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

F. Allen, The Cambridge Structural Database: a quarter of a million crystal structures and rising, Acta Crystallographica Section B Structural Science, vol.58, issue.3, p.380, 2002.
DOI : 10.1107/S0108768102003890

J. Yon, D. Perahia, and C. Ghelis, Conformational dynamics and enzyme activity, Biochimie, vol.80, issue.1, p.33, 1998.
DOI : 10.1016/S0300-9084(98)80054-0

D. Kern and E. R. Zuiderweg, The role of dynamics in allosteric regulation, Current Opinion in Structural Biology, vol.13, issue.6, p.748, 2003.
DOI : 10.1016/j.sbi.2003.10.008

J. Haile, Molecular Dynamics Simulation: Elementary Methods, Computers in Physics, vol.7, issue.6, p.625, 1993.
DOI : 10.1063/1.4823234

H. Lei and Y. Duan, Improved sampling methods for molecular simulation, Current Opinion in Structural Biology, vol.17, issue.2, p.187, 2007.
DOI : 10.1016/j.sbi.2007.03.003

R. C. Bernardi, M. C. Melo, and K. Schulten, Enhanced sampling techniques in molecular dynamics simulations of biological systems, Biochimica et Biophysica Acta (BBA) - General Subjects, vol.1850, issue.5, p.872, 2015.
DOI : 10.1016/j.bbagen.2014.10.019

G. Henkelman, B. P. Uberuaga, and H. Jónsson, A climbing image nudged elastic band method for finding saddle points and minimum energy paths, The Journal of Chemical Physics, vol.13, issue.22, p.9901, 2000.
DOI : 10.1103/PhysRevLett.85.618

L. Jaillet, F. J. Corcho, J. J. Pérez, and J. Cortés, Randomized tree construction algorithm to explore energy landscapes, Journal of Computational Chemistry, vol.319, issue.16, p.3464, 2011.
DOI : 10.1016/S0009-2614(00)00081-6

URL : http://www.iri.upc.edu/download/scidoc/1270/

D. R. Weiss and M. Levitt, Can Morphing Methods Predict Intermediate Structures?, Journal of Molecular Biology, vol.385, issue.2, p.665, 2009.
DOI : 10.1016/j.jmb.2008.10.064

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2691871/pdf

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

D. W. Farrell, K. Speranskiy, and M. Thorpe, Generating stereochemically acceptable protein pathways, Proteins: Structure, Function, and Bioinformatics, vol.104, issue.14, p.2908, 2010.
DOI : 10.1002/prot.22810

T. Igarashi, T. Moscovich, and J. F. Hughes, As-rigid-as-possible shape manipulation, ACM Transactions on Graphics, vol.24, issue.3, p.1134, 2005.
DOI : 10.1145/1073204.1073323

URL : http://www.cs.brown.edu/people/tm/papers/rigid2005.pdf

H. Guo, X. Fu, F. Chen, H. Yang, Y. Wang et al., As-rigid-as-possible shape deformation and interpolation, Journal of Visual Communication and Image Representation, vol.19, issue.4, p.245, 2008.
DOI : 10.1016/j.jvcir.2008.01.003

Z. Levi and C. Gotsman, Visualization and Computer Graphics, IEEE Transactions on, vol.21, issue.2, p.264, 2015.

Y. S. Liu, H. B. Yan, and R. R. Martin, As-Rigid-As-Possible Surface Morphing, Journal of Computer Science and Technology, vol.14, issue.3, p.548, 2011.
DOI : 10.1109/TVCG.2008.28

URL : http://ralph.cs.cf.ac.uk/papers/Geometry/ARAP_Morphing.pdf

M. Kilian, N. J. Mitra, and H. Pottmann, Geometric modeling in shape space, ACM Transactions on Graphics, vol.26, issue.3, p.64, 2007.
DOI : 10.1145/1276377.1276457

URL : http://www.dmg.tuwien.ac.at/pottmann/2007/kilian-2007-gmss/paper_docs/shape_space_sig_07.pdf

Z. Zhang, G. Li, H. Lu, Y. Ouyang, M. Yin et al., Fast as-isometric-as-possible shape interpolation, Computers & Graphics, vol.46, p.244, 2015.
DOI : 10.1016/j.cag.2014.09.005

H. B. Yan, S. M. Hu, and R. R. Martin, 3D Morphing Using Strain Field Interpolation, Journal of Computer Science and Technology, vol.22, issue.1, p.147, 2007.
DOI : 10.1007/s11390-007-9020-z

Y. Lipman, O. Sorkine, D. Levin, and D. Cohen-or, Linear rotation-invariant coordinates for meshes, ACM Transactions on Graphics, vol.24, issue.3, p.479, 2005.
DOI : 10.1145/1073204.1073217

D. Xu, H. Zhang, Q. Wang, and H. Bao, Poisson shape interpolation, Graphical Models, vol.68, issue.3, p.268, 2006.
DOI : 10.1016/j.gmod.2006.03.001

M. Botsch and O. Sorkine, Visualization and Computer Graphics, IEEE Transactions on, vol.14, issue.1, p.213, 2008.

S. K. Kearsley, On the orthogonal transformation used for structural comparisons, Acta Crystallographica Section A Foundations of Crystallography, vol.45, issue.2, p.208, 1989.
DOI : 10.1107/S0108767388010128

G. Guennebaud and B. Jacob, Eigen v3, 2010.

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

T. Schlick, Molecular modeling and simulation: an interdisciplinary guide: an interdisciplinary guide, 2010.
DOI : 10.1007/978-0-387-22464-0

URL : https://link.springer.com/content/pdf/bfm%3A978-1-4419-6351-2%2F1.pdf

A. Shehu and L. E. Kavraki, Modeling Structures and Motions of Loops in Protein Molecules, Entropy, vol.42, issue.12, p.252, 2012.
DOI : 10.1002/prot.23134

J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid et al., Scalable molecular dynamics with NAMD, Journal of Computational Chemistry, vol.84, issue.16, p.1781, 2005.
DOI : 10.1515/9783110879476

URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2486339/pdf

G. M. Torrie and J. P. Valleau, Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling, Journal of Computational Physics, vol.23, issue.2, p.187, 1977.
DOI : 10.1016/0021-9991(77)90121-8