Swelfe: a detector of internal repeats in sequences and structures, Bioinformatics, vol.24, issue.13, pp.241536-241543, 2008. ,
DOI : 10.1093/bioinformatics/btn234
URL : https://hal.archives-ouvertes.fr/pasteur-00336123
A comprehensive analysis of non-sequential alignments between all protein structures, BMC Structural Biology, vol.7, issue.1, p.78, 2007. ,
DOI : 10.1186/1472-6807-7-78
Analysis of topological and nontopological structural similarities in the PDB : new examples with old structures, Proteins, vol.25, issue.3, pp.354-65, 1996. ,
A_purva : User Manual 1), pp.0-2, 2011. ,
Protein Repeats: Structures, Functions, and Evolution, Journal of Structural Biology, vol.134, issue.2-3, pp.117-148, 2001. ,
DOI : 10.1006/jsbi.2001.4392
SCOP2 prototype: a new approach to protein structure mining, Nucleic Acids Research, vol.42, issue.D1, pp.310-314, 2014. ,
DOI : 10.1093/nar/gkt1242
SISYPHUS--structural alignments for proteins with non-trivial relationships, Nucleic Acids Research, vol.35, issue.Database, pp.253-262, 2007. ,
DOI : 10.1093/nar/gkl746
MolLoc: a web tool for the local structural alignment of molecular surfaces, Nucleic Acids Research, vol.37, issue.Web Server, pp.565-70, 2009. ,
DOI : 10.1093/nar/gkp405
MatAlign: PRECISE PROTEIN STRUCTURE COMPARISON BY MATRIX ALIGNMENT, Journal of Bioinformatics and Computational Biology, vol.04, issue.06, pp.1197-1216, 2006. ,
DOI : 10.1142/S0219720006002417
BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations, Nucleic Acids Research, vol.29, issue.1, pp.323-329, 2001. ,
DOI : 10.1093/nar/29.1.323
The Protein Data Bank, Nucleic Acids Research, vol.28, issue.1, pp.235-242, 2000. ,
DOI : 10.1093/nar/28.1.235
Expansion of protein domain repeats, PLoS Computational Biology, vol.2, pp.959-0970, 2006. ,
Domain rearrangements in protein evolution, Journal of Molecular Biology, vol.353, issue.4, pp.911-923, 2005. ,
Detection of circular permutations within protein structures using CE-CP, Bioinformatics, vol.31, issue.8, pp.311316-1318, 2014. ,
DOI : 10.1093/bioinformatics/btu823
Circular Permutation in Proteins, PLoS Computational Biology, vol.26, issue.3, p.1002445, 2012. ,
DOI : 10.1371/journal.pcbi.1002445.s002
The ASTRAL compendium for protein structure and sequence analysis, Nucleic Acids Research, vol.28, issue.1, pp.254-260, 2000. ,
DOI : 10.1093/nar/28.1.254
The ProDom database of protein domain families: more emphasis on 3D, Nucleic Acids Research, vol.33, issue.Database issue, 2005. ,
DOI : 10.1093/nar/gki034
URL : https://hal.archives-ouvertes.fr/hal-01214150
Are protein ?protein interfaces more conserved in sequence than the rest of the protein surface, pp.190-202, 2004. ,
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
Protein???Protein Binding Site Prediction by Local Structural Alignment, Journal of Chemical Information and Modeling, vol.50, issue.10, pp.1906-1919, 2010. ,
DOI : 10.1021/ci100265x
Computing the volume of a union of balls, ACM Transactions on Mathematical Software, vol.38, issue.1, pp.1-19, 2011. ,
DOI : 10.1145/2049662.2049665
URL : https://hal.archives-ouvertes.fr/hal-00849809
PRIGSA: Protein repeat identification by graph spectral analysis, Journal of Bioinformatics and Computational Biology, vol.12, issue.06, p.1442009, 2014. ,
DOI : 10.1142/S0219720014420098
Parallel seed-based approach to protein structure similarity detection, Parallel Processing and Applied Mathematics, pp.278-287, 2014. ,
URL : https://hal.archives-ouvertes.fr/hal-00881507
Hristo Djidjev , and Dominique Lavenier. Parallel seed-based approach to multiple protein structure similarities detection, Scientific Programming, 2015. ,
Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison, BMC Structural Biology, vol.6, issue.1, p.18, 2006. ,
DOI : 10.1186/1472-6807-6-18
Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison, BMC Structural Biology, vol.6, issue.1, p.18, 2006. ,
DOI : 10.1186/1472-6807-6-18
MALIDUP: A database of manually constructed structure alignments for duplicated domain pairs, Proteins: Structure, Function, and Bioinformatics, vol.34, issue.Part 5, pp.1162-1168, 2008. ,
DOI : 10.1002/prot.21783
Systematic comparison of SCOP and CATH: a new gold standard for protein structure analysis, BMC Structural Biology, vol.9, issue.1, p.23, 2009. ,
DOI : 10.1186/1472-6807-9-23
Favin versus concanavalin A: Circularly permuted amino acid sequences, Proceedings of the National Academy of Sciences, pp.3218-3222, 1979. ,
DOI : 10.1073/pnas.76.7.3218
A novel method to compare protein structures using local descriptors, BMC Bioinformatics, vol.12, issue.1, p.344, 2011. ,
DOI : 10.1103/PhysRevLett.57.2607
MASS: multiple structural alignment by secondary structures, Bioinformatics, vol.19, issue.Suppl 1, pp.95-104, 2003. ,
DOI : 10.1093/bioinformatics/btg1012
HingeProt: Automated prediction of hinges in protein structures, Proteins: Structure, Function, and Bioinformatics, vol.34, issue.3/4, pp.1219-1246, 2008. ,
DOI : 10.1002/prot.21613
The REPRO server : finding protein internal sequence repeats through the Web, Trends in biochemical sciences, vol.25, issue.10, pp.515-517, 2000. ,
Structural Mechanisms for Domain Movements in Proteins, Biochemistry, vol.33, issue.22, pp.6739-6749, 1994. ,
DOI : 10.1021/bi00188a001
The structural alignment between two proteins : is there a unique answer ? Protein science : a publication of the, pp.1325-1363, 1996. ,
Regularities in interaction patterns of globular proteins, "Protein Engineering, Design and Selection", vol.6, issue.8, pp.801-810, 1993. ,
DOI : 10.1093/protein/6.8.801
Fold independent structural comparisons of protein-ligand binding sites for exploring functional relationships, Journal of molecular biology, vol.355, issue.5, pp.1112-1136, 2006. ,
Algorithmic aspects of protein structure similarity, 40th Annual Symposium on Foundations of Computer Science (Cat. No.99CB37039), 1999. ,
DOI : 10.1109/SFFCS.1999.814624
The CATH domain structure database : new protocols and classification levels give a more comprehensive resource for exploring evolution, Nucleic acids research, pp.35-291, 2007. ,
STRATEGIES OF NON-SEQUENTIAL PROTEIN STRUCTURE ALIGNMENTS, Genome Informatics 2009, pp.21-29, 2010. ,
DOI : 10.1142/9781848165786_0003
Advances and pitfalls of protein structural alignment, Current Opinion in Structural Biology, vol.19, issue.3, pp.341-349, 2009. ,
DOI : 10.1016/j.sbi.2009.04.003
Meta-analysis of protein structural alignment, 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, pp.72-76, 2012. ,
DOI : 10.1109/BIBMW.2012.6470218
STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins, Nucleic Acids Research, vol.32, issue.Web Server, pp.500-502, 2004. ,
DOI : 10.1093/nar/gkh429
A classification of glycosyl hydrolases based on amino acid sequence similarities, Biochemical Journal, vol.280, issue.2, pp.309-325, 1991. ,
DOI : 10.1042/bj2800309
URL : https://hal.archives-ouvertes.fr/hal-00310263
New families in the classification of glycosyl hydrolases based on amino acid sequence similarities, Biochemical Journal, vol.293, issue.3, pp.781-789, 1993. ,
DOI : 10.1042/bj2930781
URL : https://hal.archives-ouvertes.fr/hal-00310595
DaliLite workbench for protein structure comparison, Bioinformatics, vol.16, issue.6, pp.566-567, 2000. ,
DOI : 10.1093/bioinformatics/16.6.566
Protein Structure Comparison by Alignment of Distance Matrices, Journal of Molecular Biology, vol.233, issue.1, pp.123-161, 1993. ,
DOI : 10.1006/jmbi.1993.1489
Parser for protein folding units, Proteins: Structure, Function, and Genetics, vol.347, issue.3, pp.256-68, 1994. ,
DOI : 10.1002/prot.340190309
Dali: a network tool for protein structure comparison, Trends in Biochemical Sciences, vol.20, issue.11, pp.478-480, 1995. ,
DOI : 10.1016/S0968-0004(00)89105-7
Searching protein structure databases with DaliLite v.3, Bioinformatics, vol.24, issue.23, pp.2780-2781, 2008. ,
DOI : 10.1093/bioinformatics/btn507
ConSole: using modularity of Contact maps to locate Solenoid domains in protein structures, BMC Bioinformatics, vol.15, issue.1, p.119, 2014. ,
DOI : 10.1038/35100529
The PROSITE database, Nucleic Acids Research, vol.34, issue.90001, pp.227-257, 2006. ,
DOI : 10.1093/nar/gkj063
InterPro in 2011 : new developments in the family and domain prediction database, Database issue), pp.40-306, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00697960
T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm, Bioinformatics, vol.25, issue.20, pp.252632-252640, 2009. ,
DOI : 10.1093/bioinformatics/btp482
URL : https://hal.archives-ouvertes.fr/hal-00423755
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, vol.33, issue.12, pp.2577-637, 1983. ,
DOI : 10.1002/bip.360221211
IRIS : Internal Repeat Identification System, 2009. ,
Configurational entropy of native proteins, Biophysical Journal, vol.52, issue.6, pp.1083-1088, 1987. ,
DOI : 10.1016/S0006-3495(87)83303-9
When protein folding is simplified to protein coiling: the continuum of solenoid protein structures, Trends in Biochemical Sciences, vol.25, issue.10, pp.509-515, 2000. ,
DOI : 10.1016/S0968-0004(00)01667-4
Comprehensive Evaluation of Protein Structure Alignment Methods: Scoring by Geometric Measures, Journal of Molecular Biology, vol.346, issue.4, pp.1173-88, 2005. ,
DOI : 10.1016/j.jmb.2004.12.032
An improved branch and bound algorithm for the maximum clique problem, pp.569-590, 2007. ,
ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment, Bioinformatics, vol.26, issue.9, pp.1160-1168, 2010. ,
DOI : 10.1093/bioinformatics/btq100
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions, Acta Crystallographica Section D Biological Crystallography, vol.60, issue.12, pp.2256-2268, 2004. ,
DOI : 10.1107/S0907444904026460
On the relationship between sequence and structure similarities in proteomics, Bioinformatics, vol.23, issue.6, pp.717-740, 2007. ,
DOI : 10.1093/bioinformatics/btm006
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
PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids, Nucleic Acids Research, vol.33, issue.Database issue, pp.266-268, 2005. ,
DOI : 10.1093/nar/gki001
The protein threading problem with sequence amino acid interaction preferences is NP-complete, "Protein Engineering, Design and Selection", vol.7, issue.9, pp.1059-68, 1994. ,
DOI : 10.1093/protein/7.9.1059
Détection de novo de structures répétées au sein des protéines, JOBIM 2015 ,
Nature of the protein universe, Proceedings of the National Academy of Sciences of the United States of America, pp.11079-84, 2009. ,
DOI : 10.1073/pnas.0905029106
Circular permutations of natural protein sequences: structural evidence, Current Opinion in Structural Biology, vol.7, issue.3, pp.422-427, 1997. ,
DOI : 10.1016/S0959-440X(97)80061-9
SCOP database in 2002: refinements accommodate structural genomics, Nucleic Acids Research, vol.30, issue.1, pp.264-267, 2002. ,
DOI : 10.1093/nar/30.1.264
Using Dominances for Solving the Protein Family Identification Problem, pp.201-212, 2011. ,
DOI : 10.1093/nar/gki524
URL : https://hal.archives-ouvertes.fr/inria-00609432
CDD: a Conserved Domain Database for the functional annotation of proteins, Nucleic Acids Research, vol.39, issue.Database, pp.39-225, 2011. ,
DOI : 10.1093/nar/gkq1189
A census of protein repeats, Journal of Molecular Biology, vol.293, issue.1, pp.151-60, 1999. ,
DOI : 10.1006/jmbi.1999.3136
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
Methods, algorithms and tools in computational proteomics: A practical point of view, PROTEOMICS, vol.23, issue.16, pp.2815-2847, 2007. ,
DOI : 10.1002/pmic.200700116
MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C?? only models, Alternative alignments, and Non-sequential alignments, BMC Bioinformatics, vol.14, issue.1, p.24, 2013. ,
DOI : 10.1016/j.jmb.2005.12.084
Toward the detection and validation of repeats in protein structure, Proteins, vol.57, issue.2, pp.365-80, 2004. ,
New protein folds, Current Opinion in Structural Biology, vol.4, issue.3, pp.441-449, 1994. ,
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. ,
Cliquer User's Guide, Version 1.0, 2003. ,
hydrolase fold, "Protein Engineering, Design and Selection", vol.5, issue.3, pp.197-211, 1992. ,
DOI : 10.1093/protein/5.3.197
Classifying a Protein in the CATH Database of Domain Structures, Acta Crystallographica Section D Biological Crystallography, issue.6, pp.541155-1167, 1998. ,
Classifying a Protein in the CATH Database of Domain Structures, Acta Crystallographica Section D Biological Crystallography, vol.54, issue.6, pp.1155-1167, 1998. ,
DOI : 10.1107/S0907444998007501
CATH ??? a hierarchic classification of protein domain structures, Structure, vol.5, issue.8, pp.1093-1108, 1993. ,
DOI : 10.1016/S0969-2126(97)00260-8
The CATH Database provides insights into protein structure/function relationships, Nucleic Acids Research, vol.27, issue.1, pp.275-284, 1999. ,
DOI : 10.1093/nar/27.1.275
Protein families and their evolution-a structural perspective Annual review of biochemistry, pp.867-900, 2005. ,
MAMMOTH (Matching molecular models obtained from theory) : An automated method for model comparison, pp.2606-2621, 2002. ,
Fr-TM-align : a new protein structural alignment method based on fragment alignments and the TM-score, BMC bioinformatics, vol.9, p.531, 2008. ,
Detecting Repetitions and Periodicities in Proteins by Tiling the Structural Space, The Journal of Physical Chemistry B, vol.117, issue.42, pp.12887-97, 2013. ,
DOI : 10.1021/jp402105j
Christine Orengo. The CATH domain structure database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis, Nucleic Acids ResearchDATABASE ISS, vol.33, 2005. ,
Protein Structure and Function, 2004. ,
UCSF Chimera?a visualization system for exploratory research and analysis, Journal of computational chemistry, issue.13, pp.251605-251617, 2004. ,
CATHEDRAL : a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures, PLoS computational biology, vol.3, issue.11, p.232, 2007. ,
FlexSnap : Flexible nonsequential protein structure alignment, In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics, vol.5724, pp.273-285, 2009. ,
DOI : 10.1186/1748-7188-5-12
URL : http://doi.org/10.1186/1748-7188-5-12
FlexSnap : flexible nonsequential protein structure alignment. Algorithms for molecular biology, p.12, 2010. ,
Database of homology-derived protein structures and the structural meaning of sequence alignment, Proteins: Structure, Function, and Genetics, vol.4, issue.1, pp.56-68, 1991. ,
DOI : 10.1002/prot.340090107
Circular permuted proteins in the universe of protein folds, Proteins: Structure, Function, and Bioinformatics, vol.25, issue.Part 12, Part 1, pp.1618-1630, 2010. ,
DOI : 10.1002/prot.22678
A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology, Journal of Molecular Biology, vol.323, issue.2, pp.387-406, 2002. ,
DOI : 10.1016/S0022-2836(02)00811-2
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
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path, Protein Engineering Design and Selection, vol.11, issue.9, pp.739-786, 1998. ,
DOI : 10.1093/protein/11.9.739
Déjà vu all over again : finding and analyzing protein structure similarities, Structure, vol.12, issue.12, pp.2103-2114, 1993. ,
Detection of spatial correlations in protein structures and molecular complexes, Structure, vol.20, issue.4, pp.718-746, 1993. ,
Towards the development of standardized methods for comparison, ranking and evaluation of structure alignments, Bioinformatics, vol.29, issue.1, pp.47-53, 2013. ,
Combined use of sequence similarity and codon bias for coding region identification, Journal of computational biology : a journal of computational molecular cell biology, vol.1, issue.1, pp.39-50, 1994. ,
SANA: an algorithm for sequential and non-sequential protein structure alignment, Amino Acids, vol.19, issue.2, pp.417-442, 2010. ,
DOI : 10.1007/s00726-009-0457-y
Protein structure alignment beyond spatial proximity. Scientific reports, p.1448, 2013. ,
Evolution of Circular Permutations in Multidomain Proteins, Molecular Biology and Evolution, vol.23, issue.4, pp.734-777, 2006. ,
DOI : 10.1093/molbev/msj091
Exact Protein Structure Classification Using the Maximum Contact Map Overlap Metric, Algorithms for Computational Biology, pp.262-273, 2014. ,
DOI : 10.1007/978-3-319-07953-0_21
URL : https://hal.archives-ouvertes.fr/hal-01093776
CSA: comprehensive comparison of pairwise protein structure alignments, Nucleic Acids Research, vol.40, issue.W1, pp.303-312, 2012. ,
DOI : 10.1093/nar/gks362
URL : https://hal.archives-ouvertes.fr/hal-00667920
RESEARCH ARTICLES Protein Domain Movements : Detection of Rigid Domains and Visualization of Hinges in Comparisons of Atomic Coordinates, pp.1-14, 1996. ,
How significant is a protein structure similarity with TM-score = 0.5?, Bioinformatics, vol.26, issue.7, pp.889-95, 2010. ,
DOI : 10.1093/bioinformatics/btq066
Database searching by flexible protein structure alignment Protein science : a publication of the, pp.1841-1850, 2004. ,
FATCAT: a web server for flexible structure comparison and structure similarity searching, Nucleic Acids Research, vol.32, issue.Web Server, pp.582-587, 2004. ,
DOI : 10.1093/nar/gkh430
Histoire de la science des protéines, 2006. ,
Prediction of protein B-factor profiles, Proteins: Structure, Function, and Bioinformatics, vol.50, issue.4, pp.905-917, 2005. ,
DOI : 10.1002/prot.20375
STRALCP structure alignment-based clustering of proteins, Nucleic Acids Research, vol.35, issue.22, p.150, 2007. ,
DOI : 10.1093/nar/gkm1049
Scoring function for automated assessment of protein structure template quality, Proteins: Structure, Function, and Bioinformatics, vol.101, issue.4, pp.702-712, 2004. ,
DOI : 10.1002/prot.20264
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
Levinthal's paradox., Proceedings of the National Academy of Sciences, pp.20-22, 1992. ,
DOI : 10.1073/pnas.89.1.20
1 (Atome lourd) Dans le cas des protéines, atome lourd désigne tout atome (majoritairement C, N, O, S) qui ne soit pas un hydrogène (H) ,
2 (Electronegativité) Capacité d'un atome à attirer les électrons, plus un atome est électronégatif ,
3 (Polarité) Capacité à créer des liaisons électrostatiques avec des molécules d'eau (H 2 O) ,
Capacité d'un atome à repousser l'eau, un composé hydrophobe ne contient pas de groupe chargé ou d'atome capable de former des liaisons hydrogène ,
6 (Liaison ionique) Liaison entre deux atomes avec une trop forte différence d'électronégativité ,
Liaison Hydrogène) Attraction entre un atome d'hydrogène et un atome électronégatif. Lorsqu'un atome d'hydrogène déjà lié à un atome subit l'attraction d'un second atome électronégatif (souvent N ou O) ,
11 (Groupe hydroxyle) Atome d'hydrogène (H) lié à un atome d'oxygène (O) ,
Groupe carbonyle) Est caractérisé par une double liaison entre un atome d'oxygène (O) et de carbone, ce dernier étant autrement lié à des atomes de carbone (C) ou d'hydrogène (H) exclusivement ,
Groupe carboxyle) Atome d'oxygène (O) uni par une double liaison à un carbone (C) lié à un groupement hydroxyle. Le groupement carboxyle a également des propriétés d'acide car il a tendance à s'ioniser en perdant un proton (H + ) Ce groupement est un ,
14 (Groupe amine) Comprend un atome d'azote (N) lié ou non à un ou plusieurs atomes d'hydrogène (H) ,
15 (Groupe thiol) Atome de soufre (S) lié à une hydrogène et attaché à un radical ,
16 (Cycles aromatiques) Structure plane et stable, les atomes peuvent s'associer et former des cycles, partageant ainsi des électrons qui, délocalisés ,
17 (Groupement aliphatique) Du grec alipheir (graisse) : hydrocarbure non-aromatique. Pour les protéines, le groupement aliphatique est restreint aux portions de chaîne latérale hydrocarbures saturées ,
définitions générales Définition A.18 (Acide aminé) Acide carboxylique possédant entre autre un groupement amine ,
20 (Enzyme) Protéines qui catalyse (favorise) une ou plusieurs réactions chimiques ,