X. Huang, M. Britto, J. Kear-scott, C. Boone, J. Rocca et al., The Role of Select Subtype Polymorphisms on HIV-1 Protease Conformational Sampling and Dynamics, Journal of Biological Chemistry, vol.289, issue.24, pp.17203-17214, 2014.
DOI : 10.1074/jbc.M114.571836

V. Kanelis, J. Forman-kay, and L. Kay, Multidimensional NMR Methods for Protein Structure Determination, IUBMB Life (International Union of Biochemistry and Molecular Biology: Life), vol.52, issue.6, pp.291-302, 2001.
DOI : 10.1080/152165401317291147

A. Sinz, Chemical cross-linking and mass spectrometry for mapping three-dimensional structures of proteins and protein complexes, Journal of Mass Spectrometry, vol.26, issue.12, pp.1225-1237, 2003.
DOI : 10.1002/jms.559

M. Marti-renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo et al., Comparative Protein Structure Modeling of Genes and Genomes, Annual Review of Biophysics and Biomolecular Structure, vol.29, issue.1, pp.291-325, 2000.
DOI : 10.1146/annurev.biophys.29.1.291

S. Vajda and D. Kozakov, Convergence and combination of methods in protein???protein docking, Current Opinion in Structural Biology, vol.19, issue.2, pp.164-170, 2009.
DOI : 10.1016/j.sbi.2009.02.008

M. Bello, M. Martínez-archundia, and J. Correa-basurto, Automated docking for novel drug discovery, Expert 637 Opinion Drug Discovery, pp.821-834, 2013.
DOI : 10.1016/j.jmgm.2010.02.001

G. Crippen and T. Havel, Distance Geometry and Molecular Conformation, p.639, 1988.

L. Liberti, C. Lavor, N. Maculan, and A. Mucherino, Euclidean Distance Geometry and Applications, SIAM Review, vol.56, issue.1, pp.3-69, 2014.
DOI : 10.1137/120875909
URL : https://hal.archives-ouvertes.fr/hal-01093056

M. Nilges, A. Gronenborn, A. Brünger, and G. Clore, Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints. Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2, "Protein Engineering, Design and Selection", vol.2, issue.1, pp.27-38, 1988.
DOI : 10.1093/protein/2.1.27

B. Alipanahi, N. Krislock, A. Ghodsi, H. Wolkowicz, L. Donaldson et al., Determining Protein Structures from NOESY Distance Constraints by Semidefinite Programming, Journal of Computational Biology, vol.20, issue.4, pp.296-310, 2013.
DOI : 10.1089/cmb.2012.0089
URL : https://hal.archives-ouvertes.fr/hal-00684488

C. Wang, T. Lozano-pérez, and B. Tidor, AmbiPack: A systematic algorithm for packing of macromolecular structures with ambiguous distance constraints, Proteins: Structure, Function, and Genetics, vol.112, issue.1, pp.26-42, 1998.
DOI : 10.1002/(SICI)1097-0134(19980701)32:1<26::AID-PROT5>3.0.CO;2-C

S. Potluri, A. Yan, B. Donald, and C. Bailey-kellogg, A complete algorithm to resolve ambiguity for intersubunit NOE assignment in structure determination of symmetric homo-oligomers, Protein Science, vol.16, issue.1, pp.69-81, 2007.
DOI : 10.1110/ps.062427307

J. Martin, A. Yan, C. Bailey-kellogg, P. Zhou, and B. Donald, A Geometric Arrangement Algorithm for Structure Determination of Symmetric Protein Homo-Oligomers from NOEs and RDCs, Journal of Computational Biology, vol.18, issue.11, pp.1507-1523, 2011.
DOI : 10.1089/cmb.2011.0173

J. Martin, A. Yan, C. Bailey-kellogg, P. Zhou, and B. Donald, A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers, Protein Science, vol.32, issue.6, pp.970-985, 2011.
DOI : 10.1002/pro.620

P. Reardon, H. Sage, S. Dennison, J. Martin, B. Donald et al., Structure of an 661 HIV-1-neutralizing antibody target, the lipid-bound gp41 envelope membrane proximal region trimer, 662 Proceedings National Academy Sciences USA 111, pp.1391-1396, 2014.

J. Zeng, J. Boyles, C. Tripathy, L. Wang, A. Yan et al., High-resolution protein structure 664 determination starting with a global fold calculated from exact solutions to the rdc equations, J Biomol NMR, vol.665, pp.45-265, 2009.

D. Gordon, G. Hom, S. Mayo, and N. Pierce, Exact rotamer optimization for protein design, Journal of Computational Chemistry, vol.230, issue.2, pp.232-243, 2003.
DOI : 10.1002/jcc.10121

C. Kingsford, B. Chazelle, and M. Singh, Solving and analyzing side-chain positioning problems using linear and integer programming, Bioinformatics, vol.21, issue.7, pp.1028-1036, 2005.
DOI : 10.1093/bioinformatics/bti144

L. Wang and B. Donald, An efficient and accurate algorithm for assigning nuclear Overhauser effect restraints 671 using a rotamer library ensemble and residual dipolar couplings. The IEEE computational systems 672 bioinformatics conference (CSB), pp.189-202, 2005.

L. Wang, R. Mettu, and B. Donald, A polynomial-time algorithm for de novo protein backbone structure 674 determination from NMR data, J Comput Biol, vol.13, pp.1276-1288, 2006.

O. Neil, R. Lilien, R. Donald, B. Stroud, R. Anderson et al., Phylogenetic classification of protozoa based on 676 the structure of the linker domain in the bifunctional enzyme, dihydrofolate reductase-thymidylate synthase, J, vol.677

C. Lavor, L. Liberti, N. Maculan, and A. Mucherino, The discretizable molecular distance geometry problem, Computational Optimization and Applications, vol.11, issue.3, pp.115-146, 2012.
DOI : 10.1007/s10589-011-9402-6
URL : https://hal.archives-ouvertes.fr/hal-00756940

C. Lavor, L. Liberti, and A. Mucherino, The interval Branch-and-Prune Algorithm for the Discretizable Molecular 681

R. A. Engh and R. Huber, Accurate bond and angle parameters for x-ray protein structure refinement. Acta 683 Crystallographica Section A: Foundations of, Crystallography, vol.47, issue.4, pp.392-400, 1991.

W. Rocchia, E. Alexov, and B. Honig, Extending the applicability of the nonlinear poisson-boltzmann equation, p.685

B. Honig and A. Nicholls, Classical electrostatics in biology and chemistry, Science, vol.268, issue.5214, pp.1144-1149, 1995.
DOI : 10.1126/science.7761829

L. Liberti, B. Masson, J. Lee, C. Lavor, and A. Mucherino, On the number of realizations of certain Henneberg graphs arising in protein conformation, Discrete Applied Mathematics, vol.165, pp.213-232, 2014.
DOI : 10.1016/j.dam.2013.01.020
URL : https://hal.archives-ouvertes.fr/hal-01093060

I. Coope, Reliable computation of the points of intersection of $n$ spheres in $R^n$, ANZIAM Journal, vol.42, pp.461-477, 2000.
DOI : 10.21914/anziamj.v42i0.608

J. Berg, J. Tymoczko, and L. Stryer, Biochemistry: International Edition, p.694, 2006.

P. Güntert, C. Mumenthaler, and K. Wüthrich, Torsion angle dynamics for NMR structure calculation with the new program Dyana, Journal of Molecular Biology, vol.273, issue.1, pp.283-298, 1997.
DOI : 10.1006/jmbi.1997.1284

P. Güntert and K. Wüthrich, Sampling of conformation space in torsion angle dynamics calculations, Comp Phys 697 Commun, pp.155-169, 2001.
DOI : 10.1016/S0010-4655(01)00204-1

B. López-méndez and P. Güntert, Automated Protein Structure Determination from NMR Spectra, Journal of the American Chemical Society, vol.128, issue.40, p.699
DOI : 10.1021/ja061136l

A. Mucherino, C. Lavor, T. Malliavin, L. Liberti, M. Nilges et al., Influence of pruning devices on the 701 solution of molecular distance geometry problems, Lecture Notes, p.702

Q. Dong and Z. Wu, A geometric build-up algorithm for solving the molecular distance geometry problem with 704 sparse distance data, Journal of Global Optimization, vol.26, issue.3, pp.321-333, 2003.
DOI : 10.1023/A:1023221624213

C. Lavor, L. Liberti, A. Mucherino, and N. Maculan, On a discretizable subclass of instances of the molecular 706 distance geometry problem, Proceedings of the 2009 ACM Symposium on Applied Computing, pp.804-805, 2009.

R. W. Floyd, Algorithm 97: Shortest path, Communications of the ACM, vol.5, issue.6, pp.345-709, 1962.
DOI : 10.1145/367766.368168

Y. Shen, F. Delaglio, G. Cornilescu, and A. Bax, TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts, Journal of Biomolecular NMR, vol.21, issue.4, pp.213-223, 2009.
DOI : 10.1007/s10858-009-9333-z

A. Grishaev and A. Bax, An Empirical Backbone???Backbone Hydrogen-Bonding Potential in Proteins and Its Applications to NMR Structure Refinement and Validation, Journal of the American Chemical Society, vol.126, issue.23, pp.7281-7292, 2004.
DOI : 10.1021/ja0319994

W. Kabsch and C. Sander, Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, vol.33, issue.12, pp.2577-2637, 1983.
DOI : 10.1002/bip.360221211

D. Abrahams and A. Gurtovoy, C++ Template Metaprogramming: Concepts, Tools, and Techniques from Boost 717 and Beyond, p.718, 2004.

M. H. Austern, Generic Programming and the STL: Using and Extending the C++ Standard Template Library

N. Josuttis, The C++ Standard Library: a Tutorial and Reference, p.721

S. Hammarling, A. Mckenney, and D. Sorensen, LAPACK Users' Guide, Society for Industrial and 724 Applied Mathematics, p.725, 1999.

L. Lee and A. Lumsdaine, The Boost Graph Library: User Guide and Reference Manual

H. Brönnimann, G. Melquiond, and S. Pion, The design of the boost interval arithmetic library. Theoretical 728, Computer Science, vol.351, issue.1, pp.111-118, 2006.

H. Brönnimann, G. Melquiond, and S. Pion, The boost interval arithmetic library, Real Numbers and 730 Computers, pp.65-80, 2003.

J. Saxe, Embeddability of weighted graphs in k-space is strongly NP-hard, Proceedings of 17th Allerton 732

L. Liberti, C. Lavor, and N. Maculan, A Branch-and-Prune algorithm for the Molecular Distance Geometry Problem, International Transactions in Operational Research, vol.23, issue.13, pp.1-17, 2008.
DOI : 10.1111/j.1475-3995.2007.00622.x

C. Lavor, A. Mucherino, L. Liberti, and N. Maculan, On the computation of protein backbones by using artificial backbones of hydrogens, Journal of Global Optimization, vol.43, issue.3???4, pp.329-344, 2011.
DOI : 10.1007/s10898-010-9584-y

V. Costa, A. Mucherino, C. Lavor, A. Cassioli, L. Carvalho et al., Discretization orders for protein side chains, Journal of Global Optimization, vol.39, issue.Suppl 9, pp.333-349, 2014.
DOI : 10.1007/s10898-013-0135-1
URL : https://hal.archives-ouvertes.fr/hal-01093052

L. Liberti, C. Lavor, and A. Mucherino, The discretizable molecular distance geometry problem seems easier on 742 proteins, Distance Geometry: Theory, Methods, 743 and Applications, p.744, 2013.

A. Cassioli, O. Günlük, C. Lavor, and L. Liberti, Discretization vertex orders in distance geometry, Discrete 745 Applied Mathematics, p.746
DOI : 10.1016/j.dam.2014.08.035

L. Liberti, B. Masson, C. Lavor, J. Lee, and A. Mucherino, On the number of realizations of certain Henneberg graphs arising in protein conformation, Discrete Applied Mathematics, vol.165, pp.213-232, 2014.
DOI : 10.1016/j.dam.2013.01.020
URL : https://hal.archives-ouvertes.fr/hal-01093060

C. Lavor, J. Lee, . Lee-st, A. John, L. Liberti et al., Discretization orders for distance geometry problems, Optimization Letters, vol.2, issue.3, pp.783-796, 2012.
DOI : 10.1007/s11590-011-0302-6
URL : https://hal.archives-ouvertes.fr/hal-00756941

H. Berman, G. Kleywegt, H. Nakamura, and J. Markley, The future of the protein data bank, Biopolymers, vol.246, issue.3, pp.218-222, 2013.
DOI : 10.1002/bip.22132

M. Respondek, T. Madl, C. Göbl, R. Golser, and K. Zangger, Mapping the Orientation of Helices in Micelle-Bound Peptides by Paramagnetic Relaxation Waves, Journal of the American Chemical Society, vol.129, issue.16, pp.5228-5234, 2007.
DOI : 10.1021/ja069004f

J. Lorieau, J. Louis, and A. Bax, The complete influenza hemagglutinin fusion domain adopts a tight helical 755 hairpin arrangement at the lipid:water interface, Proceedings National Academy Sciences USA 107, pp.11341-11346, 2010.

R. Laskowski, M. Macarthur, D. Moss, and J. Thornton, PROCHECK: a program to check the stereochemical quality of protein structures, Journal of Applied Crystallography, vol.26, issue.2, pp.283-291, 1993.
DOI : 10.1107/S0021889892009944

L. Miri, G. Bouvier, A. Kettani, A. Mikou, L. Wakrim et al., Stabilization of the 760 integrase-DNA complex by Mg2+ ions and prediction of key residues for binding HIV-1 integrase inhibitors, Proteins, vol.82, pp.761-466, 2014.

T. Malliavin, Functional motions modulating VanA ligand binding unraveled by self-organizing maps, Journal 764 Chemical Information Modeling, vol.54, pp.289-301, 2014.

T. Kohonen, Self-organizing Maps, p.766, 2001.

H. Fan and A. Mark, Relative stability of protein structures determined by X-ray crystallography or NMR spectroscopy: A molecular dynamics simulation study, Proteins: Structure, Function, and Bioinformatics, vol.22, issue.1, pp.111-120, 2003.
DOI : 10.1002/prot.10496

S. Nabuurs, C. Spronk, G. Vuister, and G. Vriend, Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors, PLoS Computational Biology, vol.16, issue.2, pp.9-770, 2006.
DOI : 1367-4803(2000)016[0404:TPPSPS]2.0.CO;2

W. Braun and N. G¯-o, Calculation of protein conformations by proton-proton distance constraints, Journal of Molecular Biology, vol.186, issue.3
DOI : 10.1016/0022-2836(85)90134-2

W. Rieping, M. Habeck, B. Bardiaux, A. Bernard, T. Malliavin et al., ARIA2: Automated NOE assignment and data integration in NMR structure calculation, Bioinformatics, vol.23, issue.3, pp.381-382, 2007.
DOI : 10.1093/bioinformatics/btl589

P. Guntert, Automated NMR Structure Calculation With CYANA, Methods Molecular Biology, vol.278, pp.353-378, 2004.
DOI : 10.1385/1-59259-809-9:353

P. Guerry and T. Herrmann, Comprehensive Automation for NMR Structure Determination of Proteins, Methods Molecular Biology, vol.777, issue.831, pp.429-451, 2012.
DOI : 10.1007/978-1-61779-480-3_22
URL : https://hal.archives-ouvertes.fr/hal-00955857

K. Lasker, A. Sali, and H. Wolfson, Determining macromolecular assembly structures by molecular docking and fitting into an electron density map, Proteins: Structure, Function, and Bioinformatics, vol.9, issue.15, pp.3205-3211, 2010.
DOI : 10.1002/prot.22845

C. Lavor, R. Alves, W. Figueiredo, A. Petraglia, and N. Maculan, Clifford Algebra and the discretizable 781 molecular distance geometry problem, Adv Appl Clifford Algebras, p.782, 2015.

A. Bernard, W. Vranken, B. Bardiaux, M. Nilges, and T. Malliavin, Bayesian estimation of NMR restraint potential and weight: A validation on a representative set of protein structures, Proteins: Structure, Function, and Bioinformatics, vol.69, issue.5, pp.1525-1537, 2008.
DOI : 10.1002/prot.22980