M. M. Woolfson, An Introduction to X-ray Crystallography, 1997.

L. E. Kay, NMR studies of protein structure and dynamics, Journal of Magnetic Resonance, vol.173, issue.2, pp.193-207, 2005.
DOI : 10.1016/j.jmr.2004.11.021

O. F. Lange, N. A. Lakomek, C. Farès, G. F. Schröder, K. F. Walter et al., Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution, Science, vol.117, issue.7147, pp.1471-1475, 2008.
DOI : 10.1038/nature05858

R. B. Fenwick, H. Van-den-bedem, J. S. Fraser, and P. Wright, Integrated description of protein dynamics from room-temperature X-ray crystallography and NMR, Proc. Natl. Acad. Sci. USA 2014, pp.445-454
DOI : 10.1063/1.448692

A. Leach, Molecular Modelling: Principles and Applications, 2001.

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

D. Wales, Energy Landscapes: Applications to Clusters, Biomolecules and Glasses, 2003.

B. Donald, Algorithms in Structural Molecular Biology, 2011.

I. Al-bluwi, T. Siméon, and J. Cortés, Motion planning algorithms for molecular simulations: A survey, Computer Science Review, vol.6, issue.4, pp.125-143
DOI : 10.1016/j.cosrev.2012.07.002

B. Gipson, D. Hsu, L. Kavraki, and J. C. Latombe, 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

A. Shehu and E. Plaku, A Survey of Computational Treatments of Biomolecules by Robotics-Inspired Methods Modeling Equilibrium Structure and Dynamic, J. Artif. Intell. Res, vol.57, pp.509-572, 2016.

J. Cortés and I. Bluwi, A Robotics Approach to Enhance Conformational Sampling of Proteins, Volume 4: 36th Mechanisms and Robotics Conference, Parts A and B, pp.12-15, 2012.
DOI : 10.1115/DETC2012-70105

D. Parsons and J. Canny, Geometric Problems in Molecular Biology and Robotics, Proc. Int. Conf. Intell. Syst. Mol. Biol, vol.2, pp.322-330, 1994.

N. Metropolis, A. Rosenbluth, M. Rosenbluth, A. Teller, and E. Teller, Equation of State Calculations by Fast Computing Machines, The Journal of Chemical Physics, vol.21, issue.6, pp.1087-1092, 1953.
DOI : 10.1063/1.1700747

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

L. R. Dodd, T. D. Boone, and D. 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

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

N. G. Wu and M. W. Deem, Efficient Monte Carlo methods for cyclic peptides, Molecular Physics, vol.98, issue.4, pp.559-580, 1999.
DOI : 10.1007/BF00576711

M. R. Betancourt, Efficient Monte Carlo trial moves for polypeptide simulations, The Journal of Chemical Physics, vol.123, issue.17, p.174905, 2005.
DOI : 10.1073/pnas.96.20.11311

I. W. Davis, W. B. Arendall, D. C. Iii-;-richardson, and J. S. Richardson, The Backrub Motion: How Protein Backbone Shrugs When a Sidechain Dances, Structure, vol.14, issue.2, pp.265-274, 2006.
DOI : 10.1016/j.str.2005.10.007

S. Bottaro, W. Boomsma, K. E. Johansson, C. Andreetta, T. Hamelryck et al., Subtle Monte Carlo Updates in Dense Molecular Systems, Journal of Chemical Theory and Computation, vol.8, issue.2, pp.695-702, 2012.
DOI : 10.1021/ct200641m

A. Vitalis and R. Pappu, Chapter 3 Methods for Monte Carlo Simulations of Biomacromolecules, Annu. Rep. Comput. Chem, vol.5, pp.49-76, 2009.
DOI : 10.1016/S1574-1400(09)00503-9

P. Kollman, R. Dixon, W. Cornell, T. Fox, C. Chipot et al., The development/application of a ???minimalist??? organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data, In Computer Simulation of Biomolecular Systems, vol.3, pp.83-96, 1997.
DOI : 10.1007/978-94-017-1120-3_2

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

N. Kurochkina and U. Guha, SH3 domains: modules of protein???protein interactions, Biophysical Reviews, vol.22, issue.1, pp.29-39, 2013.
DOI : 10.1091/mbc.E10-12-0969

S. Brocca, M. Samalíkovà, V. N. Uversky, M. Lotti, M. Vanoni et al., Order propensity of an intrinsically disordered protein, the cyclin-dependent-kinase inhibitor Sic1, Proteins: Structure, Function, and Bioinformatics, vol.1, issue.3, pp.731-746, 2009.
DOI : 10.1016/j.bbapap.2005.12.016

P. Bernadó, L. Blanchard, P. Timmins, D. Marion, R. Ruigrok et al., A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering, Proc. Natl. Acad. Sci. USA 2005, pp.17002-17005
DOI : 10.1073/pnas.0506078102

G. G. Krivov, M. V. Shapovalov, R. L. Dunbrack, and . 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 : 10.1007/978-1-4899-3324-9

J. P. Ulmschneider and W. L. Jorgensen, Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias, The Journal of Chemical Physics, vol.42, issue.9, pp.4261-4271, 2003.
DOI : 10.1021/jp961992r

C. M. Pickart and M. J. Eddins, Ubiquitin: structures, functions, mechanisms, Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, vol.1695, issue.1-3, pp.1695-55, 2004.
DOI : 10.1016/j.bbamcr.2004.09.019
URL : https://doi.org/10.1016/j.bbamcr.2004.09.019

R. Scott and H. Scheraga, Conformational Analysis of Macromolecules. II. The Rotational Isomeric States of the Normal Hydrocarbons, The Journal of Chemical Physics, vol.2, issue.8, pp.3054-3069, 1966.
DOI : 10.1063/1.1776947

J. P. Ulmschneider and W. L. Jorgensen, Polypeptide Folding Using Monte Carlo Sampling, Concerted Rotation, and Continuum Solvation, Journal of the American Chemical Society, vol.126, issue.6, pp.1849-1857, 2004.
DOI : 10.1021/ja0378862

J. J. Craig, Introduction to Robotics, 1989.

J. Nilmeier, L. Hua, E. A. Coutsias, and M. P. Jacobson, Assessing Protein Loop Flexibility by Hierarchical Monte Carlo Sampling, Journal of Chemical Theory and Computation, vol.7, issue.5, pp.1564-1574, 2011.
DOI : 10.1021/ct1006696
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3129859/pdf

J. Nilmeier and M. P. Jacobson, Multiscale Monte Carlo Sampling of Protein Sidechains: Application to Binding Pocket Flexibility, Journal of Chemical Theory and Computation, vol.4, issue.5, pp.835-846, 2008.
DOI : 10.1021/ct700334a

J. Nilmeier and M. P. Jacobson, Monte Carlo Sampling with Hierarchical Move Sets: POSH Monte Carlo, Journal of Chemical Theory and Computation, vol.5, issue.8, pp.1968-1984, 2009.
DOI : 10.1021/ct8005166

N. G. Wu and M. W. Deem, isomerization in proline-containing, cyclic peptides, The Journal of Chemical Physics, vol.11, issue.14, pp.6625-6632, 1999.
DOI : 10.1115/1.2919218

A. A. Canutescu, R. L. Dunbrack, and . Jr, Cyclic coordinate descent: A robotics algorithm for protein loop closure, Protein Science, vol.14, issue.5, pp.963-972, 2003.
DOI : 10.1002/jcc.540140508

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

M. Renaud, Calcul des Modèles Géométriques Inverses des Robots Manipulateurs 6R; Rapport LAAS 06332, 2006.

H. Y. Lee and C. G. Liang, A new vector theory for the analysis of spatial mechanisms, Mechanism and Machine Theory, vol.23, issue.3, pp.209-217, 1988.
DOI : 10.1016/0094-114X(88)90106-1

H. Y. Lee and C. G. Liang, Displacement analysis of the general spatial 7-link 7R mechanism, Mechanism and Machine Theory, vol.23, issue.3, pp.219-226, 1988.
DOI : 10.1016/0094-114X(88)90107-3

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
URL : http://www.csd.uch.gr/~emiris/algebraic99/mopapers/manocha/ieeetra.ps.Z

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 : 10.1089/10665270252935395

J. Cortés, S. Carrión, D. Curco, M. Renaud, and C. Aleman, 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

A. R. Dinner, Local deformations of polymers with nonplanar rigid main-chain internal coordinates, Journal of Computational Chemistry, vol.75, issue.13, pp.1132-1144, 2000.
DOI : 10.1080/00268979200100061

E. A. Coutsias, C. Seok, M. P. Jacobson, and K. A. Dill, A kinematic view of loop closure, Journal of Computational Chemistry, vol.35, issue.4, pp.510-528, 2004.
DOI : 10.1007/978-0-8176-4771-1

M. Mezei, Efficient Monte Carlo sampling for long molecular chains using local moves, tested on a solvated lipid bilayer, The Journal of Chemical Physics, vol.118, issue.8, pp.3874-3879, 2003.
DOI : 10.1080/00268978700101321

Y. Okamoto, Generalized-ensemble algorithms: enhanced sampling techniques for Monte Carlo and molecular dynamics simulations, Journal of Molecular Graphics and Modelling, vol.22, issue.5, pp.425-439, 2004.
DOI : 10.1016/j.jmgm.2003.12.009

J. M. Carr and D. J. Wales, Global optimization and folding pathways of selected alpha-helical proteins, J. Chem. Phys, 2005.

J. Cortés, D. Le, R. Iehl, and T. 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

D. J. Mandell and T. Kortemme, Backbone flexibility in computational protein design, Current Opinion in Biotechnology, vol.20, issue.4, pp.420-428, 2009.
DOI : 10.1016/j.copbio.2009.07.006