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ITSNAP (2009-2014) Intelligent techniques for structures of nucleic acids and proteins |
Principal Investigators:
- Dr. Julie Bernauer, AMIB project-team, Inria Saclay Île-de-France
- Prof. Michael Levitt, Stanford University
- Dr Henry van den Bedem, Stanford Synchrotron Radiation Laboratory, SLAC
Research objectives:
RNA molecules are key biomolecules that are involved in a wide range of important biological processes for therapeutics such as gene regulation. To better understand the role of nucleic acids and specifically RNA in the cell, its folding, dynamics and interactions with ions and proteins should be studied. The ITSNAP team aimed at developing methods based on recent improvements in biogeometry, statistics and machine learning to improve RNA structure modeling, possibly dynamics simulations, junction characterization and protein-RNA interactions.Scientific achievements:
Results span: (i) developing inverse-kinematics strategies for RNA sampling (KGSrna), (ii) improving on the initial sampling to handle protein assemblies for experimental fitting and refinement, (iii) extending the KB potentials to drive the RNA sampling and docking, and (iv) developing a new full-flexible protein-RNA procedure that incorporates biological information.
Publications and Awards:
- 4 Journal articles.
- 4 Conference papers.
- KGSrna software for RNA conformation sampling at http://albios.saclay.inria.fr/kgsrna/
- NA KB potential Web server at http://csb.stanford.edu/rna
- Recipient of a 2014-15 France Stanford Research grant.
Selected publication:
Fonseca R, Pachov DV, Bernauer J, van den Bedem H: Characterizing RNA ensembles from NMR data with kinematic models. Nucleic Acids Res. 2014, 42(15): 9562- 72. PMID: 25114056.
Follow up :
ITSNAP proved essential in shedding light on the undertaken activities to the international community but also on Inria in the Computational Structural Biology community. Hopefully, the Inria Associate team and Inria@SiliconValley programs will continue successfully promoting the teams’ activities and creating an active scientific community and local social networks internationally
