H. A. Carlson, Protein flexibility is an important component of structure-based drug discovery, Curr Pharm Des, vol.8, pp.1571-1578, 2002.

C. N. Cavasotto, A. Orry, and R. A. Abagyan, The challenge of considering receptor flexibility in ligand docking and virtual screening, Curr Comput Aided Drug Des, vol.1, pp.423-440, 2005.

J. Janin, Assessing predictions of protein-protein interaction: the CAPRI experiment, Protein Sci, vol.14, pp.278-283, 2005.

L. P. Ehrlich, M. Nilges, and R. C. Wade, The impact of protein flexibility on protein-protein docking, Proteins, vol.58, pp.126-133, 2005.

N. Floquet, J. Marechal, M. Badet-denisot, C. H. Robert, M. Dauchez et al., Normal mode analysis as a prerequisite for drug design: application to matrix metalloproteinases inhibitors, FEBS Letters, vol.580, pp.5130-5136, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00105805

A. R. Leach, Molecular modeling: principles and applications. Essex: Longman, 1996.

T. Schlick, Molecular modeling and simulation-an interdisciplinary guide, 2002.

M. S. Apaydin, D. L. Brutlag, C. Guestrin, D. Hsu, J. Latombe et al., Stochastic roadmap simulation: an efficient representation and algorithm for analyzing molecular motion, J Comput Biol, vol.10, pp.257-281, 2003.

J. Cortés, T. Siméon, V. Ruiz-deangulo, D. Guieysse, M. Remaud-siméon et al., A path planning approach for computing large-amplitude motions of flexible molecules, Bioinformatics, vol.21, pp.116-125, 2005.

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.

A. Enosh, S. J. Fleishman, N. Ben-tal, and D. Halperin, Prediction and simulation of motion in pairs of transmembrane ?-helices, Bioinformatics, vol.23, pp.212-218, 2007.

Q. Cui and I. Bahar, Normal mode analysis: theory and applications to biological and chemical systems, 2006.

B. R. Brooks and M. Karplus, Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme, Proc Natl Acad Sci, vol.82, pp.4995-4999, 1985.

K. Hinsen, Analysis of domain motions by approximate normal mode calculations, Proteins, vol.33, pp.417-429, 1998.
URL : https://hal.archives-ouvertes.fr/hal-02159766

F. Tama and Y. H. Sanejouand, Conformational change of proteins arising from normal mode analysis, Protein Eng, vol.14, pp.1-6, 2001.

V. Alexandrov, U. Lehnert, N. Echols, D. Milburn, D. Engelman et al., Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool, Protein Sci, vol.14, pp.633-643, 2005.

L. Mouawad and D. Perahia, Motions in hemoglobin studied by normal mode analysis and energy minimization: evidence for the existence of tertiary T-like, quaternary R-like intermediate structures, J Mol Biol, vol.258, pp.393-410, 1996.

O. Miyashita, J. N. Onuchic, and P. G. Wolynes, Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins, Proc Natl Acad Sci, vol.100, pp.12570-12575, 2003.

F. Tama, O. Miyashita, I. Brooks, and . Cl, Normal mode based flexible fitting of highresolution structure into low-resolution experimental data from cryo-EM, J Struct Biol, vol.147, pp.315-341, 2004.

J. I. Jeong, E. E. Lattman, and G. S. Chirikjian, A method for finding candidate conformations for molecular replacement using relative rotation between domains of a known structure, Acta Cryst, vol.62, pp.398-409, 2006.

M. M. Tirion, Large amplitude elastic motions in proteins from a single-parameter, atomic analysis, Phys Rev Lett, vol.77, pp.1905-1908, 1996.

F. Tama, I. Brooks, and . Cl, The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus, J Mol Biol, vol.318, pp.733-747, 2002.

I. Bahar, A. R. Atilgan, and B. Erman, Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential, Fold Des, vol.2, pp.173-181, 1997.

C. N. Cavasotto, J. A. Kovacs, and R. A. Abagyan, Representing receptor flexibility in ligand docking through relevant normal modes, J Am Chem Soc, pp.127-9632, 2005.

M. K. Kim, R. L. Jernigan, and G. S. Chirikjian, Efficient Generation of Feasible Pathways for Protein Conformational Transitions, Biophys J, vol.83, pp.1620-1630, 2002.

P. Maragakis and M. Karplus, Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase, J Mol Biol, vol.352, pp.807-822, 2005.

K. Suhre and Y. H. Sanejouand, ElNémo: a normal mode web-server for protein movement analysis and the generation of templates for molecular replacement, Nucleic Acids Res, vol.32, pp.610-614, 2004.

F. Tama, F. X. Gadea, O. Marques, and Y. H. Sanejouand, Building-block approach for determining low-frequency normal modes of macromolecules, Proteins, vol.41, pp.1-7, 2000.

J. Latombe, Robot motion planning, 1991.

S. M. Lavalle, Planning algorithms, 2006.
URL : https://hal.archives-ouvertes.fr/hal-01993243

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.239-255, 2003.

V. Ruiz-de-angulo, J. Cortés, and T. Siméon, BioCD: an efficient algorithm for self-collision and distance computation between highly articulated molecular models, Robotics: Science and Systems I, pp.6-11, 2005.
URL : https://hal.archives-ouvertes.fr/hal-01988238

S. M. Lavalle and J. J. Kuffner, Rapidly-exploring random trees: progress and prospects, Algorithmic and computational robotics: new directions (WAFR2000), pp.293-308, 2001.

K. Lindorff-larsen, R. B. Best, M. A. Depristo, C. M. Dobson, and M. Vendruscolo, Simultaneous determination of protein structure and dynamics, Nature, vol.433, pp.128-132, 2005.

C. W. Müller and G. E. Schulz, Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 ? Aresolution. A model for a catalytic transition state, J Mol Biol, vol.224, pp.159-177, 1992.

C. W. Müller, G. J. Schlauderer, J. Reinstein, and G. E. Schulz, Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding, Structure, vol.4, pp.147-156, 1996.

O. Dror, H. Benyamini, R. Nussinov, and H. Wolfson, MASS: Multiple structural alignment by secondary structures, Bioinformatics, vol.19, pp.95-104, 2003.

M. A. Depristo, P. 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.

S. Flores, N. Echols, D. Milburn, B. Hespenheide, K. Keating et al., The Database of Macromolecular Motions: new features added at the decade mark, Nucleic Acids Res, vol.34, pp.296-301, 2006.

L. Mouawad and D. Perahia, Diagonalization in a mixed basis: a method to compute low-frequency normal modes for large macromolecules, Biopolymers, vol.33, pp.599-611, 1993.