]. R. Abagyan, M. Totrov, and &. D. Kuznetsov, ICM?A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation, Journal of Computational Chemistry, vol.8, issue.5, pp.488-506, 1994.
DOI : 10.1002/jcc.540150503

P. Agarwal, L. Guibas, A. Nguyen, D. Russel, and &. L. Zhang, Collision detection for deforming necklaces, Computational Geometry, vol.28, issue.2-3, pp.137-163, 2004.
DOI : 10.1016/j.comgeo.2004.03.008

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 Science, vol.14, issue.3, pp.633-643, 2005.
DOI : 10.1110/ps.04882105

A. Altis, P. H. Nguyen, R. Hegger, and &. G. Stock, Dihedral angle principal component analysis of molecular dynamics simulations, The Journal of Chemical Physics, vol.126, issue.24, p.244111, 2007.
DOI : 10.1063/1.2746330

]. N. Amato-98, O. B. Amato, L. K. Bayazit, C. Dale, &. D. Jones et al., OBPRM: An obstacle-based PRM for 3D workspaces, Robotics: The Algorithmic Perspective: 1998 Workshop on the Algorithmic Foundations of Robotics, pp.155-168, 1998.

K. A. Amato, &. G. Dill, and . Song, Using motion planning to map protein folding landscapes and analyze folding kinetics of known native structures, Journal of Computational Biology, vol.10, pp.3-4, 2003.

]. J. Angeles-07 and . Angeles, Fundamentals of robotic mechanical systems: Theory, methods, and algorithms, Mechanical Engineering Series, 2007.
DOI : 10.1007/b97597

A. P. Apaydin, D. L. Singh, &. J. Brutlag, and . Latombe, Capturing molecular energy landscapes with probabilistic conformational roadmaps, Proceedings 2001 ICRA. IEEE International Conference on Robotics and Automation (Cat. No.01CH37164), pp.932-939, 2001.
DOI : 10.1109/ROBOT.2001.932670

. Latombe, Stochastic roadmap simulation for the study of ligandprotein interactions, Bioinformatics, vol.18, issue.2, pp.18-26, 2002.

M. S. Apaydin, D. L. Brutlag, C. Guestrin, D. Hsu, J. C. Latombe et al., Stochastic roadmap simulation, Proceedings of the sixth annual international conference on Computational biology , RECOMB '02, pp.3-4, 2003.
DOI : 10.1145/565196.565199

D. L. Apaydin, D. Brutlag, &. J. Hsu, and . Latombe, Stochastic Conformational Roadmaps for Computing Ensemble Properties of Molecular Motion, Algorithmic Foundations of Robotics V, pp.131-147, 2004.
DOI : 10.1007/978-3-540-45058-0_9

J. Apostolakis, A. Plückthun, and &. A. Caflisch, Docking small ligands in flexible binding sites, Journal of Computational Chemistry, vol.221, issue.1, pp.21-37, 1998.
DOI : 10.1002/(SICI)1096-987X(19980115)19:1<21::AID-JCC2>3.0.CO;2-0

A. Atilgan, . Sr-durell, . Jernigan, O. Mc-demirel, &. I. Keskin et al., Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model, Biophysical Journal, vol.80, issue.1, pp.505-515, 2001.
DOI : 10.1016/S0006-3495(01)76033-X

&. S. Atramentov and . Lavalle, Efficient nearest neighbor searching for motion planning, Proceedings 2002 IEEE International Conference on Robotics and Automation (Cat. No.02CH37292), pp.632-637, 2002.
DOI : 10.1109/ROBOT.2002.1013429

I. Bahar, A. R. Atilgan, and &. B. Erman, Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential, Folding and Design, vol.2, issue.3, pp.173-181, 1997.
DOI : 10.1016/S1359-0278(97)00024-2

J. Balbach, V. Forge, N. A. Van-nuland, S. L. Winder, P. J. Hore et al., Following protein folding in real time using NMR spectroscopy, Nature Structural Biology, vol.4, issue.10, pp.865-870, 1995.
DOI : 10.1107/S0021889891004399

S. Barbe, J. Cortés, T. Siméon, P. Monsan, and M. , A mixed molecular modeling-robotics approach to investigate lipase large molecular motions, Proteins: Structure, Function, and Bioinformatics, vol.81, issue.Web Server issu, pp.2517-2529, 2011.
DOI : 10.1002/prot.23075

H. M. Berman, T. Battistuz, W. F. Tn-bhat, P. E. Bluhm, K. Bourne et al., The Protein Data Bank, Acta Crystallographica Section D Biological Crystallography, vol.58, issue.6, pp.899-907, 2002.
DOI : 10.1107/S0907444902003451

P. Bernadu, L. Blanchard, P. Timmins, D. Marion, R. W. Ruigrok et al., A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering, Proceedings of the National Academy of Sciences of the U.S.A, pp.17002-17005, 2005.
DOI : 10.1073/pnas.0506202102

M. R. Betancourt, Efficient Monte Carlo trial moves for polypeptide simulations, The Journal of Chemical Physics, vol.123, issue.17, p.174905, 2005.
DOI : 10.1063/1.2102896

A. Bondi, van der Waals Volumes and Radii, The Journal of Physical Chemistry, vol.68, issue.3, pp.441-451, 1964.
DOI : 10.1021/j100785a001

R. Bonneau and &. Baker, Ab Initio Protein Structure Prediction: Progress and Prospects, Annual Review of Biophysics and Biomolecular Structure, vol.30, issue.1, pp.173-189, 2001.
DOI : 10.1146/annurev.biophys.30.1.173

&. O. Tj-brunette and . Brock, Guiding conformation space search with an all-atom energy potential, Proteins: Structure, Function, and Bioinformatics, vol.22, issue.Suppl. 6, pp.958-972, 2008.
DOI : 10.1002/prot.22123

M. Brut, A. Estève, G. Landa, G. Renvez, and &. Rouhani, The Static Modes: An alternative approach for the treatment of macro- and bio-molecular induced-fit flexibility, The European Physical Journal E, vol.28, issue.1, pp.17-25, 2009.
DOI : 10.1140/epje/i2008-10397-0

URL : https://hal.archives-ouvertes.fr/hal-01481817

J. D. Bryngelson, J. N. Onuchic, N. D. Socci, and &. P. Wolynes, Funnels, pathways, and the energy landscape of protein folding: A synthesis, Proteins: Structure, Function, and Genetics, vol.90, issue.3, pp.167-195, 1995.
DOI : 10.1002/prot.340210302

U. Burkert and &. L. Allinger, Molecular mechanics, 1982.

J. F. Canny, The complexity of robot motion planning, 1988.

A. A. Canutescu and &. R. Dunbrack-jr, Cyclic coordinate descent: A robotics algorithm for protein loop closure, Protein Science, vol.14, issue.5, pp.963-972, 2003.
DOI : 10.1110/ps.0242703

J. Cavanagh, Protein NMR spectroscopy: principles and practices, Royal Society of Chemistry, 2006.

]. C. Cavasotto-05a, J. A. Cavasotto, &. R. Kovacs, and . Abagyan, Representing Receptor Flexibility in Ligand Docking through Relevant Normal Modes, Journal of the American Chemical Society, vol.127, issue.26, pp.9632-9640, 2005.
DOI : 10.1021/ja042260c

]. C. Cavasotto-05b, A. J. Cavasotto, &. R. Orry, and . Abagyan, The Challenge of Considering Receptor Flexibility in Ligand Docking and Virtual Screening, Current Computer Aided-Drug Design, vol.1, issue.4, pp.423-440, 2005.
DOI : 10.2174/157340905774330291

C. K. Chan, Y. Hu, S. Takahashi, D. L. Rousseau, W. A. Eaton et al., Submillisecond protein folding kinetics studied by ultrarapid mixing, Proceedings of the National Academy of Sciences, vol.94, issue.5, pp.1779-1784, 1997.
DOI : 10.1073/pnas.94.5.1779

P. Cheng and &. S. Lavalle, Resolution complete rapidly-exploring random trees, Proceedings 2002 IEEE International Conference on Robotics and Automation (Cat. No.02CH37292), pp.267-272, 2002.
DOI : 10.1109/ROBOT.2002.1013372

D. Apaydin, D. Brutlag, &. J. Hsu, and . Latombe, Predicting experimental quantities in protein folding kinetics using stochastic roadmap simulation, Research in Computational Molecular Biology, pp.410-424, 2006.

D. L. Apaydin, D. Brutlag, &. J. Hsu, and . Latombe, Using stochastic roadmap simulation to predict experimental quantities in protein folding kinetics: folding rates and phi-values, Journal of Computational Biology, vol.14, issue.5, pp.578-593, 2007.

&. S. Kavraki and . Thrun, Principles of robot motion: theory, algorithms, and implementation. Intelligent robotics and autonomous agents, 2005.

]. J. Cohen, M. C. Lin, D. Manocha, and &. M. Ponamgi, I-COLLIDE, Proceedings of the 1995 symposium on Interactive 3D graphics , SI3D '95, pp.189-196, 1995.
DOI : 10.1145/199404.199437

J. Cortés, T. Siméon, M. Remaud-siméon, and &. V. Tran, Geometric algorithms for the conformational analysis of long protein loops, Journal of Computational Chemistry, vol.9, issue.Suppl, pp.956-967, 2004.
DOI : 10.1002/jcc.20021

]. J. Cortés-05a, &. T. Cortés, and . Siméon, Sampling-based motion planning under kinematic loop-closure constraints, Algorithmic Foundations of Robotics VI, pp.75-90, 2005.

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.Suppl 1, pp.116-125, 2005.
DOI : 10.1093/bioinformatics/bti1017

J. Cortés, L. Jaillet, and &. T. Siméon, Molecular disassembly with RRTlike algorithms, Proceedings of the IEEE International Conference on Robotics and Automation, pp.3301-3306, 2007.

J. Cortés, L. Jaillet, and &. T. Siméon, Disassembly Path Planning for Complex Articulated Objects, IEEE Transactions on Robotics, vol.24, issue.2, pp.475-481, 2008.
DOI : 10.1109/TRO.2008.915464

]. J. Cortés-10a, S. Cortés, D. Carrión, M. Curcó, &. C. Renaud et al., Relaxation of amorphous multichain polymer systems using inverse kinematics, Polymer, vol.51, issue.17, pp.4008-4014, 2010.
DOI : 10.1016/j.polymer.2010.06.019

]. J. Cortés-10b, D. T. Cortés, R. Le, &. T. Iehl, and . Siméon, Simulating ligand-induced conformational changes in proteins using a mechanical disassembly method, Physical Chemistry Chemical Physics, vol.16, issue.7, pp.8268-8276, 2010.
DOI : 10.1039/c002811h

]. E. Coutsias, C. Seok, M. P. Jacobson, and &. K. Dill, A kinematic view of loop closure, Journal of Computational Chemistry, vol.35, issue.4, pp.510-528, 2004.
DOI : 10.1002/jcc.10416

]. J. Craig, Introduction to robotics: Mechanics and control, 1989.

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.
DOI : 10.1201/9781420035070

P. Das, M. Moll, H. Stamati, L. E. Kavraki, and &. C. Clementi, Lowdimensional , free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction, Proceedings of the National Academy of Sciences, pp.9885-9890, 2006.

V. R. 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.241-248, 2005.
DOI : 10.15607/RSS.2005.I.032

]. D. Devaurs, T. Siméon, and &. J. Cortés, Parallelizing RRT on distributed-memory architectures, 2011 IEEE International Conference on Robotics and Automation, pp.2261-2266
DOI : 10.1109/ICRA.2011.5979751

URL : https://hal.archives-ouvertes.fr/hal-00872218

E. W. Dijkstra, A note on two problems in connexion with graphs, Numerische Mathematik, vol.4, issue.1, pp.269-271, 1959.
DOI : 10.1007/BF01386390

]. K. Dill, S. B. Ozkan, M. S. Shell, and &. R. , The Protein Folding Problem, Annual Review of Biophysics, vol.37, issue.1, pp.289-316, 2008.
DOI : 10.1146/annurev.biophys.37.092707.153558

L. R. Dodd, T. D. Boone, and &. N. Theodorou, A concerted rotation algorithm for atomistic Monte Carlo simulation of polymer melts and glasses, Molecular Physics, vol.28, issue.4, pp.961-996, 1993.
DOI : 10.1021/ma00191a079

H. J. Dyson and &. E. Wright, Unfolded Proteins and Protein Folding Studied by NMR, Chemical Reviews, vol.104, issue.8, pp.3607-3622, 2004.
DOI : 10.1021/cr030403s

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.
DOI : 10.1093/bioinformatics/btl448

A. Falicov and &. F. Cohen, A Surface of Minimum Area Metric for the Structural Comparison of Proteins, Journal of Molecular Biology, vol.258, issue.5, pp.871-892, 1996.
DOI : 10.1006/jmbi.1996.0294

L. Feng, A. Yang, &. R. Kloczkowski, and . Jernigan, The energy profiles of atomic conformational transition intermediates of adenylate kinase, Proteins: Structure, Function, and Bioinformatics, vol.70, issue.3, pp.551-558, 2009.
DOI : 10.1002/prot.22467

D. Frenkel and &. B. Smit, Understanding Molecular Simulation, Computers in Physics, vol.11, issue.4, 2002.
DOI : 10.1063/1.4822570

R. Geraerts and &. M. Overmars, A Comparative Study of Probabilistic Roadmap Planners, Algorithmic Foundations of Robotics V, pp.43-58, 2004.
DOI : 10.1007/978-3-540-45058-0_4

]. B. Gipson, D. Hsu, L. E. Kavraki, &. Latombe, and J. , Computational Models of Protein Kinematics and Dynamics: Beyond Simulation, Annual Review of Analytical Chemistry, vol.5, issue.1, pp.273-291, 2012.
DOI : 10.1146/annurev-anchem-062011-143024

. G¯-o-70-]-n, &. H. G¯-o, and . Scheraga, Ring Closure and Local Conformational Deformations of Chain Molecules, Macromolecules, vol.3, pp.178-187, 1970.

]. D. Goldberg-89 and . Goldberg, Genetic algorithms in search, optimization, and machine learning, 1989.

K. Goldberg, Completeness in robot motion planning, Proceedings of the workshop on Algorithmic foundations of robotics, pp.419-429, 1995.

G. H. Golub and &. C. Van-loan, Matrix computations, 1996.

D. S. Goodsell, G. M. Morris, and &. J. Olson, Automated docking of flexible ligands: Applications of autodock, Journal of Molecular Recognition, vol.106, issue.1, pp.1-5, 1996.
DOI : 10.1002/(SICI)1099-1352(199601)9:1<1::AID-JMR241>3.0.CO;2-6

]. S. Gottschalk, M. C. Lin, and &. D. Manocha, OBBTree, Proceedings of the 23rd annual conference on Computer graphics and interactive techniques , SIGGRAPH '96, pp.171-180, 1996.
DOI : 10.1145/237170.237244

]. D. Griffiths, Introduction to quantum mechanics, 2005.

D. Guieysse, J. Cortés, S. Puech-guenot, S. Barbe, V. Lafaquì-ere et al., A Structure-Controlled Investigation of Lipase Enantioselectivity by a Path-Planning Approach, ChemBioChem, vol.10, issue.8, pp.1308-1317, 2008.
DOI : 10.1002/cbic.200700548

]. P. Hajduk and &. J. Greer, A decade of fragment-based drug design: strategic advances and lessons learned, Nature Reviews Drug Discovery, vol.11, issue.8, pp.211-219, 2007.
DOI : 10.1038/nrd2220

I. Jolliffe, Principal component analysis, 2002.
DOI : 10.1007/978-1-4757-1904-8

M. Jones, E. R. Henry, Y. Hu, C. K. Chan, S. D. Luck et al., Fast events in protein folding initiated by nanosecond laser photolysis., Proceedings of the National Academy of Sciences, vol.90, issue.24, pp.11860-11864, 1993.
DOI : 10.1073/pnas.90.24.11860

]. G. Jones-97a, P. Jones, R. C. Willett, A. R. Glen, &. R. Leach et al., Development and validation of a genetic algorithm for flexible docking, Journal of Molecular Biology, vol.267, issue.3, pp.727-748, 1997.
DOI : 10.1006/jmbi.1996.0897

]. G. Jones-97b, P. Jones, R. C. Willett, A. R. Glen, &. R. Leach et al., Development and validation of a genetic algorithm for flexible docking, Journal of Molecular Biology, vol.267, issue.3, pp.727-748, 1997.
DOI : 10.1006/jmbi.1996.0897

]. W. Jorgensen, D. S. Maxwell, and &. J. Tirado-rives, Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids, Journal of the American Chemical Society, vol.118, issue.45, pp.11225-11236, 1996.
DOI : 10.1021/ja9621760

L. E. Kavraki, P. Svestka, J. C. Latombe, and &. M. Overmars, Probabilistic roadmaps for path planning in high-dimensional configuration spaces, IEEE Transactions on Robotics and Automation, vol.12, issue.4, pp.566-580, 1996.
DOI : 10.1109/70.508439

L. E. Kavraki, Geometric Methods in Structural Computational Biology, 2007.

M. K. Kim, R. L. Jernigan, and &. S. Chirikjian, Efficient Generation of Feasible Pathways for Protein Conformational Transitions, Biophysical Journal, vol.83, issue.3, pp.1620-1630, 2002.
DOI : 10.1016/S0006-3495(02)73931-3

S. Kirillova, J. Cortés, A. Stefaniu, and &. T. Siméon, An NMA-guided path planning approach for computing large-amplitude conformational changes in proteins, Proteins: Structure, Function, and Bioinformatics, vol.33, issue.1, pp.131-143, 2008.
DOI : 10.1002/prot.21570

]. S. Kirkpatrick, C. D. Gelatt, and &. M. Vecchi, Optimization by Simulated Annealing, Science, vol.220, issue.4598, pp.671-680, 1983.
DOI : 10.1126/science.220.4598.671

A. Koli´nskikoli´nski, Multiscale approaches to protein modeling, 2010.

R. Kolodny, L. Guibas, M. Levitt, and &. P. Koehl, Inverse Kinematics in Biology: The Protein Loop Closure Problem, The International Journal of Robotics Research, vol.24, issue.2-3, pp.151-163, 2005.
DOI : 10.1177/0278364905050352

]. G. Krivov, M. V. Shapovalov, and &. R. Dunbrack-jr, Improved prediction of protein side-chain conformations with SCWRL4, Proteins: Structure, Function, and Bioinformatics, vol.3, issue.Pt 1, pp.778-795, 2009.
DOI : 10.1002/prot.22488

J. J. Kuffner-jr and &. S. Lavalle, RRT-connect: An efficient approach to single-query path planning, Proceedings 2000 ICRA. Millennium Conference. IEEE International Conference on Robotics and Automation. Symposia Proceedings (Cat. No.00CH37065), pp.995-1001, 2000.
DOI : 10.1109/ROBOT.2000.844730

A. M. Ladd and &. E. Kavraki, Fast Tree-Based Exploration of State Space for Robots with Dynamics, pp.297-312, 2005.
DOI : 10.1007/10991541_21

. Lafaquì-ere-09-]-v, S. Lafaquì-ere, S. Barbe, D. Puech-guenot, J. Guieysse et al., Control of Lipase Enantioselectivity by Engineering the Substrate Binding Site and Access Channel, ChemBioChem, vol.14, issue.3, pp.2760-2771, 2009.
DOI : 10.1002/cbic.200900439

A. Laio and &. M. Parrinello, Escaping free-energy minima, Proceedings of the National Academy of Sciences, vol.99, issue.20, pp.12562-12566, 2002.
DOI : 10.1073/pnas.202427399

D. P. Landau and &. K. Binder, A guide to monte carlo simulations in statistical physics, 2005.

J. C. Latombe, Robot motion planning, 1990.
DOI : 10.1007/978-1-4615-4022-9

S. M. Lavalle, P. W. Finn, L. E. Kavraki, and &. J. Latombe, A randomized kinematics-based approach to pharmacophore-constrained conformational search and database screening, Journal of Computational Chemistry, vol.39, issue.9, pp.731-747, 2000.
DOI : 10.1002/(SICI)1096-987X(20000715)21:9<731::AID-JCC3>3.0.CO;2-R

]. S. Lavalle-01a, &. J. Lavalle, and . Kuffner, Rapidly-exploring random trees: Progress and prospects, Algorithmic and computational robotics: new directions: the fourth Workshop on the Algorithmic Foundations of Robotics, pp.293-308, 2001.

]. S. Lavalle-01b, &. J. Lavalle, and . Kuffner-jr, Randomized Kinodynamic Planning, The International Journal of Robotics Research, vol.20, issue.5, pp.378-400, 2001.
DOI : 10.1177/02783640122067453

S. M. Lavalle, Planning algorithms, 2006.
DOI : 10.1017/CBO9780511546877

A. R. Leach, Molecular modelling: Principles and applications, 2001.

H. Y. Lee and &. G. Liang, Displacement Analysis of the General Spatial 7-Link 7R Mechanisms. Mechanism and Machine Theory, pp.219-226, 1988.

H. Y. Lee and &. G. Liang, A New Vector Theory for the Analysis of Spatial Mechanisms. Mechanism and Machine Theory A methodology for efficiently sampling the conformation space of molecular structures, pp.209-217, 1988.

T. Lengauer and &. M. Rarey, Computational methods for biomolecular docking, Current Opinion in Structural Biology, vol.6, issue.3, pp.402-406, 1996.
DOI : 10.1016/S0959-440X(96)80061-3

E. Leontidis, J. J. De-pablo, M. Laso, and &. U. Suter, A critical evaluation of novel algorithms for the off-lattice Monte Carlo simulation of condensed polymer phases, Advances in Polymer Science, vol.116, pp.283-318, 1994.
DOI : 10.1007/BFb0080202

D. Li, H. Yang, L. Han, and &. S. Huo, Predicting the Folding Pathway of Engrailed Homeodomain with a Probabilistic Roadmap Enhanced Reaction-Path Algorithm, Biophysical Journal, vol.94, issue.5, pp.1622-1629, 2008.
DOI : 10.1529/biophysj.107.119214

&. D. Lin and . Manocha, Collision and Proximity Queries, Handbook of Discrete and Computational Geometry, 2003.

S. R. Lindemann and &. S. Lavalle, Current Issues in Sampling-Based Motion Planning, Robotics Research, pp.36-54, 2005.
DOI : 10.1007/11008941_5

]. I. Lotan, F. Schwarzer, D. Halperin, and &. J. Latombe, Efficient maintenance and self-collision testing for Kinematic Chains, Proceedings of the eighteenth annual symposium on Computational geometry , SCG '02, pp.43-52, 2002.
DOI : 10.1145/513400.513406

I. Lotan and &. F. Schwarzer, Approximation of Protein Structure for Fast Similarity Measures, Journal of Computational Biology, vol.11, issue.2-3, pp.299-317, 2004.
DOI : 10.1089/1066527041410355

T. Lozano-peréz, Spatial planning: A configuration space approach, IEEE Transactions on Computers, vol.32, issue.2, pp.108-120, 1983.

D. Manocha and &. J. Canny, Efficient inverse kinematics for general 6R manipulators, IEEE Transactions on Robotics and Automation, vol.10, issue.5, pp.648-657, 1994.
DOI : 10.1109/70.326569

D. Manocha, Y. Zhu, and &. W. Wright, Conformational analysis of molecular chains using nano-kinematics, Bioinformatics, vol.11, issue.1, pp.71-86, 1995.
DOI : 10.1093/bioinformatics/11.1.71

E. Marinari and &. G. Parisi, Simulated Tempering: A New Monte Carlo Scheme, Europhysics Letters (EPL), vol.19, issue.6, pp.451-458, 1992.
DOI : 10.1209/0295-5075/19/6/002

O. Marques and &. Y. Sanejouand, Hinge-bending motion in citrate synthase arising from normal mode calculations, Proteins: Structure, Function, and Genetics, vol.112, issue.4, pp.557-560, 1995.
DOI : 10.1002/prot.340230410

A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and &. E. Teller, Equation of State Calculations by Fast Computing Machines, Journal of Chemical Physics, vol.21, pp.1087-1092, 1953.

O. Miyashita, &. Onuchic, and . Wolynes, Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins, Proceedings of the National Academy of Sciences of the United States of America, p.12570, 2003.
DOI : 10.1073/pnas.2135471100

M. Moll, D. Schwarz, &. Lydia, and E. Kavraki, Roadmap methods for protein folding, 2007.

L. Monticelli, S. K. Kandasamy, X. Periole, R. G. Larson, D. P. Tieleman et al., The MARTINI Coarse-Grained Force Field: Extension to Proteins, Journal of Chemical Theory and Computation, vol.4, issue.5, pp.819-834, 2008.
DOI : 10.1021/ct700324x

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, Journal of Molecular Biology, vol.258, issue.2, pp.393-410, 1996.
DOI : 10.1006/jmbi.1996.0257

Y. Mu, P. H. Nguyen, and &. G. Stock, Energy landscape of a small peptide revealed by dihedral angle principal component analysis, Proteins: Structure, Function, and Bioinformatics, vol.295, issue.1, pp.45-52, 2005.
DOI : 10.1002/prot.20310

C. W. Müller and &. G. Schulz, Structure of the complex between adenylate kinase from Escherichia coli and the inhibitor Ap5A refined at 1.9 ?? resolution, Journal of Molecular Biology, vol.224, issue.1, pp.159-177, 1992.
DOI : 10.1016/0022-2836(92)90582-5

C. Müller, J. Gj-schlauderer, &. Reinstein, and . Schulz, Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding, Structure, vol.4, issue.2, pp.147-156, 1996.
DOI : 10.1016/S0969-2126(96)00018-4

V. Muñoz, Protein folding, misfolding and aggregation: classical themes and novel approaches. RSC biomolecular sciences, Royal Society of Chemistry, 2008.

]. K. Noonan, D. O-'brien, and &. J. Snoeyink, Probik: Protein Backbone Motion by Inverse Kinematics, The International Journal of Robotics Research, vol.24, issue.11, pp.971-982, 2005.
DOI : 10.1177/0278364905059108

J. N. Onuchic, &. P. Wolynes, and R. H. Pain, Theory of protein folding, Current Opinion in Structural Biology, vol.14, issue.1, pp.70-75, 2000.
DOI : 10.1016/j.sbi.2004.01.009

Y. Pak and &. S. Wang, Application of a Molecular Dynamics Simulation Method with a Generalized Effective Potential to the Flexible Molecular Docking Problems, The Journal of Physical Chemistry B, vol.104, issue.2, pp.354-359, 2000.
DOI : 10.1021/jp993073h

D. Parsons and &. J. Canny, Geometric problems in molecular biology and robotics, Proceedings of the International Conference on Intelligent Systems for Molecular Biology, pp.322-220, 1994.

]. E. Plaku-07a, H. Plaku, C. Stamati, &. L. Clementi, and . Kavraki, Fast and reliable analysis of molecular motion using proximity relations and dimensionality reduction, Proteins: Structure, Function, and Bioinformatics, vol.108, issue.4, pp.897-907, 2007.
DOI : 10.1002/prot.21337

]. E. Plaku-07b, H. Plaku, C. Stamati, &. L. Clementi, and . Kavraki, Fast and reliable analysis of molecular motion using proximity relations and dimensionality reduction, Proteins: Structure, Function, and Bioinformatics, vol.108, issue.4, pp.897-907, 2007.
DOI : 10.1002/prot.21337

J. W. Ponder and &. D. Case, Force Fields for Protein Simulations, Advances in protein chemistry, vol.66, pp.27-85, 2003.
DOI : 10.1016/S0065-3233(03)66002-X

H. Rangwala and &. G. Karypis, Protein structure methods and algorithms, of Wiley Series in Bioinformatics: Computational Techniques and Engineering, 2010.

S. T. Rao and &. G. Rossmann, Comparison of super-secondary structures in proteins, Journal of Molecular Biology, vol.76, issue.2, pp.241-256, 1973.
DOI : 10.1016/0022-2836(73)90388-4

D. C. Rapaport, The art of molecular dynamics simulation, 2007.

M. Rarey, B. Kramer, T. Lengauer, and &. G. Klebe, A Fast Flexible Docking Method using an Incremental Construction Algorithm, Journal of Molecular Biology, vol.261, issue.3, pp.470-489, 1996.
DOI : 10.1006/jmbi.1996.0477

B. Raveh, A. Enosh, O. Schueler-furman, and &. D. Halperin, Rapid Sampling of Molecular Motions with Prior Information Constraints, PLoS Computational Biology, vol.22, issue.2, p.1000295, 2009.
DOI : 10.1371/journal.pcbi.1000295.s013

J. H. Reif, Complexity of the mover's problem and generalizations, 20th Annual Symposium on Foundations of Computer Science (sfcs 1979), pp.421-427, 1979.
DOI : 10.1109/SFCS.1979.10

P. Robustelli, K. Kohlhoff, A. Cavalli, and &. M. Vendruscolo, Using NMR Chemical Shifts as Structural Restraints in Molecular Dynamics Simulations of Proteins, Structure, vol.18, issue.8, pp.923-933, 2010.
DOI : 10.1016/j.str.2010.04.016

S. Rodriguez, X. Tang, J. M. Lien, and &. N. Amato, An obstaclebased rapidly-exploring random tree, Proceedings of the IEEE International Conference on Robotics and Automation, pp.895-900, 2006.

C. E. Rohl, K. Strauss, &. D. Misura, and . Baker, Protein Structure Prediction Using Rosetta, Methods in enzymology, vol.383, pp.66-93, 2004.
DOI : 10.1016/S0076-6879(04)83004-0

M. G. Rossmann and &. P. Argos, Exploring structural homology of proteins, Journal of Molecular Biology, vol.105, issue.1, pp.75-95, 1976.
DOI : 10.1016/0022-2836(76)90195-9

G. Sánchez and &. J. Latombe, A Single-Query Bi-Directional Probabilistic Roadmap Planner with Lazy Collision Checking, Robotics Research, pp.403-417, 2003.
DOI : 10.1007/3-540-36460-9_27

J. T. Schwartz and &. M. Sharir, On the ???piano movers'??? problem I. The case of a two-dimensional rigid polygonal body moving amidst polygonal barriers, Communications on Pure and Applied Mathematics, vol.22, issue.3, pp.345-398, 1983.
DOI : 10.1002/cpa.3160360305

&. M. Peitsch, Computational structural biology: Methods and applications, 2008.

L. Sciavicco and &. B. Siciliano, Modelling and control of robot manipulators Advanced Textbooks in Control and Signal Processing, 2001.

R. A. Scott and &. H. Scheraga, Conformational Analysis of Macromolecules. II. The Rotational Isomeric States of the Normal Hydrocarbons, The Journal of Chemical Physics, vol.44, issue.8, p.3054, 1966.
DOI : 10.1063/1.1727180

D. J. Selkoe, Folding proteins in fatal ways, Nature, vol.426, issue.6968, pp.900-904, 2003.
DOI : 10.1038/nature02264

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.330, issue.6002, pp.341-346, 2010.
DOI : 10.1126/science.1187409

A. Shehu and &. B. Olson, Guiding the Search for Native-like Protein Conformations with an Ab-initio Tree-based Exploration, The International Journal of Robotics Research, vol.31, issue.8, pp.1106-1127, 2010.
DOI : 10.1177/027836402320556458

&. O. Siciliano and . Khatib, Springer handbook of robotics. Gale virtual reference library, 2008.

T. Simeon, J. P. Laumond, and &. C. Nissoux, Visibility-based probabilistic roadmaps for motion planning, Advanced Robotics, vol.14, issue.6, pp.477-493, 2000.
DOI : 10.1163/156855300741960

A. P. Singh, J. C. Latombe, and &. D. Brutlag, A Motion Planning Approach to Flexible Ligand Binding, Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, pp.252-261, 1999.

G. Song and &. M. Amato, Using motion planning to study protein folding pathways, Proceedings of the fifth annual international conference on Computational biology , RECOMB '01, pp.149-168, 2002.
DOI : 10.1145/369133.369239

M. Soss, J. Erickson, and &. M. Overmars, Preprocessing chains for fast dihedral rotations is hard or even impossible, Computational Geometry, vol.26, issue.3, pp.235-246, 2003.
DOI : 10.1016/S0925-7721(02)00156-6

]. S. Sousa-06, P. A. Sousa, &. J. Fernandes, and . Ramos, Protein-ligand docking: Current status and future challenges, Proteins: Structure, Function, and Bioinformatics, vol.219, issue.1, pp.15-26, 2006.
DOI : 10.1002/prot.21082

M. W. Spong, S. Hutchinson, and &. M. Vidyasagar, Robot modeling and control, 2006.

M. J. Sternberg, Protein structure prediction: A practical approach . The Practical Approach Series, 1996.

&. I. S-¸ucan and . Kavraki, Kinodynamic Motion Planning by Interior-Exterior Cell Exploration, Algorithmic Foundation of Robotics VIII, vol.57, pp.449-464, 2009.
DOI : 10.1007/978-3-642-00312-7_28

Y. Sugita and &. Y. Okamoto, Replica-exchange molecular dynamics method for protein folding, Chemical Physics Letters, vol.314, issue.1-2, pp.141-151, 1999.
DOI : 10.1016/S0009-2614(99)01123-9

]. F. Tama and &. Y. Sanejouand, Conformational change of proteins arising from normal mode calculations, Protein Engineering Design and Selection, vol.14, issue.1, pp.1-6, 2001.
DOI : 10.1093/protein/14.1.1

F. Tama, O. Miyashita, &. C. Brooks, and . Iii, Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM, Journal of Structural Biology, vol.147, issue.3, pp.315-326, 2004.
DOI : 10.1016/j.jsb.2004.03.002

X. Tang, B. Kirkpatrick, S. Thomas, G. Song, and &. M. Amato, Using Motion Planning to Study RNA Folding Kinetics, Journal of Computational Biology, vol.12, issue.6, pp.862-881, 2005.
DOI : 10.1089/cmb.2005.12.862

X. Tang, S. Thomas, L. Tapia, D. P. Giedroc, and &. N. Amato, Simulating RNA Folding Kinetics on Approximated Energy Landscapes, Journal of Molecular Biology, vol.381, issue.4, pp.1055-1067, 2008.
DOI : 10.1016/j.jmb.2008.02.007

]. L. Tapia, X. Tang, S. Thomas, and &. M. Amato, Kinetics analysis methods for approximate folding landscapes, Bioinformatics, vol.23, issue.13, pp.539-548, 2007.
DOI : 10.1093/bioinformatics/btm199

]. L. Tapia, S. Thomas, and &. M. Amato, A Motion Planning Approach to Studying Molecular Motions, Communications in Information & Systems, vol.10, issue.1, pp.53-68, 2010.

J. B. Tenenbaum, V. Silva, and &. J. Langford, A Global Geometric Framework for Nonlinear Dimensionality Reduction, Science, vol.290, issue.5500, pp.2319-2323, 2000.
DOI : 10.1126/science.290.5500.2319

M. L. Teodoro, G. N. Phillips-jr, and &. L. Kavraki, Molecular docking: a problem with thousands of degrees of freedom, Proceedings 2001 ICRA. IEEE International Conference on Robotics and Automation (Cat. No.01CH37164), pp.960-965, 2001.
DOI : 10.1109/ROBOT.2001.932674

S. Thomas, G. Song, and &. M. Amato, Protein folding by motion planning, Physical Biology, vol.2, issue.4, pp.148-155, 2005.
DOI : 10.1088/1478-3975/2/4/S09

S. Thomas, X. Tang, L. Tapia, and &. M. Amato, Simulating Protein Motions with Rigidity Analysis, Journal of Computational Biology, vol.14, issue.6, pp.839-855, 2007.
DOI : 10.1089/cmb.2007.R019

&. P. Thorpe and . Duxbury, Rigidity theory and applications: edited by m.f thorpe and p.m. duxbury, 1999.
DOI : 10.1007/b115749

I. Konstantinos, . Tsianos, &. L. Ioan-alexandru-sucan, and . Kavraki, Sampling-based robot motion planning: Towards realistic applications, Computer Science Review, vol.1, pp.2-11, 2007.

]. R. Unger and &. J. Moult, Genetic Algorithms for Protein Folding Simulations, Journal of Molecular Biology, vol.231, issue.1, pp.75-81, 1993.
DOI : 10.1006/jmbi.1993.1258

L. J. Van-der-maaten, E. O. Postma, and &. H. Van-den-herik, Dimensionality Reduction: A Comparative Review, 2009.

S. Wallin, J. Farwer, and &. U. Bastolla, Testing similarity measures with continuous and discrete protein models, Proteins: Structure, Function, and Bioinformatics, vol.9, issue.Suppl, pp.144-157, 2003.
DOI : 10.1002/prot.10271

S. Wells, S. Menor, B. Hespenheide, and &. M. Thorpe, Constrained geometric simulation of diffusive motion in proteins, Physical Biology, vol.2, issue.4, pp.127-136, 2005.
DOI : 10.1088/1478-3975/2/4/S07

S. A. Wilmarth, N. M. Amato, and &. F. Stiller, MAPRM: a probabilistic roadmap planner with sampling on the medial axis of the free space, Proceedings 1999 IEEE International Conference on Robotics and Automation (Cat. No.99CH36288C), pp.1024-1031, 2002.
DOI : 10.1109/ROBOT.1999.772448

N. G. Wu and &. W. Deem, isomerization in proline-containing, cyclic peptides, The Journal of Chemical Physics, vol.111, issue.14, pp.6625-6632, 1999.
DOI : 10.1063/1.479952

H. Yang, H. Wu, D. Li, L. Han, and &. S. Huo, Temperature-Dependent Probabilistic Roadmap Algorithm for Calculating Variationally Optimized Conformational Transition Pathways, Journal of Chemical Theory and Computation, vol.3, issue.1, pp.17-25, 2007.
DOI : 10.1021/ct0502054

P. Yao, A. Dhanik, N. Marz, R. Propper, C. Kou et al., Efficient Algorithms to Explore Conformation Spaces of Flexible Protein Loops, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.5, issue.4, pp.534-545, 2008.
DOI : 10.1109/TCBB.2008.96

M. J. Zaki and &. C. Bystroff, Protein structure prediction, Methods in Molecular Biology, 2008.
DOI : 10.1007/978-1-59745-574-9

M. Zhang and &. E. Kavraki, A New Method for Fast and Accurate Derivation of Molecular Conformations, Journal of Chemical Information and Computer Sciences, vol.42, issue.1, pp.64-70, 2002.
DOI : 10.1021/ci010327z

I. Norman and . Badler, Inverse kinematics positioning using nonlinear programming for highly articulated figures, ACM Trans. Graph, vol.13, issue.4, pp.313-336, 1994.