N. M. Amato, K. A. Dill, and G. Song, Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures, J. Comput. Biol, vol.10, pp.149-168, 2003.

M. S. Apaydin, D. L. Brutlag, C. Guestrin, D. Hsu, and J. Latombe, Stochastic roadmap simulation: an efficient representation and algorithm for analyzing molecular motion, Proceedings of RECOMB, pp.12-21, 2002.

M. S. Apaydin, D. L. Brutlag, C. Guestrin, D. Hsu, and J. Latombe, Stochastic conformational roadmaps for computing ensemble properties of molecular motion, Algorithmic Foundations of Robotics V (WAFR'02), pp.131-147, 2004.

H. A. Carlson, Protein flexibility and drug design: how to hit a moving target, Cur. Opin. Chem. Biol, vol.6, pp.447-452, 2002.

J. Cortés, T. Siméon, and J. Laumond, A random loop generator for planning the motions of closed kinematic chains using PRM methods, Proceedings of IEEE International Conference on Robotics and Automation, pp.2141-2146, 2002.

J. Cortés, T. Siméon, M. Remaud-siméon, and V. Tran, Geometric algorithms for the conformational analysis of long protein loops, J. Comput. Chem, vol.25, pp.956-967, 2004.

J. Cortés and T. Siméon, Sampling-based motion planning under kinematic loop-closure constraints, Algorithmic Foundations of Robotics VI (WAFR'04), 2004.

M. A. Depristo, P. I. De-bakker, S. C. Lovell, and T. L. Blundell, Ab initio construction of polypeptide fragments: efficient generation of accurate, representative ensembles, Proteins, vol.51, pp.41-55, 2003.

D. Guieysse, C. Salagnad, P. Monsan, M. Remaud-simeon, and V. Tran, Towards a novel explanation of Pseudomonas Cepacia lipase enantioselectivity via molecular modelling of the enantiomer trajectory into the active site, Tetrahedron: Asymmetry, vol.14, pp.1807-1817, 2003.

R. M. Jackson, H. A. Gabb, and M. J. Stenberg, Rapid refinement of protein interfaces incorporating solvation: application to the docking problem, J. Mol. Biol, vol.276, pp.265-285, 1998.

L. C. James, P. Roversi, and D. S. Tawfik, Antibody multispecificity mediated by conformational diversity, Science, vol.299, pp.1362-1367, 2003.

J. Janin, K. Henrick, J. Moult, L. T. Eyck, M. J. Sternberg et al., CAPRI: a critical assessment of predicted interactions, Proteins, vol.52, pp.2-9, 2003.

L. E. Kavraki, P. Svestka, J. Latombe, and M. H. Overmars, Probabilistic roadmaps for path planning in high-dimensional configuration spaces, IEEE Trans. Robotics Autom, vol.12, pp.566-580, 1996.

I. D. Kuntz, J. M. Blaney, S. J. Oatley, R. Langridge, and T. E. Ferrin, A geometric approach to macromolecule-ligand interactions, J. Mol. Biol, vol.161, pp.269-288, 1982.

J. Latombe, Robot Motion Planning, 1991.

S. M. Lavalle, J. J. Kuffner, and A. K. Peters, Rapidly-exploring random trees: progress and prospects, Algorithmic and Computational Robotics: New Directions (WAFR2000), pp.293-308, 2001.

A. R. Leach, Molecular Modeling: Principles and Applications, 1996.

M. Lei, L. A. Kuhn, M. I. Zavodszky, and M. F. Thorpe, Sampling protein conformations and pathways, J. Comput. Chem, vol.25, pp.1133-1148, 2004.

E. F. De-lemos, F. Esteves, V. Ruelle, J. Lamotte-brasseur, B. Quinting et al., Acidophilic adaptation of family 11 endo-?-1,4-xylanases: modeling and mutational analysis, Protein Sci, vol.13, pp.1209-1218, 2004.

I. Lotan, F. Schwarzer, D. Halperin, and J. Latombe, Efficient maintenance and self-collision testing for kinematic chains, Proceedings of the 18th ACM Symposium on Computational Geometry, pp.43-52, 2002.

D. Manocha and J. Canny, Efficient inverse kinematics of general 6R manipulators, IEEE Trans. Robotics Autom, vol.10, pp.648-657, 1994.

A. W. Moore, A. Connolly, C. Genovese, A. Gray, L. Grone et al., Fast algorithms and efficient statistics: N-point correlation Functions, Proceedings of MPA/MPE/ESO Conference on Mining the Sky, 2001.

J. Moult and M. N. James, An algorithm for determining the conformation of polypeptide segments in proteins by systematic search, Proteins, vol.1, pp.146-163, 1986.

J. Muilu, A. Torronen, M. Perakyla, and J. Rouvinen, Functional conformational changes of endo-1,4-xylanase II from Trichoderma reesei: a molecular dynamics study, Proteins, vol.31, pp.434-478, 1998.

M. J. Osborne, J. Schnell, S. J. Benkovic, H. J. Dyson, and P. E. Wright, Backbone dynamics in dihdydrofolate reductase complexes: role of loop flexibility in the catalytic mechanism, Biochemistry, vol.40, pp.9846-9859, 2001.

M. Rarey, B. Kramer, T. Lengauer, and G. Klebe, A fast flexible docking method using an incremental construction algorithm, J. Mol. Biol, vol.261, pp.470-489, 1996.
DOI : 10.1006/jmbi.1996.0477

M. Renaud, A simplified inverse kinematic model calculation method for all 6R type manipulators, Proceedings of International Conference on Mechanical Design and Production, pp.15-25, 2000.
DOI : 10.1016/b978-008043711-8/50002-7

V. Ruiz-de-angulo, J. Cortés, and T. Siméon, BioCD: an efficient algorithm for self-detection and distance computation between highly articulated molecular models, Proceedings of Robotics: Science and Systems, 2005.

A. P. Singh, J. Latombe, and D. L. Brutlag, A motion planning approach to flexible ligand binding, Proceedings of ISMB, pp.252-261, 1999.

X. Tang, B. Kirkpatrick, S. Thomas, G. Song, and N. M. Amato, Using motion planning to study RNA folding kinetics, Proceedings of RECOMB, pp.252-261, 2004.
DOI : 10.1145/974614.974648

URL : http://parasol.tamu.edu/publications/download.php?file_id=77

A. Tramontano, R. Leplace, and V. Morea, Analysis and assessment of comparative modeling predictions in CASP4, Proteins, Suppl, vol.5, pp.22-38, 2001.

A. Yershova, L. Jaillet, T. Siméon, and S. M. Lavalle, Dynamic-domain RRTs: efficient exploration by controlling the sampling domain, Proc. IEEE Int. Conf. Robotics Automation, pp.3867-3872, 2005.
URL : https://hal.archives-ouvertes.fr/hal-01987538

M. Zhang and L. E. Kavraki, A New Method for Fast and Accurate Derivation of Molecular Conformations, J. Chem. Inf. Comput. Sci, vol.41, pp.64-70, 2002.