HiRE-RNA Contest

Welcome to the HiRE-RNA Contest homepage. In this contest, participants are asked to manipulate RNA structures interactively. These molecules are found in living cells, like DNA, but perform other functions.

People run Molecular Dynamics Simulations at home. By mean of a molecular visualization software, UnityMol, they can pull atoms and discover how these molecules behave and how it is related to the function.

Participants then submit their simulated RNA structures. They are then are evaluated and scored based on energy calculations.

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Principle

1

Students generate molecular structures.

2

They send their results to our web service.

3

Their files get scored and ranked by RMSD against the reference structures.

UnityMol + HiRE-RNA

Perfect Match

Molecular Dynamics Simulations are computationally costly. They take a long time to simulate very few. Coarse-grained models consist in reducing the number of simulated atoms. Thus, we get a higher throughput while still preserving foundamental and significant molecular behaviors. HiRE-RNA is one of such coarse-grained models for RNA molecules [1,2]. It allows us to simulate and capture significant molecular behavior while being computionally efficient.

UnityMol is a molecular visualization software geared towards biology. Created in 2011, it enables us to quickly prototype and validate new molecular representations. UnityMol development is based on the Unity3D video game engine, a promising new way to design research software [3,4].

By coupling the HiRE-RNA simulator with UnityMol, we get a direct insight of the molecular behavior. Users can also directly interact with the molecule using the classic computer mouse.

Meet Us

You might also have seen us at these events:

  • EuroVR 2016 - November 22-24, 2016, Athens, Greece
  • iGAMER 2015 - January 29-31, 2016, Cité des Sciences et de l'Industrie, Paris - France
  • GGMM 2015 - 19th Congress - May 26-28, 2015, Sète - France
  • IEEE VARMS workshop - Virtual and Augmented Reality dedicated to Molecular Science - March 24, 2015, Arles - France
  • igam4er 2014 - December 12-14, 2014, Cité des Sciences et de l'Industrie, Paris - France
  • Reims Image 2014 - AFIG - November 25-28, 2014, Reims - France
  • IEEE LDAV 2014 - November 9-10, 2014, Paris - France

References

  1. HiRE-RNA: a high resolution coarse- grained energy model for RNA.
    S. Pasquali and P. Derreumaux. J. Phys. Chem. B, 114(37):11957– 11966, Sept. 2010.
  2. Coarse-grained simulations of RNA and DNA duplexes.
    T. Cragnolini et al. J. Phys. Chem. B, 117(27):8047–8060, 2013.
  3. Game on, science - how video game technology may help biologists tackle visualization challenges.
    Z. Lv et al. PLoS ONE, 8(3):e57990, Mar. 2013.
  4. Three-dimensional representations of complex carbohydrates and polysaccharides - Sweet UnityMol: A video game-based computer graphic software.
    S. Pérez, T. Tubiana, A. Imberty, and M. Baaden. Glycobiology, page cwu133, Dec. 2014.
  5. UnityMol: Interactive and ludic visual manipulation of coarse-grained RNA and other biomolecules.
    S. Doutreligne et al. VARMS@IEEEVR 2015, Mar. 2015.
  6. A VR framework prototype for immersive exploration and manipulation of molecular structures based on UnityMol.
    X. Martinez et al. EuroVR 2016, Nov. 2016.

Laboratoire de Biochimie Théorique

HiRE-RNA is continously developed since 2009 at LBT - Laboratoire de Biochimie Théorique - CNRS UPR 9080. The work was initiated by Doctors Samuela Pasquali and Philippe Derreumaux. Among contributors, we find Tristan Cragnolini and Cédric Gageat.

UnityMol was created in 2011. Contributors: Marc Baaden, Zhihan Lv, Alex Tek, Mathieu Chavent, Franck Da Silva, Charly Empereur-mot, Mikael Trellet, Thibault Tubiana, Caroline Roudier, Sébastien Doutreligne, Benoist Laurent, Adrien Danzon, Xavier Martinez, Pierre Ghossoub.

The lab is located at Institut de Biologie Physico-Chimique - Paris.