H. Hegyi and M. Gerstein, The relationship between protein structure and function: a comprehensive survey with application to the yeast genome, Journal of Molecular Biology, vol.288, issue.1, pp.147-164, 1999.
DOI : 10.1006/jmbi.1999.2661

A. Marchler-bauer, C. Zheng, and F. Chitsaz, CDD: conserved domains and protein three-dimensional structure, Nucleic Acids Research, vol.41, issue.D1, pp.348-352, 2013.
DOI : 10.1093/nar/gks1243
URL : http://doi.org/10.1093/nar/gks1243

A. Andreeva and A. G. Murzin, Evolution of protein fold in the presence of functional constraints, Current Opinion in Structural Biology, vol.16, issue.3, pp.399-408, 2006.
DOI : 10.1016/j.sbi.2006.04.003

C. L. Worth, S. Gong, and T. L. Blundell, Structural and functional constraints in the evolution of protein families, Nature Reviews Molecular Cell Biology, vol.23, 2009.
DOI : 10.1038/nrm2762

S. Pascarella and P. Argos, Analysis of insertions/deletions in protein structures, Journal of Molecular Biology, vol.224, issue.2, pp.461-471, 1992.
DOI : 10.1016/0022-2836(92)91008-D

G. A. Reeves, T. J. Dallman, and O. C. Redfern, Structural Diversity of Domain Superfamilies in the CATH Database, Journal of Molecular Biology, vol.360, issue.3, pp.725-741, 2006.
DOI : 10.1016/j.jmb.2006.05.035

S. Sandhya, S. S. Rani, and B. Pankaj, Length Variations amongst Protein Domain Superfamilies and Consequences on Structure and Function, PLoS ONE, vol.58, issue.3, p.4981, 2009.
DOI : 10.1371/journal.pone.0004981.s008
URL : https://hal.archives-ouvertes.fr/hal-01198473

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

L. Holm and J. Park, DaliLite workbench for protein structure comparison, Bioinformatics, vol.16, issue.6, pp.566-567, 2000.
DOI : 10.1093/bioinformatics/16.6.566

I. N. Shindyalov and P. E. Bourne, Protein structure alignment by incremental combinatorial extension (CE) of the optimal path, Protein Engineering Design and Selection, vol.11, issue.9, pp.739-747, 1998.
DOI : 10.1093/protein/11.9.739

C. A. Orengo and W. R. Taylor, [36] SSAP: Sequential structure alignment program for protein structure comparison, Methods Enzymol, vol.266, pp.617-635, 1996.
DOI : 10.1016/S0076-6879(96)66038-8

D. Lupyan, A. Leo-macias, and A. R. Ortiz, A new progressive-iterative algorithm for multiple structure alignment, Bioinformatics, vol.21, issue.15, pp.3255-3263, 2005.
DOI : 10.1093/bioinformatics/bti527

A. Sali and T. L. Blundell, Definition of general topological equivalence in protein structures, Journal of Molecular Biology, vol.212, issue.2, pp.403-428, 1990.
DOI : 10.1016/0022-2836(90)90134-8

Y. Ye and A. Godzik, Flexible structure alignment by chaining aligned fragment pairs allowing twists, Bioinformatics, vol.19, issue.Suppl 2, pp.246-255, 2003.
DOI : 10.1093/bioinformatics/btg1086

M. Menke, B. Berger, and L. Cowen, Matt: Local Flexibility Aids Protein Multiple Structure Alignment, PLoS Computational Biology, vol.5, issue.1, p.10, 2008.
DOI : 0162-8828(1983)005[0533:QOAKAG]2.0.CO;2
URL : http://doi.org/10.1371/journal.pcbi.0040010

M. Shatsky, R. Nussinov, and H. J. Wolfson, FlexProt: Alignment of Flexible Protein Structures Without a Predefinition of Hinge Regions, Journal of Computational Biology, vol.11, issue.1, pp.83-106, 2004.
DOI : 10.1089/106652704773416902

G. Agarwal, S. Mahajan, and N. Srinivasan, Identification of Local Conformational Similarity in Structurally Variable Regions of Homologous Proteins Using Protein Blocks, PLoS ONE, vol.77, issue.3, p.17826, 2011.
DOI : 10.1371/journal.pone.0017826.s008
URL : https://hal.archives-ouvertes.fr/inserm-00586691

A. G. De-brevern, C. Etchebest, and S. Hazout, Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks, Proteins: Structure, Function, and Genetics, vol.7, issue.3, pp.271-287, 2000.
DOI : 10.1002/1097-0134(20001115)41:3<271::AID-PROT10>3.0.CO;2-Z
URL : https://hal.archives-ouvertes.fr/inserm-00132821

B. Offmann, M. Tyagi, D. Brevern, and A. G. , Local Protein Structures, Current Bioinformatics, vol.2, issue.3, pp.165-202, 2007.
DOI : 10.2174/157489307781662105
URL : https://hal.archives-ouvertes.fr/inserm-00175058

A. P. Joseph, G. Agarwal, and S. Mahajan, A short survey on protein blocks, Biophysical Reviews, vol.30, issue.3, pp.137-145, 2010.
DOI : 10.1007/s12551-010-0036-1
URL : https://hal.archives-ouvertes.fr/inserm-00512823

R. Karchin, M. Cline, and Y. Mandel-gutfreund, Hidden Markov models that use predicted local structure for fold recognition: Alphabets of backbone geometry, Proteins: Structure, Function, and Bioinformatics, vol.323, issue.1/2, pp.504-514, 2003.
DOI : 10.1002/prot.10369

J. D. Thompson, D. G. Higgins, and T. J. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-4680, 1994.
DOI : 10.1093/nar/22.22.4673

S. Balaji, S. Sujatha, and S. S. Kumar, PALI--a database of Phylogeny and ALIgnment of homologous protein structures, Nucleic Acids Research, vol.29, issue.1, pp.61-65, 2001.
DOI : 10.1093/nar/29.1.61

A. G. Murzin, S. E. Brenner, and T. Hubbard, 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

M. S. Johnson, A. Sali, and T. L. Blundell, [42] Phylogenetic relationships from three-dimensional protein structures, Methods Enzymol, vol.183, pp.670-690, 1990.
DOI : 10.1016/0076-6879(90)83044-A

M. S. Johnson, M. J. Sutcliffe, and T. L. Blundell, Molecular anatomy: Phyletic relationships derived from three-dimensional structures of proteins, Journal of Molecular Evolution, vol.170, issue.1, pp.43-59, 1990.
DOI : 10.1007/BF02102452

A. P. Joseph, N. Srinivasan, D. Brevern, and A. G. , Improvement of protein structure comparison using a structural alphabet, Biochimie, vol.93, issue.9, pp.1434-1445, 2011.
DOI : 10.1016/j.biochi.2011.04.010
URL : https://hal.archives-ouvertes.fr/inserm-00646245

A. D. Mclachlan, Rapid comparison of protein structures, Acta Crystallographica Section A, vol.38, issue.6, pp.871-873, 1982.
DOI : 10.1107/S0567739482001806

A. S. Konagurthu, J. C. Whisstock, and P. J. Stuckey, MUSTANG: A multiple structural alignment algorithm, Proteins: Structure, Function, and Bioinformatics, vol.365, issue.3, pp.559-574, 2006.
DOI : 10.1002/prot.20921