A. Godzik, The structural alignment between two proteins: Is there a unique answer?, Protein Science, vol.221, issue.7, pp.1325-1338, 1996.
DOI : 10.1002/pro.5560050711

M. Sierk and G. Kleywegt, D??j?? Vu All Over Again, Structure, vol.12, issue.12, pp.2103-2111, 2004.
DOI : 10.1016/j.str.2004.09.016

J. Konc and D. Janezic, An efficient branch-and-bound algorithm for finding a maximum clique, Discrete Mathematics and Theoretical Computer Science, vol.58, p.220, 2003.

E. Tomita and T. Seki, An improved branch and bound algorithm for the maximum clique problem, Communications in Mathematical and in Computer Chemistry / MATCH, vol.58, pp.569-590, 2007.

P. R. Östergård, A fast algorithm for the maximum clique problem, Discrete Applied Mathematics, vol.120, issue.1-3, pp.197-207, 2002.
DOI : 10.1016/S0166-218X(01)00290-6

A. Andreeva, D. Howorth, J. M. Chandonia, S. Brenner, T. Hubbard et al., Data growth and its impact on the SCOP database: new developments, Nucleic Acids Research, vol.36, issue.Database, pp.419-425, 2007.
DOI : 10.1093/nar/gkm993

D. Strickland, E. Barnes, and J. Sokol, Optimal Protein Structure Alignment Using Maximum Cliques, Operations Research, vol.53, issue.3, pp.389-402, 2005.
DOI : 10.1287/opre.1040.0189

R. Karp, Reducibility among combinatorial problems, Complexity of Computer Computations, vol.6, pp.85-103, 1972.

I. Bomze, M. Budinich, P. Pardalos, and M. Pelillo, The Maximum Clique Problem, Handbook of Combinatorial Optimization, 1999.
DOI : 10.1007/978-1-4757-3023-4_1

J. F. Gibrat, T. Madej, and S. Bryant, Surprising similarities in structure comparison, Current Opinion in Structural Biology, vol.6, issue.3, pp.377-385, 1996.
DOI : 10.1016/S0959-440X(96)80058-3

A. Godzik and J. Skolnick, Flexible algorithm for direct multiple alignment of protein structures and sequences, Bioinformatics, vol.10, issue.6, pp.587-596, 1994.
DOI : 10.1093/bioinformatics/10.6.587

R. Andonov, N. Yanev, and N. Malod-dognin, An Efficient Lagrangian Relaxation for the Contact Map Overlap Problem, WABI '08: Proceedings of the 8th international workshop on Algorithms in Bioinformatics, pp.162-173, 2008.
DOI : 10.1007/978-3-540-87361-7_14

URL : https://hal.archives-ouvertes.fr/inria-00327135

A. Caprara, R. Carr, S. Israil, G. Lancia, and B. Walenz, 1001 Optimal PDB Structure Alignments: Integer Programming Methods for Finding the Maximum Contact Map Overlap, Journal of Computational Biology, vol.11, issue.1, pp.27-52, 2004.
DOI : 10.1089/106652704773416876

M. Fredman, On computing the length of longest increasing subsequences, Discrete Mathematics, vol.11, issue.1, pp.29-35, 1975.
DOI : 10.1016/0012-365X(75)90103-X

J. Martin, G. Letellier, A. Marin, J. F. Taly, A. De-brevern et al., Protein secondary structure assignment revisited: a detailed analysis of different assignment methods, BMC Structural Biology, vol.5, issue.1, p.17, 2005.
DOI : 10.1186/1472-6807-5-17

URL : https://hal.archives-ouvertes.fr/inserm-00090199

G. Lancia, R. Carr, B. Walenz, and S. Istrail, 101 optimal PDB structure alignments, Proceedings of the fifth annual international conference on Computational biology , RECOMB '01, pp.193-202, 2001.
DOI : 10.1145/369133.369199

I. Lerman, Likelihood linkage analysis (LLA) classification method: An example treated by hand, Biochimie, vol.75, issue.5, pp.379-397, 1993.
DOI : 10.1016/0300-9084(93)90172-O