, Voter AF: A method for accelerating the molecular dynamics simulation of infrequent events, J. Chem. Phys, vol.106, issue.11, pp.4665-4677, 1997.

S. Izrailev, S. Stepaniants, B. Isralewitz, D. Kosztin, H. Lu et al., Steered molecular dynamics, Computational Molecular Dynamics: Challenges, Methods, Ideas, pp.39-65, 1998.

R. R. Sørensen and A. F. Voter, Temperature-accelerated dynamics for simulation of infrequent events, J. Comput. Phys, vol.112, pp.9599-9606, 2000.

A. Laio and M. Parrinello, Escaping free-energy minima, Proc Natl. Acad. Sci. U.S.A, vol.99, issue.20, pp.12562-12566, 2002.

D. Hamelberg, J. Morgan, and J. A. Mccammon, Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules, J. Chem. Phys, vol.120, pp.11919-11929, 2004.

D. E. Shaw, P. Maragakis, K. Lindorff-larsen, S. Piana, R. O. Dror et al., Atomic-level characterization of the structural dynamics of proteins, Science, vol.2010, issue.6002, pp.341-346

G. Mills and H. Jónsson, Quantum and thermal effects in H2 dissociative adsorption: Evaluation of free energy barriers in multidimensional quantum systems, Phys. Rev. Lett, vol.72, pp.1124-1127, 1994.

E. Ren, W. Vanden-eijnden, and E. , String method for the study of rare events, Phys. Rev. B, vol.66, p.52301, 2002.

P. G. Bolhuis, D. Chandler, C. Dellago, and P. L. Geissler, Transition path sampling and the calculation of rate constants, Annu. Rev. Phys. Chem, vol.53, pp.291-318, 2002.

J. Cortés, T. Siméon, V. Ruiz-de-angulo, D. Guieysse, M. Remaud-siméon et al., A path planning approach for computing large-amplitude motions of flexible molecules, Bioinformatics, vol.21, issue.1, pp.116-125, 2005.

B. Raveh, A. Enosh, O. Schueler-furman, and D. Halperin, Rapid sampling of molecular motions with prior information constraints, PLoS Comput. Biol, vol.5, issue.2, p.1000295, 2009.

N. Haspel, M. Moll, M. Baker, W. Chiu, and L. E. Kavraki, Tracing conformational changes in proteins, BMC Struct. Biol, issue.1, p.1, 2010.

A. Siméon, T. Cortés, and J. , Motion planning algorithms for molecular simulations: a survey, Comput. Sci. Rev, vol.2012, issue.4, pp.125-143

Q. Cui and I. Bahar, Normal mode analysis: theory and applications to biological and chemical systems. Chapman and Hall/CRC mathematical and computational biology series, 2006.

B. Brooks and M. Karplus, Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme, Proc Natl. Acad. Sci. U.S.A, vol.82, issue.15, pp.4995-4999, 1985.

K. Hinsen, Analysis of domain motions by approximate normal mode calculations, Proteins, vol.33, issue.3, 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 calculations, Prot. 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, Prot. Sci, vol.14, issue.3, pp.633-643, 2005.

S. Kirillova, J. Cortés, and A. Stefaniu, Siméon T: An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins, Proteins, vol.70, pp.131-143, 2008.

B. P. Cossins, A. Hosseini, and V. Guallar, Exploration of protein conformational change with PELE and meta-dynamics, J. Chem. Theory Comput, vol.8, pp.959-965, 2012.

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

B. Siciliano and O. Khatib, , 2008.

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.

A. R. Atilgan, S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin et al., Anisotropy of fluctuation dynamics of proteins with an elastic network model, Biophys. J, vol.80, pp.505-515, 2001.

, Tirion MM: Large amplitude elastic motions in proteins from a single-parameter, atomic analysis, Phys. Rev. Lett, vol.77, issue.9, pp.1905-1908, 1996.

M. K. Kim, R. L. Jernigan, and G. S. Chirikjian, Efficient generation of feasible pathways for protein conformational transitions, Biophys. J, vol.83, issue.3, pp.1620-1630, 2002.

F. Tama, O. Miyashita, I. Brooks, and . Cl, Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM, J. Struc. Biol, vol.147, issue.3, pp.315-326, 2004.

C. N. Cavasotto, J. A. Kovacs, and R. A. Abagyan, Representing receptor flexibility in ligand docking through relevant normal modes, J. Am. Chem. Soc, vol.127, issue.26, pp.9632-9640, 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, issue.2, pp.393-410, 1996.

A. D. Schuyler and G. S. Chirikjian, Efficient determination of low-frequency normal modes of large protein structures by cluster-NMA, J. Mol. Graph. Model, vol.24, pp.46-58, 2005.

O. Demerdash and J. C. Mitchell, Density-cluster NMA: a new protein decomposition technique for coarse-grained normal mode analysis, Proteins, vol.2012, issue.7, pp.1766-1779

E. Eyal, L. W. Yang, and I. Bahar, Anisotropic network model: systematic evaluation and a new web interface, Bioinformatics, vol.22, issue.21, pp.2619-2627, 2006.

J. Cortés and I. Al-bluwi, A robotics approach to enhance conformational sampling of proteins, Proc. IDETC/CIE, 2012.

M. Renaud, A simplified inverse kinematic model calculation method for all 6R type manipulators, Current Advances in Mechanical Design and Production VII, pp.57-66, 2000.

H. Y. Lee and C. G. Liang, A new vector theory for the analysis of spatial mechanisms, Mech. Mach. Theory, vol.23, issue.3, pp.209-217, 1988.

D. Manocha and J. F. Canny, Efficient inverse kinematics for general 6R manipulators, IEEE Trans. Robot. Autom, vol.10, issue.5, pp.648-657, 1994.

E. A. Coutsias, C. Seok, M. P. Jacobson, and K. A. Dill, A kinematic view of loop closure, J. Comput. Chem, vol.25, issue.4, pp.510-528, 2004.

A. Atramentov and S. M. Lavalle, Efficient nearest neighbor searching for motion planning, Proc. IEEE Int. Conf. Robot. Autom, pp.632-637, 2002.

, Research Collaboratory for Structural Bioinformatics PDB

D. A. Case, T. A. Darden, I. Cheatham, . Te, C. L. Simmerling et al., , 2006.

, The PyMOL Molecular Graphics System, Version 1.5, Schrödinger, LLC

E. Plaku, H. Stamati, C. Clementi, and L. Kavraki, Fast and reliable analysis of molecular motion using proximity relations and dimensionality reduction, Proteins, vol.67, issue.4, pp.897-907, 2007.

A. Shehu and B. Olson, Guiding the search for native-like protein conformations with an ab-initio treebased exploration, Int. J. Robot. Res, vol.29, issue.8, pp.1106-1127, 2010.

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 ? A resolution. 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, issue.2, pp.147-156, 1996.

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.

Y. Feng, L. Yang, A. Kloczkowski, and R. L. Jernigan, The energy profiles of atomic conformational transition intermediates of adenylate kinase, Proteins, vol.77, issue.3, pp.551-558, 2009.

D. Devaurs, T. Siméon, and J. Cortés, Parallelizing RRT on distributed-memory architectures, Proc. IEEE Int. Conf. Robot. Autom, pp.2261-2266, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00872218

L. Jaillet, J. Cortés, and T. Siméon, Sampling-based path planning on configuration-space costmaps, IEEE Trans. Robot, vol.26, issue.4, pp.635-646, 2010.
URL : https://hal.archives-ouvertes.fr/hal-01986202

L. Jaillet, F. J. Corcho, J. J. Pérez, and J. Cortés, Randomized tree construction algorithm to explore energy landscapes, J. Comput. Chem, vol.32, issue.16, pp.3464-3474, 2011.
URL : https://hal.archives-ouvertes.fr/hal-01894030