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, A. Prli?, T. J. Hubbard, and A. G. Murzin, SISYPHUS--structural alignments for proteins with non-trivial relationships, Nucleic Acids Research, vol.35, issue.Database, pp.253-259, 2007.
DOI : 10.1093/nar/gkl746

C. Berbalk, C. S. Schwaiger, and P. Lackner, Accuracy analysis of multiple structure alignments, Protein Science, vol.40, issue.10, 2009.
DOI : 10.1002/pro.213

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. Istrail, 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

G. Csaba, F. Birzele, and R. Zimmer, Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis, BMC Structural Biology, vol.9, issue.1, pp.23-23, 2009.
DOI : 10.1186/1472-6807-9-23

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

L. H. Greene, T. E. Lewis, S. Addou, A. Cuff, T. Dallman et al., The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution, Nucleic Acids Research, vol.35, issue.Database, pp.35291-297, 2007.
DOI : 10.1093/nar/gkl959

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

L. Holm and C. Sander, Dictionary of recurrent domains in protein structures, Proteins: Structure, Function, and Genetics, vol.22, issue.1, pp.88-96, 1998.
DOI : 10.1002/(SICI)1097-0134(19981001)33:1<88::AID-PROT8>3.0.CO;2-H

T. Kawabata and K. Nishikawa, Protein structure comparison using the Markov transition model of evolution, Proteins: Structure, Function, and Genetics, vol.24, issue.1, pp.108-122, 2000.
DOI : 10.1002/1097-0134(20001001)41:1<108::AID-PROT130>3.0.CO;2-S

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, Experimental Algorithms, pp.106-117, 2010.
DOI : 10.1007/978-3-642-13193-6_10
URL : https://hal.archives-ouvertes.fr/inria-00536700

N. Malod-dognin, M. L. Boudic-jamin, P. Kamath, and R. Andonov, Using Dominances for Solving the Protein Family Identification Problem, Lecture Notes in Computer Science, vol.33, issue.4, pp.201-212, 2011.
DOI : 10.1093/nar/gki524
URL : https://hal.archives-ouvertes.fr/inria-00609432

G. Mayr, F. S. Domingues, and P. Lackner, Comparative Analysis of Protein Structure Alignments, BMC Structural Biology, vol.7, issue.1, pp.50-50, 2007.
DOI : 10.1186/1472-6807-7-50

A. G. Murzin, S. E. Brenner, T. Hubbard, and C. Chothia, SCOP: A structural classification of proteins database for the investigation of sequences and structures, Journal of Molecular Biology, vol.247, issue.4, pp.536-540, 1995.
DOI : 10.1016/S0022-2836(05)80134-2

W. R. Taylor and C. A. Orengo, Protein structure alignment, Journal of Molecular Biology, vol.208, issue.1, pp.1-22, 1989.
DOI : 10.1016/0022-2836(89)90084-3

I. Wohlers, F. S. Domingues, and G. W. Klau, Towards optimal alignment of protein structure distance matrices, Bioinformatics, vol.26, issue.18, pp.2273-2280, 2010.
DOI : 10.1093/bioinformatics/btq420

I. Wohlers, R. Andonov, and G. W. Klau, Algorithm engineering for optimal alignment of protein structure distance matrices. Optimization Letters, pp.421-433, 2011.
URL : https://hal.archives-ouvertes.fr/inria-00586067

I. Wohlers, N. Malod-dognin, R. Andonov, and G. W. Klau, CSA: comprehensive comparison of pairwise protein structure alignments, Nucleic Acids Research, vol.40, issue.W1
DOI : 10.1093/nar/gks362
URL : https://hal.archives-ouvertes.fr/hal-00667920

W. Xie and N. V. Sahinidis, A Reduction-Based Exact Algorithm for the Contact Map Overlap Problem, Journal of Computational Biology, vol.14, issue.5, pp.637-654, 2007.
DOI : 10.1089/cmb.2007.R007