R. Andonov, N. Malod-dognin, and N. Yanev, Maximum Contact Map Overlap Revisited, Journal of Computational Biology, vol.18, issue.1, pp.27-41, 2011.
DOI : 10.1089/cmb.2009.0196

URL : https://hal.archives-ouvertes.fr/inria-00536624

A. Andreeva, D. Howorth, J. Chandonia, S. E. Brenner, T. J. 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

H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat et al., The Protein Data Bank, Nucleic Acids Research, vol.28, issue.1, pp.235-242, 2000.
DOI : 10.1093/nar/28.1.235

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

P. Di-lena, . Fariselli, . Margara, R. Vassura, and . Casadio, Fast overlapping of protein contact maps by alignment of eigenvectors, Bioinformatics, vol.26, issue.18, pp.2250-2258, 2010.
DOI : 10.1093/bioinformatics/btq402

M. Gerstein and M. Levitt, Using iterative dynamic programming to obtain accurate pair-wise and multiple alignments of protein structures, ISMB-96 Proceedings, pp.59-67, 1996.

J. Gibrat, T. Madej, and S. H. 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 seequences, CABIOS, vol.10, pp.587-596, 1994.

L. Holm and C. Sander, Protein Structure Comparison by Alignment of Distance Matrices, Journal of Molecular Biology, vol.233, issue.1, pp.123-138, 1993.
DOI : 10.1006/jmbi.1993.1489

W. Kabsch, A discussion of the solution for the best rotation to relate two sets of vectors, Acta Crystallographica Section A, vol.34, issue.5, pp.827-828, 1978.
DOI : 10.1107/S0567739478001680

R. M. Karp, Reducibility among combinatorial problems, Complexity of Computer Computations, vol.6, pp.85-103, 1972.
DOI : 10.1007/978-3-540-68279-0_8

R. H. Lathrop, The protein threading problem with sequence amino acid interaction preferences is NP-complete, "Protein Engineering, Design and Selection", vol.7, issue.9, pp.1059-1068, 1994.
DOI : 10.1093/protein/7.9.1059

N. Malod-dognin, R. Andonov, and N. Yanev, Maximum Cliques in Protein Structure Comparison, pp.106-117, 2010.
DOI : 10.1007/978-3-642-13193-6_10

URL : https://hal.archives-ouvertes.fr/inria-00536700

N. Malod-dognin, N. Yanev, and R. Andonov, Comparing protein 3d structures using a_purva, 2010.
URL : https://hal.archives-ouvertes.fr/inria-00539939

C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells et al., CATH ??? a hierarchic classification of protein domain structures, Structure, vol.5, issue.8, pp.1093-1109, 1997.
DOI : 10.1016/S0969-2126(97)00260-8

C. A. Orengo and J. M. Thornton, PROTEIN FAMILIES AND THEIR EVOLUTION???A STRUCTURAL PERSPECTIVE, Annual Review of Biochemistry, vol.74, issue.1, pp.867-900, 2005.
DOI : 10.1146/annurev.biochem.74.082803.133029

Y. Shibberu and A. Holder, A Spectral Approach to Protein Structure Alignment, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, issue.4, pp.867-875, 2011.
DOI : 10.1109/TCBB.2011.24

Y. Zhang and J. Skolnick, TM-align: a protein structure alignment algorithm based on the TM-score, Nucleic Acids Research, vol.33, issue.7, pp.2302-2309, 2005.
DOI : 10.1093/nar/gki524

D. On and S. , 10 4.1.1 Running time comparison