of RNA secondary structure by free energy minimization
    • Mathews DH, Turner DH (2006). Prediction of RNA secondary structure by free energy minimization. Curr. Opin. Struct. Biol., 16: 270-278.
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 270-278
    • Mathews, D.H.1    Turner, D.H.2
  • 20
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker M (2003). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res., 31: 3406-3415.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 21
    • 0043123153 scopus 로고    scopus 로고
    • Vienna RNA secondary structure server
    • Hofacker IL (2003). Vienna RNA secondary structure server. Nucleic Acids Res., 31: 3429-3431.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3429-3431
    • Hofacker, I.L.1
  • 22
    • 84883563787 scopus 로고    scopus 로고
    • RNAstructure: Web servers for RNA secondary structure prediction and analysis
    • Bellaousov S, Reuter JS, Seetin MG, Methews DH (2013). RNAstructure: web servers for RNA secondary structure prediction and analysis. Nucleic Acids Res, 41: W471-W474.
    • (2013) Nucleic Acids Res , vol.41 , pp. W471-W474
    • Bellaousov, S.1    Reuter, J.S.2    Seetin, M.G.3    Methews, D.H.4
  • 23
    • 23144463133 scopus 로고    scopus 로고
    • Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots
    • Xayaphoummine A, Bucher T, Isambert H (2005). Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots. Nucleic Acids Res., 33: W605-W610.
    • (2005) Nucleic Acids Res. , vol.33 , pp. W605-W610
    • Xayaphoummine, A.1    Bucher, T.2    Isambert, H.3
  • 24
    • 25844447772 scopus 로고    scopus 로고
    • HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots
    • Ren J, Rastegari B, Condon A, Hoos HH (2005), HotKnots: Heuristic prediction of RNA secondary structures including pseudoknots. RNA, 11, 1494-1504.
    • (2005) RNA , vol.11 , pp. 1494-1504
    • Ren, J.1    Rastegari, B.2    Condon, A.3    Hoos, H.H.4
  • 25
    • 84856397817 scopus 로고    scopus 로고
    • Analysis of energy-based algorithms for RNA secondary structure prediction
    • Hajiaghayi M, Condon A, Hoos HH (2012). Analysis of energy-based algorithms for RNA secondary structure prediction BMC Bioinformatics, 13, 22.
    • (2012) BMC Bioinformatics , vol.13 , pp. 22
    • Hajiaghayi, M.1    Condon, A.2    Hoos, H.H.3
  • 26
    • 40449139010 scopus 로고    scopus 로고
    • The MC-fold and MC-sym pipeline infers RNA structure from sequence data
    • Parisien M, Major F (2008). The MC-fold and MC-sym pipeline infers RNA structure from sequence data. Nature, 452: 51-55.
    • (2008) Nature , vol.452 , pp. 51-55
    • Parisien, M.1    Major, F.2
  • 27
    • 80255140476 scopus 로고    scopus 로고
    • RNA and protein 3D structure modeling: Similarities and differences
    • Rother K, Rother M, Boniecki M, Puton T, Bujnicki JM (2011). RNA and protein 3D structure modeling: similarities and differences. J. Mol. Model, 17: 2325-2336.
    • (2011) J. Mol. Model , vol.17 , pp. 2325-2336
    • Rother, K.1    Rother, M.2    Boniecki, M.3    Puton, T.4    Bujnicki, J.M.5
  • 28
    • 75549088409 scopus 로고    scopus 로고
    • NNDB: The nearest neighbor parameter database for predicting stability of nucleic acid secondary structure
    • Turner DH, Mathews DH (2010). NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure. Nucleic Acid Res., 38: D280-D282.
    • (2010) Nucleic Acid Res. , vol.38 , pp. D280-D282
    • Turner, D.H.1    Mathews, D.H.2
  • 29
    • 84901469255 scopus 로고    scopus 로고
    • Predicting structure and stability for RNA complexes with intermolecular loop-loop base-pairing
    • Cao S, Xu X, Chen S-J (2014). Predicting structure and stability for RNA complexes with intermolecular loop-loop base-pairing. RNA, 20, 835-845.
    • (2014) RNA , vol.20 , pp. 835-845
    • Cao, S.1    Xu, X.2    Chen, S.-J.3
  • 30
    • 41549094987 scopus 로고    scopus 로고
    • Discrete state model and accurate estimation of loop entropy of RNA secondary structures
    • Zhang J, Lin M, Chen R, Wang W, Liang J (2008). Discrete state model and accurate estimation of loop entropy of RNA secondary structures. J Chem Phys, 128, 125107.
    • (2008) J Chem Phys , vol.128 , pp. 125107
    • Zhang, J.1    Lin, M.2    Chen, R.3    Wang, W.4    Liang, J.5
  • 31
    • 44149101971 scopus 로고    scopus 로고
    • Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms
    • Ding F, Sharma S, Chalasani P, Demidov VV, Broude NE, et al. (2008) Ab initio RNA folding by discrete molecular dynamics: from structure prediction to folding mechanisms. RNA, 14, 1164-1173.
    • (2008) RNA , vol.14 , pp. 1164-1173
    • Ding, F.1    Sharma, S.2    Chalasani, P.3    Demidov, V.V.4    Broude, N.E.5
  • 32
    • 50549096615 scopus 로고    scopus 로고
    • IFoldRNA: Three-dimensional RNA structure prediction and folding
    • Sharma S, Ding F, Dokholyan NV (2008). iFoldRNA: three-dimensional RNA structure prediction and folding. Bioinformatics, 24, 1951-1952.
    • (2008) Bioinformatics , vol.24 , pp. 1951-1952
    • Sharma, S.1    Ding, F.2    Dokholyan, N.V.3
  • 33
    • 77958490892 scopus 로고    scopus 로고
    • Coarse-grained model for simulation of RNA three-dimensional structures
    • Xia Z, Gardner DP, Gutell RR, Ren P (2010). Coarse-grained model for simulation of RNA three-dimensional structures. J Phys Chem B, 114, 13497-13506.
    • (2010) J Phys Chem B , vol.114 , pp. 13497-13506
    • Xia, Z.1    Gardner, D.P.2    Gutell, R.R.3    Ren, P.4
  • 34
    • 35548950310 scopus 로고    scopus 로고
    • Automated de novo prediction of native-like RNA tertiary structures
    • Das R, Baker D (2007). Automated de novo prediction of native-like RNA tertiary structures. Proc Natl Acad Sci USA, 104, 14664-14669.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 14664-14669
    • Das, R.1    Baker, D.2
  • 35
    • 77951643739 scopus 로고    scopus 로고
    • Atomic accuracy in predicting and designing noncanonical RNA structure
    • Das R, Karanicolas J, Baker D (2010). Atomic accuracy in predicting and designing noncanonical RNA structure. Nat Methods, 7, 291-294.
    • (2010) Nat Methods , vol.7 , pp. 291-294
    • Das, R.1    Karanicolas, J.2    Baker, D.3
  • 36
    • 79953795893 scopus 로고    scopus 로고
    • Physics-based de novo prediction of RNA 3D structures
    • Cao S, Chen S-J (2011). Physics-based de novo prediction of RNA 3D structures. J. Phys. Chem. B, 115: 4216-4226.
    • (2011) J. Phys. Chem. B , vol.115 , pp. 4216-4226
    • Cao, S.1    Chen, S.-J.2
  • 37
    • 79960024822 scopus 로고    scopus 로고
    • WebFR3D-a server for finding, aligning and analyzing recurrent RNA 3D motifs
    • Petrov AI, Zirbel CL, Leontis NB (2011). WebFR3D-a server for finding, aligning and analyzing recurrent RNA 3D motifs. Nucleic Acids Res, 39, W50-W55.
    • (2011) Nucleic Acids Res , vol.39 , pp. W50-W55
    • Petrov, A.I.1    Zirbel, C.L.2    Leontis, N.B.3
  • 38
    • 38549140073 scopus 로고    scopus 로고
    • RNA FRABASE version 1.0: An engine with a database to search for the three-dimensional fragments within RNA structures
    • Popenda M, Blazewicz M, Szachniuk M, Adamiak RW (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.
    • (2008) Nucleic Acids Res , vol.36 , pp. D386-D391
    • Popenda, M.1    Blazewicz, M.2    Szachniuk, M.3    Adamiak, R.W.4
  • 39
    • 28344438036 scopus 로고    scopus 로고
    • Predicting RNA folding thermodynamics with a reduced chain representation model
    • Cao S, Chen S-J (2005). Predicting RNA folding thermodynamics with a reduced chain representation model. RNA, 11: 1884-1897.
    • (2005) RNA , vol.11 , pp. 1884-1897
    • Cao, S.1    Chen, S.-J.2
  • 40
    • 33744547883 scopus 로고    scopus 로고
    • Predicting RNA psuedoknot folding thermodynamics
    • Cao S, Chen S-J (2006). Predicting RNA psuedoknot folding thermodynamics. Nucleic Acids Res., 34: 2634-2652.
    • (2006) Nucleic Acids Res. , vol.34 , pp. 2634-2652
    • Cao, S.1    Chen, S.-J.2
  • 41
    • 62549128665 scopus 로고    scopus 로고
    • Predicting structures and stabilities for H-type pseudoknots with inter-helix loop
    • Cao S, Chen S-J (2009). Predicting structures and stabilities for H-type pseudoknots with inter-helix loop. RNA, 15: 696-706.
    • (2009) RNA , vol.15 , pp. 696-706
    • Cao, S.1    Chen, S.-J.2
  • 42
    • 81755162785 scopus 로고    scopus 로고
    • Structure and stability of RNA/RNA kissing complex: With application to HIV dimerization initiation signal
    • Cao S, Chen S-J (2011). Structure and stability of RNA/RNA kissing complex: with application to HIV dimerization initiation signal. RNA, 17: 2130-2143.
    • (2011) RNA , vol.17 , pp. 2130-2143
    • Cao, S.1    Chen, S.-J.2
  • 43
    • 75649099055 scopus 로고    scopus 로고
    • Improved free energy parameters for RNA pseudoknotted secondary structure prediction
    • Andronescu MS, Pop C, Condon AE (2010). Improved free energy parameters for RNA pseudoknotted secondary structure prediction. RNA, 16, 26-42.
    • (2010) RNA , vol.16 , pp. 26-42
    • Andronescu, M.S.1    Pop, C.2    Condon, A.E.3
  • 44
    • 67650727366 scopus 로고    scopus 로고
    • VARNA: Interactive drawing and editing of the RNA secondary structure
    • Darty K, Denise A, Ponty Y (2009). VARNA: Interactive drawing and editing of the RNA secondary structure Bioinformatics, 25: 1974-1975.
    • (2009) Bioinformatics , vol.25 , pp. 1974-1975
    • Darty, K.1    Denise, A.2    Ponty, Y.3
  • 45
    • 0037225166 scopus 로고    scopus 로고
    • Bistable secondary structures of small RNAs and their structural probing by comparative imino proton NMR spectroscopy
    • Hobartner C, Micura R (2003). Bistable secondary structures of small RNAs and their structural probing by comparative imino proton NMR spectroscopy. J Mol Biol, 325: 421-431.
    • (2003) J Mol Biol , vol.325 , pp. 421-431
    • Hobartner, C.1    Micura, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.