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, T. J. Prli?, A. Hubbard, and . 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

D. Barthel, J. Hirst, E. Blazewicz, N. Burke, and . Krasnogor, ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information, BMC Bioinformatics, vol.8, issue.1, pp.416-416, 2007.
DOI : 10.1186/1471-2105-8-416

C. Berbalk, C. Schwaiger, and P. Lackner, Accuracy analysis of multiple structure alignments, Protein Science, vol.40, issue.10, pp.2027-2035, 2009.
DOI : 10.1002/pro.213

H. Berman, . Westbrook, . Feng, T. Gilliland, . 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

O. Camoglu, A. Can, and . Singh, Integrating multi-attribute similarity networks for robust representation of the protein space, Bioinformatics, vol.22, issue.13, pp.1585-1592, 2006.
DOI : 10.1093/bioinformatics/btl130

O. Carugo and S. Pongor, A normalized root-mean-spuare distance for comparing protein three-dimensional structures, Protein Science, vol.301, issue.7, pp.1470-1473, 2001.
DOI : 10.1110/ps.690101

U. Emekli, D. Schneidman-duhovny, H. J. Wolfson, T. Nussinov, and . Haliloglu, HingeProt: Automated prediction of hinges in protein structures, Proteins: Structure, Function, and Bioinformatics, vol.34, issue.3/4, pp.1219-1227, 2008.
DOI : 10.1002/prot.21613

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

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

T. Hamelryck and B. Manderick, PDB file parser and structure class implemented in Python, Bioinformatics, vol.19, issue.17, pp.2308-2310, 2003.
DOI : 10.1093/bioinformatics/btg299

H. Hasegawa and L. Holm, Advances and pitfalls of protein structural alignment, Current Opinion in Structural Biology, vol.19, issue.3, pp.341-348, 2009.
DOI : 10.1016/j.sbi.2009.04.003

R. Hoffmann and A. Valencia, Implementing the iHOP concept for navigation of biomedical literature, Bioinformatics, vol.21, issue.Suppl 2, pp.252-258, 2005.
DOI : 10.1093/bioinformatics/bti1142

L. Holm and P. Rosenström, Dali server: conservation mapping in 3D, Nucleic Acids Research, vol.38, issue.Web Server, pp.545-549, 2010.
DOI : 10.1093/nar/gkq366

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

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

T. Kawabata, MATRAS: a program for protein 3D structure comparison, Nucleic Acids Research, vol.31, issue.13, pp.313367-3369, 2003.
DOI : 10.1093/nar/gkg581

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

N. Malod-dognin, R. Andonov, and N. Yanev, Maximum Cliques in Protein Structure Comparison, Lecture Notes in Computer Science, vol.6049, pp.106-117, 2010.
DOI : 10.1007/978-3-642-13193-6_10

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

T. Margraf, A. Schenk, and . Torda, The SALAMI protein structure search server, Nucleic Acids Research, vol.37, issue.Web Server, pp.480-484, 2009.
DOI : 10.1093/nar/gkp431

G. Mayr, F. 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

R. Mosca and T. Schneider, RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes, Nucleic Acids Research, vol.36, issue.Web Server, pp.42-46, 2008.
DOI : 10.1093/nar/gkn197

S. Shih, S. Prag, M. Francis, J. Sutanto, L. Hurley et al., A ubiquitin-binding motif required for intramolecular monoubiquitylation, the CUE domain, The EMBO Journal, vol.22, issue.6, pp.1273-1281, 2003.
DOI : 10.1093/emboj/cdg140

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

Y. Zhang and J. Skolnick, Scoring function for automated assessment of protein structure template quality, Proteins: Structure, Function, and Bioinformatics, vol.101, issue.4, pp.702-710, 2004.
DOI : 10.1002/prot.20264

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