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

A. Mitsutake and Y. Okamoto, Multidimensional generalized-ensemble algorithms for complex systems, The Journal of Chemical Physics, vol.130, issue.21, p.214105, 2009.
DOI : 10.1063/1.3127783

A. P. Lyubartsev, A. A. Martsinovski, S. V. Shevkunov, and P. N. Vorontsov-velyaminov, New approach to Monte Carlo calculation of the free energy: Method of expanded ensembles, The Journal of Chemical Physics, vol.96, issue.3, pp.1776-83, 1992.
DOI : 10.1063/1.462133

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

Z. Li and H. A. Scheraga, Monte Carlo-minimization approach to the multiple-minima problem in protein folding., Proceedings of the National Academy of Sciences, vol.84, issue.19, pp.6611-6615, 1987.
DOI : 10.1073/pnas.84.19.6611

C. Michael, . Prentiss, J. David, . Wales, G. Peter et al., Protein structure prediction using basin-hopping, The Journal of Chemical Physics, vol.128, issue.22, p.225106, 2008.

R. Elber and M. Karplus, Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin, Science, vol.235, issue.4786, pp.318-321, 1987.
DOI : 10.1126/science.3798113

J. M. Troyer, F. E. Cohen, and . Becker, Protein conformational landscapes: Energy minimization and clustering of a long molecular dynamics trajectory, Proteins: Structure, Function, and Genetics, vol.48, issue.1, pp.97-110, 1995.
DOI : 10.1002/prot.340230111

M. Wevers, J. C. Schön, and M. Jansen, Global aspects of the energy landscape of metastable crystal structures in ionic compounds, Journal of Physics: Condensed Matter, vol.11, issue.33, p.6487, 1999.
DOI : 10.1088/0953-8984/11/33/316

F. Wang and D. Landau, Efficient, multiple-range random walk algorithm to calculate the density of states. Physical review letters, p.2050, 2001.

A. Laio and M. Parrinello, Escaping free-energy minima, Proceedings of the National Academy of Sciences, vol.99, issue.20, pp.9912562-12566, 2002.
DOI : 10.1073/pnas.202427399

L. Jaillet, F. J. Corcho, J. Pérez, and J. Cortés, Randomized tree construction algorithm to explore energy landscapes, Journal of Computational Chemistry, vol.319, issue.16, pp.3464-3474, 2011.
DOI : 10.1002/jcc.21931

C. Michael, . Prentiss, J. David, . Wales, G. Peter et al., The energy landscape, folding pathways and the kinetics of a knotted protein, PLoS computational biology, vol.6, issue.7, p.1000835, 2010.

G. G. Henkelman, G. Jóhannesson, and H. Jónsson, Methods for Finding Saddle Points and Minimum Energy Paths, Theoretical Methods in Condensed Phase Chemistry, pp.269-302, 2002.
DOI : 10.1007/0-306-46949-9_10

D. J. Wales, Discrete path sampling, Molecular Physics, vol.18, issue.20, pp.3285-3305, 2002.
DOI : 10.1063/1.1315348

D. J. Wales, Energy Landscapes, 2003.
DOI : 10.1017/CBO9780511721724
URL : https://hal.archives-ouvertes.fr/hal-01423280

M. Steven, J. Lavalle, and . Jr, Rapidly-exploring random trees: Progress and prospects, Algorithmic and Computational Robotics: New Directions, pp.293-308, 2001.

J. James, . Kuffner, M. Steven, and . Lavalle, Rrt-connect: An efficient approach to singlequery path planning, Robotics and Automation Proceedings. ICRA'00. IEEE International Conference on, pp.995-1001, 2000.

H. Samet, Foundations of multidimensional and metric data structures, 2006.

N. Peter and . Yianilos, Data structures and algorithms for nearest neighbor search in general metric spaces, ACM SODA, pp.311-321, 1993.

S. O. Hara and B. A. Draper, Are you using the right approximate nearest neighbor algorithm, Applications of Computer Vision (WACV), 2013 IEEE Workshop on, pp.9-14, 2013.

D. Devaurs, T. Siméon, and J. Cortes, Enhancing the transition-based RRT to deal with complex cost spaces, 2013 IEEE International Conference on Robotics and Automation, pp.4120-4125, 2013.
DOI : 10.1109/ICRA.2013.6631158
URL : https://hal.archives-ouvertes.fr/hal-00872224

S. Brown, N. J. Fawzi, and T. Head-gordon, Coarse-grained sequences for protein folding and design, Proceedings of the National Academy of Sciences, vol.100, issue.19, pp.10712-10717, 2003.
DOI : 10.1073/pnas.1931882100
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC196869

M. T. Oakley, D. J. Wales, and R. Johnston, Energy Landscape and Global Optimization for a Frustrated Model Protein, The Journal of Physical Chemistry B, vol.115, issue.39, pp.11525-11529, 2011.
DOI : 10.1021/jp207246m

F. Cazals, T. Dreyfus, D. Mazauric, A. Roth, and C. H. Robert, Conformational ensembles and sampled energy landscapes: Analysis and comparison, Journal of Computational Chemistry, vol.32, issue.16, p.2015
DOI : 10.1002/jcc.23913
URL : https://hal.archives-ouvertes.fr/hal-01076317