Students generate molecular structures.
They send their results to our web service.
Their files get scored and ranked by RMSD against the reference structures.
UnityMol + HiRE-RNA
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.
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
- 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.
- Coarse-grained simulations of RNA and DNA duplexes.
T. Cragnolini et al. J. Phys. Chem. B, 117(27):8047–8060, 2013.
- Game on, science - how video game technology may help biologists tackle visualization challenges.
Z. Lv et al. PLoS ONE, 8(3):e57990, Mar. 2013.
- 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.
- UnityMol: Interactive and ludic visual manipulation of coarse-grained RNA and other biomolecules.
S. Doutreligne et al. VARMS@IEEEVR 2015, Mar. 2015.
- A VR framework prototype for immersive exploration and manipulation of molecular structures based on UnityMol.
X. Martinez et al. EuroVR 2016, Nov. 2016.