F. Alber, S. Dokudovskaya, L. M. Veenhoff, W. Zhang, J. Kipper et al., Determining the architectures of macromolecular assemblies, Nature, vol.450, issue.7170, pp.683-694, 2007.

A. R. Atilgan, S. R. Durell, R. L. Jernigan, M. C. Demirel, O. Keskin et al., Anisotropy of Fluctuation Dynamics of Proteins with an Elastic Network Model, Biophysical Journal, vol.80, issue.1, pp.505-515, 2001.

A. Bakan, L. M. Meireles, and I. Bahar, ProDy: Protein Dynamics Inferred from Theory and Experiments, Bioinformatics, vol.27, issue.11, pp.1575-1577, 2011.

N. I. Brodie, K. I. Popov, E. V. Petrotchenko, N. V. Dokholyan, and C. H. Borchers, Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations, Science Advances, vol.3, issue.7, p.e1700479, 2017.

A. T. Brunger, Version 1.2 of the Crystallography and NMR system, Nature Protocols, vol.2, issue.11, pp.2728-2733, 2007.

A. T. Brünger, P. D. Adams, G. M. Clore, W. L. Delano, P. Gros et al., Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination, Acta Crystallographica Section D Biological Crystallography, vol.54, issue.5, pp.905-921, 1998.

J. M. Bullock, J. Schwab, K. Thalassinos, and M. Topf, The Importance of Non-accessible Crosslinks and Solvent Accessible Surface Distance in Modeling Proteins with Restraints From Crosslinking Mass Spectrometry, Molecular & Cellular Proteomics, vol.15, issue.7, pp.2491-2500, 2016.

J. M. Bullock, N. Sen, K. Thalassinos, and M. Topf, Modeling Protein Complexes Using Restraints from Crosslinking Mass Spectrometry, Structure, vol.26, issue.7, pp.1015-1024.e2, 2018.

Z. A. Chen, A. Jawhari, L. Fischer, C. Buchen, S. Tahir et al., Architecture of the RNA polymerase II?TFIIF complex revealed by cross-linking and mass spectrometry, The EMBO Journal, vol.29, issue.4, pp.717-726, 2010.

M. T. Degiacomi, C. Schmidt, A. J. Baldwin, and J. L. Benesch, Accommodating Protein Dynamics in the Modeling of Chemical Crosslinks, Structure, vol.25, issue.11, pp.1751-1757.e5, 2017.

M. T. Degiacomi, C. Schmidt, A. J. Baldwin, and J. L. Benesch, Accommodating Protein Dynamics in the Modeling of Chemical Crosslinks, Structure, vol.25, issue.11, pp.1751-1757.e5, 2017.

I. Farabella, D. Vasishtan, A. P. Joseph, A. P. Pandurangan, H. Sahota et al., TEMPy: a Python library for assessment of three-dimensional electron microscopy density fits, Journal of Applied Crystallography, vol.48, issue.4, pp.1314-1323, 2015.

M. Ferber, J. Kosinski, A. Ori, U. J. Rashid, M. Moreno-morcillo et al., Automated structure modeling of large protein assemblies using crosslinks as distance restraints, Nature Methods, vol.13, issue.6, pp.515-520, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01337283

A. J. Ferrari, F. C. Gozzo, and L. Martinez, Statistical Force-Field for Structural Modeling Using Chemical Cross-Linking/mass Spectrometry Distance Constraints, 2018.

A. J. Ferrari, M. A. Clasen, L. Kurt, P. C. Carvalho, F. C. Gozzo et al., TopoLink: evaluation of structural models using chemical crosslinking distance constraints, Bioinformatics, vol.35, issue.17, pp.3169-3170, 2019.

D. J. Hand, Measuring classifier performance: a coherent alternative to the area under the ROC curve, Machine Learning, vol.77, issue.1, pp.103-123, 2009.

K. Henzler-wildman and D. Kern, Dynamic personalities of proteins, Nature, vol.450, issue.7172, pp.964-972, 2007.

A. N. Holding, XL-MS: Protein cross-linking coupled with mass spectrometry, Methods, vol.89, pp.54-63, 2015.

E. Jones, T. Oliphant, and P. Peterson, SciPy: Open source scientific tools for Python, 2001.

A. Kahraman, F. Herzog, A. Leitner, G. Rosenberger, R. Aebersold et al., Cross-Link Guided Molecular Modeling with ROSETTA, PLoS ONE, vol.8, issue.9, p.e73411, 2013.

A. Kahraman, L. Malmström, and R. Aebersold, Xwalk: computing and visualizing distances in cross-linking experiments, Bioinformatics, vol.27, issue.15, pp.2163-2164, 2011.

K. Lasker, F. Forster, S. Bohn, T. Walzthoeni, E. Villa et al., Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach, Proceedings of the National Academy of Sciences, vol.109, issue.5, pp.1380-1387, 2012.

K. Lasker, J. L. Phillips, D. Russel, J. Velázquez-muriel, D. Schneidman-duhovny et al., Integrative Structure Modeling of Macromolecular Assemblies from Proteomics Data, Molecular & Cellular Proteomics, vol.9, issue.8, pp.1689-1702, 2010.

A. Leitner, M. Faini, F. Stengel, and R. Aebersold, Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines, Trends in Biochemical Sciences, vol.41, issue.1, pp.20-32, 2016.

A. Leitner, T. Walzthoeni, A. Kahraman, F. Herzog, O. Rinner et al., Probing Native Protein Structures by Chemical Cross-linking, Mass Spectrometry, and Bioinformatics, Molecular & Cellular Proteomics, vol.9, issue.8, pp.1634-1649, 2010.

A. D. Mackerell, D. Bashford, M. Bellott, R. L. Dunbrack, J. D. Evanseck et al., All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins?, The Journal of Physical Chemistry B, vol.102, issue.18, pp.3586-3616, 1998.

E. D. Merkley, S. Rysavy, A. Kahraman, R. P. Hafen, V. Daggett et al., Distance restraints from crosslinking mass spectrometry: Mining a molecular dynamics simulation database to evaluate lysine-lysine distances, Protein Science, vol.23, issue.6, pp.747-759, 2014.

J. Rappsilber, The beginning of a beautiful friendship: Cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes, Journal of Structural Biology, vol.173, issue.3, pp.530-540, 2011.

P. J. Robinson, M. J. Trnka, R. Pellarin, C. H. Greenberg, D. A. Bushnell et al., Molecular architecture of the yeast Mediator complex, eLife, vol.4, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-01401346

A. W. Schüttelkopf and D. M. Van-aalten, PRODRG: a tool for high-throughput crystallography of protein?ligand complexes, Acta Crystallographica Section D Biological Crystallography, vol.60, issue.8, pp.1355-1363, 2004.

I. Unal, Defining an Optimal Cut-Point Value in ROC Analysis: An Alternative Approach, Computational and Mathematical Methods in Medicine, vol.2017, pp.1-14, 2017.

A. B. Ward, A. Sali, and I. A. Wilson, Integrative Structural Biology, Science, vol.339, issue.6122, pp.913-915, 2013.