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Volumn 14, Issue 6, 2018, Pages

Solving the RNA design problem with reinforcement learning

Author keywords

[No Author keywords available]

Indexed keywords

REINFORCEMENT LEARNING; STRUCTURAL DESIGN;

EID: 85049380253     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1006176     Document Type: Article
Times cited : (35)

References (28)
  • 1
    • 79551675216 scopus 로고    scopus 로고
    • Nanoparticle-mediated delivery of siRNA targeting Parp1 extends survival of mice bearing tumors derived from Brca1-deficient ovarian cancer cells
    • pmid:21187397
    • Goldberg MS, Xing D, Ren Y, Orsulic S, Bhatia SN, Sharp PA, Nanoparticle-mediated delivery of siRNA targeting Parp1 extends survival of mice bearing tumors derived from Brca1-deficient ovarian cancer cells. Proc Natl Acad Sci. 2011;108: 745–750. doi: 10.1073/pnas.1016538108 pmid: 21187397
    • (2011) Proc Natl Acad Sci , vol.108 , pp. 745-750
    • Goldberg, M.S.1    Xing, D.2    Ren, Y.3    Orsulic, S.4    Bhatia, S.N.5    Sharp, P.A.6
  • 2
    • 54249113318 scopus 로고    scopus 로고
    • Higher-Order Cellular Information Processing with Synthetic RNA Devices
    • pmid:18927397
    • Win MN, Smolke CD, Higher-Order Cellular Information Processing with Synthetic RNA Devices. Science. 2008;322: 456–460. doi: 10.1126/science.1160311 pmid: 18927397
    • (2008) Science , vol.322 , pp. 456-460
    • Win, M.N.1    Smolke, C.D.2
  • 3
    • 79960697001 scopus 로고    scopus 로고
    • Organization of Intracellular Reactions with Rationally Designed RNA Assemblies
    • pmid:21700839
    • Delebecque CJ, Lindner AB, Silver PA, Aldaye FA, Organization of Intracellular Reactions with Rationally Designed RNA Assemblies. Science. 2011;333: 470–474. doi: 10.1126/science.1206938 pmid: 21700839
    • (2011) Science , vol.333 , pp. 470-474
    • Delebecque, C.J.1    Lindner, A.B.2    Silver, P.A.3    Aldaye, F.A.4
  • 4
    • 84901275902 scopus 로고    scopus 로고
    • Construction of RNA nanocages by re-engineering the packaging RNA of Phi29 bacteriophage
    • pmid:24835104
    • Hao C, Li X, Tian C, Jiang W, Wang G, Mao C, Construction of RNA nanocages by re-engineering the packaging RNA of Phi29 bacteriophage. Nat Commun. 2014;5. doi: 10.1038/ncomms4890 pmid: 24835104
    • (2014) Nat Commun , vol.5
    • Hao, C.1    Li, X.2    Tian, C.3    Jiang, W.4    Wang, G.5    Mao, C.6
  • 7
    • 85019112209 scopus 로고    scopus 로고
    • Applicability of a computational design approach for synthetic riboswitches
    • pmid:27994029
    • Domin G, Findeiß S, Wachsmuth M, Will S, Stadler PF, Mörl M, Applicability of a computational design approach for synthetic riboswitches. Nucleic Acids Res. 2017;45: 4108–4119. doi: 10.1093/nar/gkw1267 pmid: 27994029
    • (2017) Nucleic Acids Res , vol.45 , pp. 4108-4119
    • Domin, G.1    Findeiß, S.2    Wachsmuth, M.3    Will, S.4    Stadler, P.F.5    Mörl, M.6
  • 8
    • 84922379183 scopus 로고    scopus 로고
    • Complete RNA inverse folding: computational design of functional hammerhead ribozymes
    • pmid:25209235
    • Dotu I, Garcia-Martin JA, Slinger BL, Mechery V, Meyer MM, Clote P, Complete RNA inverse folding: computational design of functional hammerhead ribozymes. Nucleic Acids Res. 2014;42: 11752–11762. doi: 10.1093/nar/gku740 pmid: 25209235
    • (2014) Nucleic Acids Res , vol.42 , pp. 11752-11762
    • Dotu, I.1    Garcia-Martin, J.A.2    Slinger, B.L.3    Mechery, V.4    Meyer, M.M.5    Clote, P.6
  • 9
    • 27944493648 scopus 로고    scopus 로고
    • Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes
    • pmid:16244657
    • Penchovsky R, Breaker RR, Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nat Biotechnol. 2005;23: 1424–1433. doi: 10.1038/nbt1155 pmid: 16244657
    • (2005) Nat Biotechnol , vol.23 , pp. 1424-1433
    • Penchovsky, R.1    Breaker, R.R.2
  • 10
    • 84876376374 scopus 로고    scopus 로고
    • De novo design of a synthetic riboswitch that regulates transcription termination
    • pmid:23275562
    • Wachsmuth M, Findeiß S, Weissheimer N, Stadler PF, Mörl M, De novo design of a synthetic riboswitch that regulates transcription termination. Nucleic Acids Res. 2013;41: 2541–2551. doi: 10.1093/nar/gks1330 pmid: 23275562
    • (2013) Nucleic Acids Res , vol.41 , pp. 2541-2551
    • Wachsmuth, M.1    Findeiß, S.2    Weissheimer, N.3    Stadler, P.F.4    Mörl, M.5
  • 12
    • 0842268067 scopus 로고    scopus 로고
    • A New Algorithm for RNA Secondary Structure Design
    • pmid:15095976
    • Andronescu M, Fejes AP, Hutter F, Hoos HH, Condon A, A New Algorithm for RNA Secondary Structure Design. J Mol Biol. 2004;336: 607–624. doi: 10.1016/j.jmb.2003.12.041 pmid: 15095976
    • (2004) J Mol Biol , vol.336 , pp. 607-624
    • Andronescu, M.1    Fejes, A.P.2    Hutter, F.3    Hoos, H.H.4    Condon, A.5
  • 13
    • 33747840719 scopus 로고    scopus 로고
    • INFO-RNA—a fast approach to inverse RNA folding
    • pmid:16709587
    • Busch A, Backofen R, INFO-RNA—a fast approach to inverse RNA folding. Bioinformatics. 2006;22: 1823–1831. doi: 10.1093/bioinformatics/btl194 pmid: 16709587
    • (2006) Bioinformatics , vol.22 , pp. 1823-1831
    • Busch, A.1    Backofen, R.2
  • 14
    • 84867350994 scopus 로고    scopus 로고
    • Dynamics in Sequence Space for RNA Secondary Structure Design
    • pmid:26593011
    • Matthies MC, Bienert S, Torda AE, Dynamics in Sequence Space for RNA Secondary Structure Design. J Chem Theory Comput. 2012;8: 3663–3670. doi: 10.1021/ct300267j pmid: 26593011
    • (2012) J Chem Theory Comput , vol.8 , pp. 3663-3670
    • Matthies, M.C.1    Bienert, S.2    Torda, A.E.3
  • 16
    • 79961002039 scopus 로고    scopus 로고
    • MODENA: a multi-objective RNA inverse folding
    • Taneda A, MODENA: a multi-objective RNA inverse folding. Adv Appl Bioinforma Chem AABC. 2010;4: 1–12.
    • (2010) Adv Appl Bioinforma Chem AABC , vol.4 , pp. 1-12
    • Taneda, A.1
  • 17
    • 84893831061 scopus 로고    scopus 로고
    • RNA design rules from a massive open laboratory
    • pmid:24469816
    • Lee J, Kladwang W, Lee M, Cantu D, Azizyan M, Kim H, et al. RNA design rules from a massive open laboratory. Proc Natl Acad Sci. 2014;111: 2122–2127. doi: 10.1073/pnas.1313039111 pmid: 24469816
    • (2014) Proc Natl Acad Sci , vol.111 , pp. 2122-2127
    • Lee, J.1    Kladwang, W.2    Lee, M.3    Cantu, D.4    Azizyan, M.5    Kim, H.6
  • 18
    • 84958581697 scopus 로고    scopus 로고
    • Principles for Predicting RNA Secondary Structure Design Difficulty
    • pmid:26902426
    • Anderson-Lee J, Fisker E, Kosaraju V, Wu M, Kong J, Lee J, et al. Principles for Predicting RNA Secondary Structure Design Difficulty. J Mol Biol. 2016;428: 748–757. doi: 10.1016/j.jmb.2015.11.013 pmid: 26902426
    • (2016) J Mol Biol , vol.428 , pp. 748-757
    • Anderson-Lee, J.1    Fisker, E.2    Kosaraju, V.3    Wu, M.4    Kong, J.5    Lee, J.6
  • 24
    • 85031918331 scopus 로고    scopus 로고
    • Mastering the game of Go without human knowledge
    • pmid:29052630
    • Silver D, Schrittwieser J, Simonyan K, Antonoglou I, Huang A, Guez A, et al. Mastering the game of Go without human knowledge. Nature. 2017;550: 354–359. doi: 10.1038/nature24270 pmid: 29052630
    • (2017) Nature , vol.550 , pp. 354-359
    • Silver, D.1    Schrittwieser, J.2    Simonyan, K.3    Antonoglou, I.4    Huang, A.5    Guez, A.6
  • 27
    • 85049363996 scopus 로고    scopus 로고
    • DeepChem: Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology [Internet]. deepchem; 2017. Available
    • DeepChem: Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology [Internet]. deepchem; 2017. Available: https://github.com/deepchem/deepchem


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.