R. Henderson, The potential and limitations of neutrons, electrons and x-rays for atomic resolution microscopy of unstained biological molecules, Q. Rev. Biophys, vol.28, pp.171-193, 1995.

W. K?-uhlbrandt, Biochemistry. The resolution revolution. Science, vol.343, pp.1443-1444, 2014.

X. C. Bai, G. Mcmullan, and S. H. Scheres, How cryo-EM is revolutionizing structural biology, Trends Biochem. Sci, vol.40, pp.49-57, 2015.

E. Callaway, The revolution will not be crystallized: a new method sweeps through structural biology, Nature, vol.525, pp.172-174, 2015.

E. Nogales, The development of cryo-EM into a mainstream structural biology technique, Nat. Methods, vol.13, pp.24-27, 2016.

R. M. Glaeser, How good can cryo-EM become?, Nat. Methods, vol.13, pp.28-32, 2016.

A. F. Brilot, J. Z. Chen, and N. Grigorieff, Beam-induced motion of vitrified specimen on holey carbon film, J. Struct. Biol, vol.177, pp.630-637, 2012.

M. Carroni and H. R. Saibil, Cryo electron microscopy to determine the structure of macromolecular complexes, Methods, vol.95, pp.78-85, 2016.

X. Li, Y. Mooney, and . Cheng, Electron counting and beaminduced motion correction enable near-atomic-resolution single-particle cryo-EM, Nat. Methods, vol.10, pp.584-590, 2013.

M. Liao, Y. Cao, and . Cheng, Structure of the TRPV1 ion channel determined by electron cryo-microscopy, Nature, vol.504, pp.107-112, 2013.

X. C. Bai, Y. Yan, and . Shi, An atomic structure of human g-secretase, Nature, vol.525, pp.212-217, 2015.

M. G. Campbell, B. Veesler, and . Carragher, 2015. 2.8 Å resolution reconstruction of the Thermoplasma acidophilum 20S proteasome using cryo-electron microscopy
URL : https://hal.archives-ouvertes.fr/hal-02004224

A. Bartesaghi, S. Merk, and . Subramaniam, 2015. 2.2 Å resolution cryo-EM structure of b-galactosidase in complex with a cell-permeant inhibitor, Science, vol.348, pp.1147-1151

I. S. Fernández, X. C. Bai, and S. H. Scheres, Molecular architecture of a eukaryotic translational initiation complex, Science, vol.342, p.1240585, 2013.

J. Zhao, S. Benlekbir, and J. L. Rubinstein, Electron cryomicroscopy observation of rotational states in a eukaryotic V-ATPase, Nature, vol.521, pp.241-245, 2015.

A. B. Ward, A. Sali, and I. A. Wilson, Biochemistry. Integrative structural biology. Science, vol.339, pp.913-915, 2013.

H. Van-den-bedem and J. S. Fraser, Integrative, dynamic structural biology at atomic resolution-it's about time, Nat. Methods, vol.12, pp.307-318, 2015.

S. H. Scheres, RELION: implementation of a Bayesian approach to cryo-EM structure determination, J. Struct. Biol, vol.180, pp.519-530, 2012.

G. F. Schröder, Hybrid methods for macromolecular structure determination: experiment with expectations, Curr. Opin. Struct. Biol, vol.31, pp.20-27, 2015.

J. R. Lopez-blanco and P. Chacon, Structural modeling from electron microscopy data, WIREs Comput. Mol. Sci, vol.5, pp.62-81, 2015.

E. F. Pettersen, T. D. Goddard, and T. E. Ferrin, UCSF Chimera-a visualization system for exploratory research and analysis, J. Comput. Chem, vol.25, pp.1605-1612, 2004.

N. Volkmann and D. Hanein, Quantitative fitting of atomic models into observed densities derived by electron microscopy, J. Struct. Biol, vol.125, pp.176-184, 1999.

M. G. Rossmann, R. Bernal, and S. V. Pletnev, Combining electron microscopic with x-ray crystallographic structures, J. Struct. Biol, vol.136, pp.190-200, 2001.

A. Sali and T. L. Blundell, Comparative protein modelling by satisfaction of spatial restraints, J. Mol. Biol, vol.234, pp.779-815, 1993.

K. Lasker, H. J. Topf, and . Wolfson, Inferential optimization for simultaneous fitting of multiple components into a CryoEM map of their assembly, J. Mol. Biol, vol.388, pp.180-194, 2009.

W. Wriggers, Conventions and workflows for using SITUS, Acta Crystallogr. D Biol. Crystallogr, vol.68, pp.344-351, 2012.

W. Zheng, Accurate flexible fitting of high-resolution protein structures into cryo-electron microscopy maps using coarse-grained pseudo-energy minimization, Biophys. J, vol.100, pp.478-488, 2011.

L. G. Trabuco, K. Villa, and . Schulten, Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics, Structure, vol.16, pp.673-683, 2008.

A. H. Ratje, C. M. Loerke, and . Spahn, Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites, Nature, vol.468, pp.713-716, 2010.

M. Topf, A. Lasker, and . Sali, Protein structure fitting and refinement guided by cryo-EM density, Structure, vol.16, pp.295-307, 2008.

M. Saha and M. C. Morais, FOLD-EM: automated fold recognition in medium-and low-resolution (4-15 Å ) electron density maps, Bioinformatics, vol.28, pp.3265-3273, 2012.

F. Dimaio, M. D. Tyka, and D. Baker, Refinement of protein structures into low-resolution density maps using ROSETTA, J. Mol. Biol, vol.392, pp.181-190, 2009.

S. Lindert, J. Alexander, and . Meiler, EM-fold: de novo atomic-detail protein structure determination from medium-resolution density maps, Structure, vol.20, pp.464-478, 2012.

D. Russel, A. Lasker, and . Sali, Putting the pieces together: integrative modeling platform software for structure determination of macromolecular assemblies, PLoS Biol, vol.10, p.1001244, 2012.

P. D. Adams, P. V. Afonine, and P. H. Zwart, The Phenix software for automated determination of macromolecular structures, Methods, vol.55, pp.94-106, 2011.

A. Singharoy, K. Teo, and . Schulten, Molecular dynamicsbased refinement and validation for sub-5 Å cryo-electron microscopy maps, vol.5, p.16105, 2016.

A. T. Br?-unger, P. D. Adams, and G. L. Warren, Crystallography & NMR system: a new software suite for macromolecular structure determination, Acta Crystallogr. D Biol. Crystallogr, vol.54, pp.905-921, 1998.

M. Bonomi, G. T. Heller, and M. Vendruscolo, Principles of protein structural ensemble determination, Curr. Opin. Struct. Biol, vol.42, pp.106-116, 2017.

P. Sormanni, M. Piovesan, and . Vendruscolo, Simultaneous quantification of protein order and disorder, Nat. Chem. Biol, vol.13, pp.339-342, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01802823

J. R. Allison, Using simulation to interpret experimental data in terms of protein conformational ensembles, Curr. Opin. Struct. Biol, vol.43, pp.79-87, 2017.

C. K. Fisher and C. M. Stultz, Constructing ensembles for intrinsically disordered proteins, Curr. Opin. Struct. Biol, vol.21, pp.426-431, 2011.

K. Gaalswyk, M. I. Muniyat, and J. Maccallum, The emerging role of physical modeling in the future of structure determination, 2017.

W. Rieping, M. Habeck, and M. Nilges, Inferential structure determination, Science, vol.309, pp.303-306, 2005.

M. Bonomi, M. Camilloni, and . Vendruscolo, Metainference: a Bayesian inference method for heterogeneous systems, Sci. Adv, vol.2, p.1501177, 2016.

K. Lindorff-larsen, R. B. Best, and M. Vendruscolo, Simultaneous determination of protein structure and dynamics, Nature, vol.433, pp.128-132, 2005.

D. Schneidman-duhovny, R. Pellarin, and A. Sali, Uncertainty in integrative structural modeling, Curr. Opin. Struct. Biol, vol.28, pp.96-104, 2014.

S. Hanot, R. Bonomi, and . Pellarin, Bayesian multi-scale modeling of macromolecular structures based on cryo-electron microscopy density maps, 2017.

A. Cavalli, C. Camilloni, and M. Vendruscolo, Molecular dynamics simulations with replica-averaged structural restraints generate structural ensembles according to the maximum entropy principle, J. Chem. Phys, vol.138, p.94112, 2013.

M. Bonomi and C. Camilloni, Integrative structural and dynamical biology with PLUMED-ISDB, Bioinformatics, vol.33, pp.3999-4000, 2017.

G. A. Tribello, G. Bonomi, and . Bussi, PLUMED 2: new feathers for an old bird, Comput. Phys. Commun, vol.185, pp.604-613, 2014.

E. Prince, International Tables for Crystallography, 2004.

R. B. Best and G. Hummer, Optimized molecular dynamics force fields applied to the helix-coil transition of polypeptides, J. Phys. Chem. B, vol.113, pp.9004-9015, 2009.

W. C. Still, T. Tempczyk, and . Hendrickson, Semianalytical treatment of solvation for molecular mechanics and dynamics, J. Am. Chem. Soc, vol.112, pp.6127-6129, 1990.

D. S. Sivia and J. Skilling, Data Analysis: A Bayesian Tutorial, 2006.

K. A. Beauchamp, Y. S. Lin, and V. S. Pande, Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements, J. Chem. Theory Comput, vol.8, pp.1409-1414, 2012.

B. Hess, P-LINCS: a parallel linear constraint solver for molecular simulation, J. Chem. Theory Comput, vol.4, pp.116-122, 2008.

G. Bussi, D. Donadio, and M. Parrinello, Canonical sampling through velocity rescaling, J. Chem. Phys, vol.126, p.14101, 2007.

M. J. Ferrarotti, G. Bottaro, and . Bussi, Accurate multiple time step in biased molecular simulations, J. Chem. Theory Comput, vol.11, pp.139-146, 2015.

A. Barducci, G. Bussi, and M. Parrinello, Well-tempered metadynamics: a smoothly converging and tunable free-energy method, Phys. Rev. Lett, vol.100, p.20603, 2008.

B. Hess, E. Kutzner, and . Lindahl, GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation, J. Chem. Theory Comput, vol.4, pp.435-447, 2008.

C. Bartolucci, H. Lamba, and . Heumann, Crystal structure of wild-type chaperonin GroEL, J. Mol. Biol, vol.354, pp.940-951, 2005.

X. Fei, G. H. Yang, and . Lorimer, Crystal structure of a GroEL-ADP complex in the relaxed allosteric state at 2.7 Å resolution, Proc. Natl. Acad. Sci. USA, vol.110, pp.2958-2966, 2013.

T. Kawabata, Multiple subunit fitting into a low-resolution density map of a macromolecular complex using a Gaussian mixture model, Biophys. J, vol.95, pp.4643-4658, 2008.

Y. Chen, O. B. Clarke, and F. Mancia, Structure of the STRA6 receptor for retinol uptake, Science, vol.353, p.6302, 2016.

R. A. Laskowski, M. W. Macarthur, and J. M. Thornton, Procheck-a program to check the stereochemical quality of protein structures, J. Appl. Cryst, vol.26, pp.283-291, 1993.

X. Daura, A. E. Gademann, and . Mark, Peptide folding: when simulation meets experiment, Angew. Chem. Int. Ed, vol.38, pp.236-240, 1999.

R. Kawaguchi, H. Yu, and . Sun, A membrane receptor for retinol binding protein mediates cellular uptake of vitamin A, Science, vol.315, pp.820-825, 2007.

R. Kawaguchi, H. Yu, and . Sun, Mapping the membrane topology and extracellular ligand binding domains of the retinol binding protein receptor, Biochemistry, vol.47, pp.5387-5395, 2008.

H. Van-esch, J. P. Jansen, and . Fryns, Encephalopathy and bilateral cataract in a boy with an interstitial deletion of Xp22 comprising the CDKL5 and NHS genes, Am. J. Med. Genet. A, vol.143, pp.364-369, 2007.

M. Zhong, H. Kawaguchi, and . Sun, Vitamin A transport and the transmembrane pore in the cell-surface receptor for plasma retinol binding protein, PLoS One, vol.8, p.73838, 2013.