Motion for structural bioinformatics

Computational tools are today of primary importance for biologists to model protein structure and function, and understand biomolecular interactions. In this context, our goal is to explore new computational routes for structural bioinformatics, using robotic algorithms. The algorithmic challenge comes from the complexity of molecular chains involving up to thousands degrees of freedom. Our results show the high potential of these new techniques for modeling macromolecular flexibility as well as studying ligand-receptor interactions.

Relevant Papers

J.CORTES , S.BARBE , M.ERARD , T.SIMEON, Encoding molecular motions in voxel maps. IEEE International Conference on Robotics and Automation (ICRA 2009), Kobe (Japon), May 2009, 6p.

D.GUIEYSSE , J.CORTES , S.PUECH-GUENOT , S.BARBE , V.LAFAQUIERE , P.MONSAN , T.SIMEON , I.ANDRE , M.REMAUD-SIMEON, A structure-controlled lipase enantioselectivity investigated by a path planning approach. ChemBioChem, Vol.9, N°8, pp.1308-1317, May 2008

S.KIRILLOVA , J.CORTES , A.B.STEFANIU , T.SIMEON, An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins. Proteins: Structure, Function, and Bioinformatics, Vol.70, N°1, pp.131-143, December2007

J.CORTES , L.JAILLET , T.SIMEON, Molecular disassembly with RRT-like algorithms. 2007 IEEE International Conference on Robotics and Automation (ICRA'07), Rome (Italie), April 2007, pp.3301-3306

J.CORTES , T.SIMEON , V.RUIZ DE ANGULO , D.GUIEYSSE , M.REMAUD-SIMEON , V.TRAN, A path planning approach for computing large-amplitude motions of flexible molecules. 13th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB'2005), Détroit (USA), 25-29 Juin 2005, Rapport LAAS N°05020, Bioinformatics, Vol.21, N°Supplement 1, pp.i116-i125, 2005

J.CORTES , T.SIMEON , M.REMAUD-SIMEON , V.TRAN, Geometric algorithms for the conformational analysis of lang protein loops. Journal of Computational Chemistry, Issue 7, Vol.25, pp.956-967, May 2004