L. Pauling, R. B. Corey, and H. R. Branson, The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain, Proceedings of the National Academy of Sciences, vol.37, issue.4, pp.205-211, 1951.
DOI : 10.1073/pnas.37.4.205

L. Pauling and R. B. Corey, The Pleated Sheet, A New Layer Configuration of Polypeptide Chains, Proceedings of the National Academy of Sciences, vol.37, issue.5, pp.251-256, 1951.
DOI : 10.1073/pnas.37.5.251

D. Eisenberg, The discovery of the ??-helix and ??-sheet, the principal structural features of proteins, Proceedings of the National Academy of Sciences, vol.100, issue.20, pp.11207-11210, 2003.
DOI : 10.1073/pnas.2034522100

L. Fourrier, C. Benros, and A. G. De-brevern, Use of a structural alphabet for analysis of short loops connecting repetitive structures, BMC Bioinformatics, vol.5, issue.1, p.58, 2004.
DOI : 10.1186/1471-2105-5-58

URL : https://hal.archives-ouvertes.fr/inserm-00112104

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

M. N. Fodje and S. Karadaghi, Occurrence, conformational features and amino acid propensities for the ??-helix, Protein Engineering Design and Selection, vol.15, issue.5, pp.353-358, 2002.
DOI : 10.1093/protein/15.5.353

J. Martin, 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

M. Heinig and D. Frishman, 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

B. Offmann, M. Tyagi, and A. G. De-brevern, 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

D. P. Klose, B. A. Wallace, and R. W. Janes, 2Struc: the secondary structure server, Bioinformatics, vol.26, issue.20, pp.2624-2625, 2010.
DOI : 10.1093/bioinformatics/btq480

P. A. Calligari and G. R. Kneller, : combining localization and description of protein secondary structure, Acta Crystallographica Section D Biological Crystallography, vol.12, issue.12, pp.1690-169310, 2012.
DOI : 10.1107/S0907444912039029

M. Tyagi, A. Bornot, B. Offmann, and A. G. De-brevern, Analysis of loop boundaries using different local structure assignment methods, Protein Science, vol.34, issue.9, pp.1869-188110, 2009.
DOI : 10.1002/pro.198

URL : https://hal.archives-ouvertes.fr/inserm-00392504

E. Kruus, P. Thumfort, C. Tang, and N. S. Wingreen, Gibbs sampling and helix-cap motifs, Nucleic Acids Research, vol.33, issue.16, pp.5343-535333, 2005.
DOI : 10.1093/nar/gki842

R. Wintjens, S. J. Wodak, and M. Rooman, Typical interaction patterns in alphabeta and betaalpha turn motifs, Protein Engineering Design and Selection, vol.11, issue.7, pp.505-522, 1998.
DOI : 10.1093/protein/11.7.505

J. Wojcik, J. P. Mornon, and J. Chomilier, New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification, Journal of Molecular Biology, vol.289, issue.5, pp.1469-1490, 1999.
DOI : 10.1006/jmbi.1999.2826

N. S. Boutonnet, A. V. Kajava, and M. J. Rooman, Structural classification of ?????? and ?????? supersecondary structure units in proteins, Proteins: Structure, Function, and Genetics, vol.3, issue.2, pp.193-212, 1998.
DOI : 10.1002/(SICI)1097-0134(19980201)30:2<193::AID-PROT9>3.0.CO;2-O

J. Bonet, ArchDB 2014: structural classification of loops in proteins, Nucleic Acids Research, vol.42, issue.D1, pp.315-319, 2014.
DOI : 10.1093/nar/gkt1189

Y. Mansiaux, A. P. Joseph, J. C. Gelly, and A. G. De-brevern, Assignment of PolyProline II Conformation and Analysis of Sequence ??? Structure Relationship, PLoS ONE, vol.59, issue.3, 2011.
DOI : 10.1371/journal.pone.0018401.s008

URL : https://hal.archives-ouvertes.fr/inserm-00586725

L. Pauling and R. B. Corey, The Structure of Fibrous Proteins of the Collagen-Gelatin Group, Proceedings of the National Academy of Sciences, vol.37, issue.5, pp.272-281, 1951.
DOI : 10.1073/pnas.37.5.272

P. M. Cowan, S. Mcgavin, and A. C. North, The Polypeptide Chain Configuration of Collagen, Nature, vol.176, issue.4492, pp.1062-1064, 1955.
DOI : 10.1021/ja01650a082

A. A. Adzhubei and M. J. Sternberg, Left-handed Polyproline II Helices Commonly Occur in Globular Proteins, Journal of Molecular Biology, vol.229, issue.2, pp.472-493, 1993.
DOI : 10.1006/jmbi.1993.1047

T. P. Creamer, Left-handed polyproline II helix formation is (very) locally driven, Proteins: Structure, Function, and Genetics, vol.24, issue.2, pp.218-226, 1998.
DOI : 10.1002/(SICI)1097-0134(19981101)33:2<218::AID-PROT6>3.0.CO;2-E

B. J. Stapley and T. P. Creamer, A survey of left-handed polyproline II helices, Protein Science, vol.117, issue.3, pp.587-595, 1999.
DOI : 10.1110/ps.8.3.587

T. P. Creamer and M. N. Campbell, Determinants of the polyproline II helix from modeling studies, Adv Protein Chem, vol.62, pp.263-282, 2002.
DOI : 10.1016/S0065-3233(02)62010-8

A. A. Adzhubei, M. J. Sternberg, and A. A. Makarov, Polyproline-II Helix in Proteins: Structure and Function, Journal of Molecular Biology, vol.425, issue.12, pp.2100-2132, 2013.
DOI : 10.1016/j.jmb.2013.03.018

P. F. Fuchs and A. J. Alix, High accuracy prediction of ??-turns and their types using propensities and multiple alignments, Proteins: Structure, Function, and Bioinformatics, vol.55, issue.4, pp.828-839, 2005.
DOI : 10.1002/prot.20461

A. Bornot and A. G. De-brevern, Protein beta-turn assignments, Bioinformation, vol.1, issue.5, pp.153-155, 2006.
DOI : 10.6026/97320630001153

URL : https://hal.archives-ouvertes.fr/inserm-00133658

B. W. Matthews, The ?? Turn. Evidence for a New Folded Conformation in Proteins, Macromolecules, vol.5, issue.6, pp.818-819, 1972.
DOI : 10.1021/ma60030a031

E. J. Milner-white, Situations of gamma-turns in proteins. Their relation to alpha-helices, beta-sheets and ligand binding sites, J Mol Biol, vol.216, pp.386-397, 1990.

D. Nataraj, N. Srinivasan, R. Sowdhamini, and C. Ramakrishnan, Alpha-turns in pro tein structures, Curr. Sci, vol.69, pp.434-447, 1995.

V. Pavone, Discovering protein secondary structures: Classification and description of isolated ??-turns, Biopolymers, vol.221, issue.6, pp.705-721, 1996.
DOI : 10.1002/(SICI)1097-0282(199606)38:6<705::AID-BIP3>3.0.CO;2-V

B. Dasgupta and P. Chakrabarti, pi-Turns: types, systematics and the context of their occurrence in protein structures, BMC Structural Biology, vol.8, issue.1, pp.1472-6807, 2008.
DOI : 10.1186/1472-6807-8-39

K. R. Rajashankar and S. Ramakumar, ??-Turns in proteins and peptides: Classification, conformation, occurrence, hydration and sequence, Protein Science, vol.4, issue.5, pp.932-946, 1996.
DOI : 10.1002/pro.5560050515

J. S. Richardson, The Anatomy and Taxonomy of Protein Structure, Adv Protein Chem, vol.34, pp.167-339, 1981.
DOI : 10.1016/S0065-3233(08)60520-3

C. M. Venkatachalam, Stereochemical criteria for polypeptides and proteins. V. Conformation of a system of three linked peptide units, Biopolymers, vol.1, issue.10, pp.1425-1436, 1968.
DOI : 10.1002/bip.1968.360061006

J. L. Crawford, W. N. Lipscomb, and C. G. Schellman, The Reverse Turn as a Polypeptide Conformation in Globular Proteins, Proceedings of the National Academy of Sciences, vol.70, issue.2, pp.538-542, 1973.
DOI : 10.1073/pnas.70.2.538

P. N. Lewis, F. A. Momany, and H. A. Scheraga, Chain reversals in proteins, Biochimica et Biophysica Acta (BBA) - Protein Structure, vol.303, issue.2, pp.211-229, 1973.
DOI : 10.1016/0005-2795(73)90350-4

E. G. Hutchinson and J. M. Thornton, A revised set of potentials for ??-turn formation in proteins, Protein Science, vol.3, issue.12, pp.2207-2216, 1994.
DOI : 10.1002/pro.5560031206

C. M. Wilmot and J. M. Thornton, Analysis and prediction of the different types of ??-turn in proteins, Journal of Molecular Biology, vol.203, issue.1, pp.221-232, 1988.
DOI : 10.1016/0022-2836(88)90103-9

A. W. Chan, E. G. Hutchinson, D. Harris, and J. M. Thornton, Identification, classification, and analysis of beta-bulges in proteins, Protein Science, vol.170, issue.10, pp.1574-1590, 1993.
DOI : 10.1002/pro.5560021004

D. V. Nataraj, N. Srinivasan, R. Sowdhamini, and C. Ramakrishnan, ? -turns in protein structures, Curr. Sci, vol.69, pp.434-447, 1995.

E. G. Hutchinson and J. M. Thornton, PROMOTIF-A program to identify and analyze structural motifs in proteins, Protein Science, vol.3, issue.2, pp.212-220, 1996.
DOI : 10.1002/pro.5560050204

A. V. Efimov, Standard conformations of a polypeptide chain in irregular protein regions], Mol Biol (Mosk), vol.20, pp.250-260, 1986.

A. Efimov, Standard structures in proteins, Progress in Biophysics and Molecular Biology, vol.60, issue.3, pp.201-239, 1993.
DOI : 10.1016/0079-6107(93)90015-C

A. Efimov, Super-secondary structures involving triple-strand ??-sheets, FEBS Letters, vol.211, issue.3, pp.253-256, 1993.
DOI : 10.1016/0014-5793(93)80688-Q

A. V. Efimov, Super-secondary Structures and Modeling of Protein Folds, Methods Mol Biol, vol.932, pp.177-189, 2013.
DOI : 10.1007/978-1-62703-065-6_11

A. Efimov, Structural trees for protein superfamilies, Proteins: Structure, Function, and Genetics, vol.3, issue.2, pp.241-260, 1997.
DOI : 10.1002/(SICI)1097-0134(199706)28:2<241::AID-PROT12>3.0.CO;2-I

A. Efimov, A structural tree for proteins containing 3??-corners, FEBS Letters, vol.247, issue.1, pp.37-41, 1997.
DOI : 10.1016/S0014-5793(97)00296-2

A. B. Gordeev, A. M. Kargatov, A. V. Efimov, and . Pcbost, PCBOST: Protein classification based on structural trees, Biochemical and Biophysical Research Communications, vol.397, issue.3, pp.470-471, 2010.
DOI : 10.1016/j.bbrc.2010.05.136

C. M. Wilmot and J. M. Thornton, -Turns and their distortions: a proposed new nomenclature, "Protein Engineering, Design and Selection", vol.3, issue.6, pp.479-493, 1990.
DOI : 10.1093/protein/3.6.479

URL : https://hal.archives-ouvertes.fr/hal-01209979

O. Koch and G. Klebe, Turns revisited: A uniform and comprehensive classification of normal, open, and reverse turn families minimizing unassigned random chain portions, Proteins: Structure, Function, and Bioinformatics, vol.74, issue.Part 5, pp.353-36710, 2009.
DOI : 10.1002/prot.22185

T. Kohonen, Self-organized formation of topologically correct feature maps, Biological Cybernetics, vol.13, issue.1, pp.59-69, 1982.
DOI : 10.1007/BF00337288

T. Kohonen, Self-Organizing Maps, 2001.

O. Koch, J. Cole, P. Block, and G. Klebe, Secbase: Database Module To Retrieve Secondary Structure Elements with Ligand Binding Motifs, Journal of Chemical Information and Modeling, vol.49, issue.10, pp.2388-240210, 2009.
DOI : 10.1021/ci900202d

M. Meissner, O. Koch, G. Klebe, and G. Schneider, Prediction of turn types in protein structure by machine-learning classifiers, Proteins: Structure, Function, and Bioinformatics, vol.8, issue.2, pp.344-35210, 2009.
DOI : 10.1002/prot.22164

N. C. Fitzkee, P. J. Fleming, and G. Rose, The Protein Coil Library: A structural database of nonhelix, nonstrand fragments derived from the PDB, Proteins: Structure, Function, and Bioinformatics, vol.326, issue.Pt 5, pp.852-854, 2005.
DOI : 10.1002/prot.20394

L. L. Perskie and G. Rose, Physical-chemical determinants of coil conformations in globular proteins, Protein Science, vol.326, issue.Suppl 8, pp.1127-1136399, 2010.
DOI : 10.1002/pro.399

L. L. Porter and G. D. Rose, Redrawing the Ramachandran plot after inclusion of hydrogen-bonding constraints, Proceedings of the National Academy of Sciences, vol.108, issue.1, pp.109-1131014674107, 2011.
DOI : 10.1073/pnas.1014674107

G. Wang, R. L. Dunbrack, and . Jr, PISCES: a protein sequence culling server, Bioinformatics, vol.19, issue.12, pp.1589-1591, 2003.
DOI : 10.1093/bioinformatics/btg224

M. Tyagi, A. Bornot, B. Offmann, and A. G. De-brevern, Protein short loop prediction in terms of a structural alphabet, Computational Biology and Chemistry, vol.33, issue.4, pp.329-333, 2009.
DOI : 10.1016/j.compbiolchem.2009.06.002

URL : https://hal.archives-ouvertes.fr/inserm-00396485

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

A. P. Joseph, 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

L. R. Rabiner, A tutorial on hidden Markov models and selected application in speech recognition, Proceedings of the IEEE, pp.257-286, 1989.

M. Tyagi, Protein Block Expert (PBE): a web-based protein structure analysis server using a structural alphabet, Nucleic Acids Research, vol.34, issue.Web Server, pp.119-123, 2006.
DOI : 10.1093/nar/gkl199

URL : https://hal.archives-ouvertes.fr/inserm-00133751

P. Poulain, PBxplore: A program to explore protein structures with Protein Blocks Available at: https://github, PBxplore, pp.21-67, 2016.

J. Schuchhardt, G. Schneider, J. Reichelt, D. Schomburg, and P. Wrede, Local structural motifs of protein backbones are classified by self-organizing neural networks, "Protein Engineering, Design and Selection", vol.9, issue.10, pp.833-842, 1996.
DOI : 10.1093/protein/9.10.833

A. G. De-brevern and S. Hazout, 'Hybrid Protein Model' for optimally defining 3D protein structure fragments, Bioinformatics, vol.19, issue.3, pp.345-353, 2003.
DOI : 10.1093/bioinformatics/btf859

URL : https://hal.archives-ouvertes.fr/inserm-00133632

J. Esque, A. Urbain, C. Etchebest, and A. G. De-brevern, Sequence???structure relationship study in all-?? transmembrane proteins using an unsupervised learning approach, Amino Acids, vol.33, issue.7, pp.2303-2322, 2015.
DOI : 10.1007/s00726-015-2010-5

R. Ihaka and R. Gentleman, R: A Language for Data Analysis and Graphics, Journal of Computational and Graphical Statistics, vol.5, pp.299-314, 1996.

G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, Stereochemistry of polypeptide chain configurations, Journal of Molecular Biology, vol.7, issue.1, pp.95-99, 1963.
DOI : 10.1016/S0022-2836(63)80023-6

C. Ramakrishnan and G. N. Ramachandran, Stereochemical Criteria for Polypeptide and Protein Chain Conformations, Biophysical Journal, vol.5, issue.6, pp.909-933, 1965.
DOI : 10.1016/S0006-3495(65)86759-5

C. Micheletti, F. Seno, and A. Maritan, Recurrent oligomers in proteins: An optimal scheme reconciling accurate and concise backbone representations in automated folding and design studies, Proteins: Structure, Function, and Genetics, vol.105, issue.4, pp.662-674, 2000.
DOI : 10.1002/1097-0134(20000901)40:4<662::AID-PROT90>3.0.CO;2-F

P. Y. Chou and G. Fasman, Prediction of beta-turns, Biophysical Journal, vol.26, issue.3, pp.367-383, 1979.
DOI : 10.1016/S0006-3495(79)85259-5

H. Singh, S. Singh, and G. P. Raghava, platform for predicting and initiating ??-turns in a protein at desired locations, Proteins: Structure, Function, and Bioinformatics, vol.21, issue.5, pp.910-92110, 2015.
DOI : 10.1002/prot.24783

J. Sammon, A Nonlinear Mapping for Data Structure Analysis, IEEE Transactions on Computers, vol.18, issue.5, pp.401-409, 1969.
DOI : 10.1109/T-C.1969.222678

K. Guruprasad and S. Rajkumar, Beta-and gamma-turns in proteins revisited: a new set of amino acid turntype dependent positional preferences and potentials, J Biosci, vol.25, pp.143-156, 2000.

A. V. Efimov, Standard structures in protein molecules. II. Beta-alpha hairpins], Mol Biol (Mosk), vol.20, pp.340-345, 1986.

N. V. Kalmankar, C. Ramakrishnan, and P. Balaram, Sparsely populated residue conformations in protein structures: Revisiting ???experimental??? Ramachandran maps, Proteins: Structure, Function, and Bioinformatics, vol.132, issue.7, pp.1101-111224384, 2014.
DOI : 10.1002/prot.24384

P. F. Fuchs, Kinetics and Thermodynamics of Type VIII ??-Turn Formation: A CD, NMR, and Microsecond Explicit Molecular Dynamics Study of the GDNP Tetrapeptide, Biophysical Journal, vol.90, issue.8, pp.2745-2759, 2006.
DOI : 10.1529/biophysj.105.074401

N. Srinivasan, V. S. Anuradha, C. Ramakrishnan, R. Sowdhamini, and P. Balaram, Conformational characteristics of asparaginyl residues in proteins, International Journal of Peptide and Protein Research, vol.7, issue.2, pp.112-122, 1994.
DOI : 10.1111/j.1399-3011.1994.tb00565.x

K. Guruprasad, M. S. Prasad, and G. Kumar, Analysis of gammabeta, betagamma, gammagamma, betabeta continuous turns in proteins, Journal of Peptide Research, vol.241, issue.4, pp.292-300, 2001.
DOI : 10.1093/bioinformatics/16.4.372

K. Guruprasad, M. S. Prasad, and G. Kumar, Analysis of gammabeta, betagamma, gammagamma, betabeta multiple turns in proteins, Journal of Peptide Research, vol.16, issue.4, pp.250-263, 2000.
DOI : 10.1107/S0907444998009378

K. Guruprasad, M. J. Rao, S. Adindla, and L. Guruprasad, Combinations of turns in proteins, Journal of Peptide Research, vol.62, issue.4, pp.167-174, 2003.
DOI : 10.1034/j.1399-3011.2003.00086.x

D. De-sanctis, Bishistidyl Heme Hexacoordination, a Key Structural Property in Drosophila melanogaster Hemoglobin, Journal of Biological Chemistry, vol.280, issue.29, pp.27222-27229, 2005.
DOI : 10.1074/jbc.M503814200

A. Becker and W. Kabsch, X-ray Structure of Pyruvate Formate-Lyase in Complex with Pyruvate and CoA: HOW THE ENZYME USES THE CYS-418 THIYL RADICAL FOR PYRUVATE CLEAVAGE, Journal of Biological Chemistry, vol.277, issue.42, pp.40036-40042, 2002.
DOI : 10.1074/jbc.M205821200

H. Dobbek, V. Svetlitchnyi, J. Liss, and O. Meyer, Carbon Monoxide Induced Decomposition of the Active Site [Ni???4Fe???5S] Cluster of CO Dehydrogenase, Journal of the American Chemical Society, vol.126, issue.17, pp.5382-538710, 2004.
DOI : 10.1021/ja037776v

C. W. Levy, Insights into Enzyme Evolution Revealed by the Structure of Methylaspartate Ammonia Lyase, Structure, vol.10, issue.1, pp.105-113, 2002.
DOI : 10.1016/S0969-2126(01)00696-7

W. P. Burmeister, D. Guilligay, S. Cusack, G. Wadell, and N. Arnberg, Crystal Structure of Species D Adenovirus Fiber Knobs and Their Sialic Acid Binding Sites, Journal of Virology, vol.78, issue.14, pp.7727-77367727, 2004.
DOI : 10.1128/JVI.78.14.7727-7736.2004

W. Grabarse, On the mechanism of biological methane formation: structural evidence for conformational changes in methyl-coenzyme M reductase upon substrate binding, Journal of Molecular Biology, vol.309, issue.1, pp.315-3304647, 2001.
DOI : 10.1006/jmbi.2001.4647

T. Hisano, Crystal Structure of the (R)-Specific Enoyl-CoA Hydratase from Aeromonas caviae Involved in Polyhydroxyalkanoate Biosynthesis, Journal of Biological Chemistry, vol.278, issue.1, pp.617-62410, 2003.
DOI : 10.1074/jbc.M205484200

Y. Zuo, Y. Wang, and A. Malhotra, Crystal Structure of Escherichia coli RNase D, an Exoribonuclease Involved in Structured RNA Processing, Structure, vol.13, issue.7, pp.973-984015, 2005.
DOI : 10.1016/j.str.2005.04.015

B. Y. Kwak, Structure and Mechanism of CTP:Phosphocholine Cytidylyltransferase (LicC) from Streptococcus pneumoniae, Journal of Biological Chemistry, vol.277, issue.6, pp.4343-4350, 2002.
DOI : 10.1074/jbc.M109163200

K. Schafer, X-ray Structures of the Maltose???Maltodextrin-binding Protein of the Thermoacidophilic Bacterium Alicyclobacillus acidocaldarius Provide Insight into Acid Stability of Proteins, Journal of Molecular Biology, vol.335, issue.1, pp.261-274, 2004.
DOI : 10.1016/j.jmb.2003.10.042

I. Hayashi and M. Ikura, Crystal Structure of the Amino-terminal Microtubule-binding Domain of End-binding Protein 1 (EB1), Journal of Biological Chemistry, vol.278, issue.38, pp.36430-3643410, 2003.
DOI : 10.1074/jbc.M305773200

E. L. Wise, D. E. Graham, R. H. White, and I. Rayment, The Structural Determination of Phosphosulfolactate Synthase from Methanococcus jannaschii at 1.7-A Resolution: AN ENOLASE THAT IS NOT AN ENOLASE, Journal of Biological Chemistry, vol.278, issue.46, pp.45858-4586310, 2003.
DOI : 10.1074/jbc.M307486200