IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0136444.html
   My bibliography  Save this article

GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies

Author

Listed:
  • Mélanie Boudard
  • Julie Bernauer
  • Dominique Barth
  • Johanne Cohen
  • Alain Denise

Abstract

Cellular processes involve large numbers of RNA molecules. The functions of these RNA molecules and their binding to molecular machines are highly dependent on their 3D structures. One of the key challenges in RNA structure prediction and modeling is predicting the spatial arrangement of the various structural elements of RNA. As RNA folding is generally hierarchical, methods involving coarse-grained models hold great promise for this purpose. We present here a novel coarse-grained method for sampling, based on game theory and knowledge-based potentials. This strategy, GARN (Game Algorithm for RNa sampling), is often much faster than previously described techniques and generates large sets of solutions closely resembling the native structure. GARN is thus a suitable starting point for the molecular modeling of large RNAs, particularly those with experimental constraints. GARN is available from: http://garn.lri.fr/.

Suggested Citation

  • Mélanie Boudard & Julie Bernauer & Dominique Barth & Johanne Cohen & Alain Denise, 2015. "GARN: Sampling RNA 3D Structure Space with Game Theory and Knowledge-Based Scoring Strategies," PLOS ONE, Public Library of Science, vol. 10(8), pages 1-21, August.
    • Handle: RePEc:plo:pone00:0136444
    DOI: 10.1371/journal.pone.0136444
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0136444
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0136444&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0136444?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Loomes, Graham & Sugden, Robert, 1982. "Regret Theory: An Alternative Theory of Rational Choice under Uncertainty," Economic Journal, Royal Economic Society, vol. 92(368), pages 805-824, December.
    2. Jes Frellsen & Ida Moltke & Martin Thiim & Kanti V Mardia & Jesper Ferkinghoff-Borg & Thomas Hamelryck, 2009. "A Probabilistic Model of RNA Conformational Space," PLOS Computational Biology, Public Library of Science, vol. 5(6), pages 1-11, June.
    3. Marc Parisien & François Major, 2008. "The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data," Nature, Nature, vol. 452(7183), pages 51-55, March.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Jun Li & Wei Zhu & Jun Wang & Wenfei Li & Sheng Gong & Jian Zhang & Wei Wang, 2018. "RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks," PLOS Computational Biology, Public Library of Science, vol. 14(11), pages 1-18, November.
    2. Georgia Perakis & Guillaume Roels, 2008. "Regret in the Newsvendor Model with Partial Information," Operations Research, INFORMS, vol. 56(1), pages 188-203, February.
    3. Jinyi Hu, 2023. "Linguistic Multiple-Attribute Decision Making Based on Regret Theory and Minimax-DEA," Mathematics, MDPI, vol. 11(20), pages 1-14, October.
    4. repec:cup:judgdm:v:15:y:2020:i:6:p:1044-1051 is not listed on IDEAS
    5. Sacha Bourgeois-Gironde, 2017. "How regret moves individual and collective choices towards rationality," Chapters, in: Morris Altman (ed.), Handbook of Behavioural Economics and Smart Decision-Making, chapter 11, pages 188-204, Edward Elgar Publishing.
    6. Martín Egozcue & Xu Guo & Wing-Keung Wong, 2015. "Optimal output for the regret-averse competitive firm under price uncertainty," Eurasian Economic Review, Springer;Eurasia Business and Economics Society, vol. 5(2), pages 279-295, December.
    7. Jhunjhunwala, Tanushree, 2021. "Searching to avoid regret: An experimental evidence," Journal of Economic Behavior & Organization, Elsevier, vol. 189(C), pages 298-319.
    8. van Dijk, Wilco W. & van der Pligt, Joop, 1997. "The Impact of Probability and Magnitude of Outcome on Disappointment and Elation," Organizational Behavior and Human Decision Processes, Elsevier, vol. 69(3), pages 277-284, March.
    9. Ming Li & Dipjyoti Majumdar, 2010. "A Psychologically Based Model of Voter Turnout," Journal of Public Economic Theory, Association for Public Economic Theory, vol. 12(5), pages 979-1002, October.
    10. Kobana Abukari & Isaac Otchere, 2020. "Dominance of hybrid contratum strategies over momentum and contrarian strategies: half a century of evidence," Financial Markets and Portfolio Management, Springer;Swiss Society for Financial Market Research, vol. 34(4), pages 471-505, December.
    11. Peng Li & Ju Liu & Cuiping Wei, 2019. "A Dynamic Decision Making Method Based on GM(1,1) Model with Pythagorean Fuzzy Numbers for Selecting Waste Disposal Enterprises," Sustainability, MDPI, vol. 11(20), pages 1-19, October.
    12. Vaida Kaduskeviciute & Sigitas Urbonavicius, 2019. "Webrooming: A Way of Dealing with Uncertainties in Purchasing," Tržište/Market, Faculty of Economics and Business, University of Zagreb, vol. 31(2), pages 139-152.
    13. Qin, Jie, 2015. "A model of regret, investor behavior, and market turbulence," Journal of Economic Theory, Elsevier, vol. 160(C), pages 150-174.
    14. Grenet, Julien & He, YingHua & Kübler, Dorothea, 2022. "Preference Discovery in University Admissions: The Case for Dynamic Multioffer Mechanisms," EconStor Open Access Articles and Book Chapters, ZBW - Leibniz Information Centre for Economics, vol. 130(6), pages 1-1.
    15. Embrey, Matthew & Seel, Christian & Philipp Reiss, J., 2024. "Gambling in risk-taking contests: Experimental evidence," Journal of Economic Behavior & Organization, Elsevier, vol. 221(C), pages 570-585.
    16. Sugden, Robert & Wang, Mengjie & Zizzo, Daniel John, 2019. "Take it or leave it: Experimental evidence on the effect of time-limited offers on consumer behaviour," Journal of Economic Behavior & Organization, Elsevier, vol. 168(C), pages 1-23.
    17. Chorus, Caspar G., 2014. "Benefit of adding an alternative to one׳s choice set: A regret minimization perspective," Journal of choice modelling, Elsevier, vol. 13(C), pages 49-59.
    18. Camille Magron & Maxime Merli, 2012. "Stocks repurchase and sophistication of individual investors," Working Papers of LaRGE Research Center 2012-02, Laboratoire de Recherche en Gestion et Economie (LaRGE), Université de Strasbourg.
    19. Michaël Lainé, 2014. "Vers une alternative au paradigme de la rationalité ? Victoires et déboires du programme spinoziste en économie," Post-Print hal-01335618, HAL.
    20. Enrico G. De Giorgi & Thierry Post, 2011. "Loss Aversion with a State-Dependent Reference Point," Management Science, INFORMS, vol. 57(6), pages 1094-1110, June.
    21. Tonin, Stefania, 2018. "Citizens’ perspectives on marine protected areas as a governance strategy to effectively preserve marine ecosystem services and biodiversity," Ecosystem Services, Elsevier, vol. 34(PB), pages 189-200.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0136444. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.