B. Brooks, R. Bruccoleri, B. Olafson, D. States, S. Swaminathan et al., CHARMM: A program for macromolecular energy, minimization, and dynamics calculations, Journal of Computational Chemistry, vol.I, issue.2, pp.187-217, 1983.
DOI : 10.1002/jcc.540040211

S. Crivelli, O. Kreylos, B. Hamann, N. Max, and W. Bethel, ProteinShop: A tool for interactive protein manipulation and steering, Journal of Computer-Aided Molecular Design, vol.18, issue.4, 2004.
DOI : 10.1023/B:JCAM.0000046822.54719.4f

S. Crouzy, S. Bernèche, R. , and B. , Channels by Tea, The Journal of General Physiology, vol.34, issue.2, pp.207-217, 2001.
DOI : 10.1126/science.2000494

D. Doyle, J. Cabral, R. Pfuetzner, A. Kuo, J. Gulbis et al., The Structure of the Potassium Channel: Molecular Basis of K+ Conduction and Selectivity, Science, vol.280, issue.5360, pp.69-77, 1998.
DOI : 10.1126/science.280.5360.69

R. Featherstone, A Divide-and-Conquer Articulated-Body Algorithm for Parallel O(log(n)) Calculation of Rigid-Body Dynamics. Part 1: Basic Algorithm, The International Journal of Robotics Research, vol.18, issue.9, pp.867-875, 1999.
DOI : 10.1177/02783649922066619

R. Featherstone, A Divide-and-Conquer Articulated-Body Algorithm for Parallel O(log(n)) Calculation of Rigid-Body Dynamics. Part 2: Trees, Loops, and Accuracy, The International Journal of Robotics Research, vol.18, issue.9, pp.876-892, 1999.
DOI : 10.1177/02783649922066628

S. Gottschalk, M. C. Lin, and D. Manocha, OBBTree, Proceedings of the 23rd annual conference on Computer graphics and interactive techniques , SIGGRAPH '96, 1996.
DOI : 10.1145/237170.237244

T. Head-gordon and C. Brooks, Virtual rigid body dynamics, Biopolymers, vol.2, issue.1, pp.77-100, 1991.
DOI : 10.1002/bip.360310108

L. Heginbotham and R. Mackinnon, The aromatic binding site for tetraethylammonium ion on potassium channels, Neuron, vol.8, issue.3, pp.483-491, 1992.
DOI : 10.1016/0896-6273(92)90276-J

P. Herzyk and R. E. Hubbard, A reduced representation of proteins for use in restraint satisfaction calculations, Proteins: Structure, Function, and Genetics, vol.4, issue.3, pp.310-324, 1993.
DOI : 10.1002/prot.340170308

J. Janin, Assessing predictions of protein-protein interaction: The CAPRI experiment, Protein Science, vol.14, issue.2, pp.278-283, 2005.
DOI : 10.1110/ps.041081905

I. Lotan, F. Schwarzer, D. Halperin, and J. Latombe, Algorithm and Data Structures for Efficient Energy Maintenance during Monte Carlo Simulation of Proteins, Journal of Computational Biology, vol.11, issue.5, pp.902-932, 2004.
DOI : 10.1089/cmb.2004.11.902

E. Neria, S. Fischer, and M. Karplus, Simulation of activation free energies in molecular systems, The Journal of Chemical Physics, vol.105, issue.5, 1996.
DOI : 10.1063/1.472061

S. Redon and M. C. Lin, An efficient, error-bounded approximation algorithm for simulating quasi-statics of complex linkages, Computer-Aided Design, vol.38, issue.4, pp.300-314, 2006.
DOI : 10.1016/j.cad.2006.01.009

URL : https://hal.archives-ouvertes.fr/hal-01148355

S. Redon, N. Gallopo, and M. C. Lin, Adaptive dynamics of articulated bodies, In ACM Transactions on Graphics, issue.3, p.24, 2005.
URL : https://hal.archives-ouvertes.fr/inria-00390315

A. Sasli and T. Blundell, Comparative Protein Modelling by Satisfaction of Spatial Restraints, Journal of Molecular Biology, vol.234, issue.3, pp.779-815, 1993.
DOI : 10.1006/jmbi.1993.1626