J. C. Kendrew, G. Bodo, H. M. Dintzis, R. G. Parrish, H. Wyckoff et al., A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis, Nature, vol.178, issue.4610, pp.662-666, 1958.
DOI : 10.1002/hlca.19490320118

L. Pauling and R. B. Corey, Atomic Coordinates and Structure Factors for Two Helical Configurations of Polypeptide Chains, Proceedings of the National Academy of Sciences, vol.37, issue.5, pp.235-240, 1951.
DOI : 10.1073/pnas.37.5.235

D. Eisenberg, The discovery of the ??-helix and ??-sheet, the principal structural features of proteins, Proceedings of the National Academy of Sciences, vol.47, issue.4, pp.11207-11210, 2003.
DOI : 10.1016/S0022-2836(63)80023-6

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

L. Pauling and R. B. Corey, TWO HYDROGEN-BONDED SPIRAL CONFIGURATIONS OF THE POLYPEPTIDE CHAIN, Journal of the American Chemical Society, vol.72, issue.11, p.53, 1950.
DOI : 10.1021/ja01167a545

B. K. Ho, A. Thomas, and R. Brasseur, Revisiting the Ramachandran plot: Hard-sphere repulsion, electrostatics, and H-bonding in the ??-helix, Protein Science, vol.285, issue.11, pp.2508-2522, 2003.
DOI : 10.1110/ps.03235203

N. Colloc-'h and F. E. Cohen, ??-Breakers: An aperiodic secondary structure, Journal of Molecular Biology, vol.221, issue.2, pp.603-613, 1991.
DOI : 10.1016/0022-2836(91)80075-6

L. Regan, Protein Structure: Born to be beta, Current Biology, vol.4, issue.7, pp.656-658, 1994.
DOI : 10.1016/S0960-9822(00)00147-0

J. S. Richardson and D. C. Richardson, Natural ??-sheet proteins use negative design to avoid edge-to-edge aggregation, Proceedings of the National Academy of Sciences, vol.268, issue.4, pp.2754-2759, 2002.
DOI : 10.1006/jmbi.1994.1691

J. S. Richardson, Handedness of crossover connections in beta sheets., Proceedings of the National Academy of Sciences, vol.73, issue.8, pp.2619-2623, 1976.
DOI : 10.1073/pnas.73.8.2619

C. Chotia, M. Levitt, and D. Richardson, Structure of proteins: packing of alpha-helices and pleated sheets., Proceedings of the National Academy of Sciences, vol.74, issue.10, pp.4130-4134, 1977.
DOI : 10.1073/pnas.74.10.4130

C. Chotia, M. Levitt, and D. Richardson, Helix to helix packing in proteins, Journal of Molecular Biology, vol.145, issue.1, pp.215-250, 1981.
DOI : 10.1016/0022-2836(81)90341-7

A. V. Efimov, Structure of coiled ??-??-hairpins and ??-??-corners, FEBS Letters, vol.224, issue.2, pp.288-292, 1991.
DOI : 10.1016/0014-5793(91)80706-9

R. Aurora, R. Srinivasan, and G. D. Rose, Rules for alpha-helix termination by glycine, Science, vol.264, issue.5162, pp.1126-1130, 1994.
DOI : 10.1126/science.8178170

E. Hutchinson, T. Sessions, . Woolfson, and . Dn, Determinants of strand register in antiparallel ??-sheets of proteins, Protein Science, vol.22, issue.11, pp.2287-2300, 1998.
DOI : 10.1002/pro.5560071106

R. Aurora and G. D. Rose, Helix capping, Protein Science, vol.31, issue.1, pp.21-38, 1998.
DOI : 10.1002/pro.5560070103

W. M. Liu and K. Chou, Singular points of protein ??-sheets, Protein Science, vol.3, issue.11, pp.2324-2330, 1998.
DOI : 10.1002/pro.5560071109

J. Donohue, Hydrogen Bonded Helical Configurations of the Polypeptide Chain, Proceedings of the National Academy of Sciences, vol.39, issue.6, pp.470-478, 1953.
DOI : 10.1073/pnas.39.6.470

L. Pal and G. Basu, Novel protein structural motifs containing two-turn and longer 310-helices, Protein Engineering Design and Selection, vol.12, issue.10, pp.811-814, 1999.
DOI : 10.1093/protein/12.10.811

L. Pal, .. G. Basu, and P. Chakrabarti, Variants of 310-helices in proteins, Proteins: Structure, Function, and Genetics, vol.32, issue.3, pp.571-579, 2002.
DOI : 10.1002/prot.10184

B. W. Low and R. B. Baybutt, THE ?? HELIX???A HYDROGEN BONDED CONFIGURATION OF THE POLYPEPTIDE CHAIN, Journal of the American Chemical Society, vol.74, issue.22, p.5806, 1952.
DOI : 10.1021/ja01142a539

B. W. Low and H. J. Greenville-wells, Generalized Mathematical Relationships for Polypeptide Chain Helices: The Coordinates of the II Helix, Proceedings of the National Academy of Sciences, vol.39, issue.8, pp.785-801, 1953.
DOI : 10.1073/pnas.39.8.785

T. M. Weaver, The ??-helix translates structure into function, Protein Science, vol.21, issue.1, pp.201-206, 2000.
DOI : 10.1110/ps.9.1.201

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

R. Sudha, M. Kohtani, G. A. Breaux, and M. F. Jarrold, ??-Helix Preference in Unsolvated Peptides, Journal of the American Chemical Society, vol.126, issue.9, pp.2777-2784, 2004.
DOI : 10.1021/ja0381353

R. Armen, D. O. Alonso, and V. Daggett, -, and ??-helix in helix???coil transitions, Protein Science, vol.31, issue.102, pp.1145-1157, 2003.
DOI : 10.1110/ps.0240103

J. P. Cartailler and H. Luecke, Structural and Functional Characterization of ?? Bulges and Other Short Intrahelical Deformations, Structure, vol.12, issue.1, pp.133-144, 2004.
DOI : 10.1016/j.str.2003.12.001

L. Pauling and R. B. Corey, The Structure of Fibrous Proteins of the Collagen- HAL author manuscript inserm-00134564, 1951.

P. M. Cowan and S. Mcgavin, Structure of Poly-L-Proline, Nature, vol.7, issue.4480, pp.501-503, 1955.
DOI : 10.1021/ja01176a005

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

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, 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

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

N. Eswar, C. Ramakrishnan, and N. Srinivasan, Stranded in isolation: structural role of isolated extended strands in proteins, Protein Engineering Design and Selection, vol.16, issue.5, pp.331-339, 2003.
DOI : 10.1093/protein/gzg046

R. Sowdhamini, N. Srinivasan, C. Ramakrishnan, and P. Balaram, Orthogonal ???? motifs in proteins, Journal of Molecular Biology, vol.223, issue.4, pp.845-851, 1992.
DOI : 10.1016/0022-2836(92)90246-G

J. S. Richardson, E. D. Getzoff, and D. C. Richardson, The beta bulge: a common small unit of nonrepetitive protein structure., Proceedings of the National Academy of Sciences, vol.75, issue.6, pp.2574-2578, 1978.
DOI : 10.1073/pnas.75.6.2574

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. D. Axe, N. W. Foster, and A. R. Fersht, An irregular beta-bulge common to a group of bacterial RNases is an important determinant of stability and function, 1999.

G. N. Ramachandran and V. Sasisekharan, Conformation of Polypeptides and Proteins, Protein Chem, vol.23, p.283, 1968.
DOI : 10.1016/S0065-3233(08)60402-7

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

URL : http://deepblue.lib.umich.edu/bitstream/2027.42/33067/1/0000453.pdf

J. S. Richardson, E. D. Getzoff, and D. C. Richardson, The beta bulge: a common small unit of nonrepetitive protein structure., Proceedings of the National Academy of Sciences, vol.75, issue.6, pp.2574-2578, 1978.
DOI : 10.1073/pnas.75.6.2574

G. Némethy and M. P. Printz, The ?? Turn, a Possible Folded Conformation of the Polypeptide Chain. Comparison with the ?? Turn, Macromolecules, vol.5, issue.6, pp.755-758, 1972.
DOI : 10.1021/ma60030a017

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, Recurring loop motif in proteins that occurs in right-handed and left-handed forms, Journal of Molecular Biology, vol.199, issue.3, pp.503-511, 1988.
DOI : 10.1016/0022-2836(88)90621-3

G. D. Rose, L. M. Gierasch, and J. A. Smith, Turns in Peptides and Proteins, Adv. Prot. Chem, vol.37, pp.1-109, 1985.
DOI : 10.1016/S0065-3233(08)60063-7

P. N. Lewis, F. A. Momany, and H. A. Scheraga, Folding of Polypeptide Chains in Proteins: A Proposed Mechanism for Folding, Proceedings of the National Academy of Sciences, vol.68, issue.9, pp.2293-2297, 1971.
DOI : 10.1073/pnas.68.9.2293

I. D. Kuntz, Protein folding, Journal of the American Chemical Society, vol.94, issue.11, pp.4009-4012, 1972.
DOI : 10.1021/ja00766a060

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

P. Y. Chou and G. D. Fasman, ??-turns in proteins, Journal of Molecular Biology, vol.115, issue.2, pp.135-175, 1977.
DOI : 10.1016/0022-2836(77)90094-8

G. D. Rose and J. P. Seltzer, A new algorithm for finding the peptide chain turns in a globular protein, Journal of Molecular Biology, vol.113, issue.1, pp.153-164, 1977.
DOI : 10.1016/0022-2836(77)90046-8

G. D. Rose and D. B. Wetlaufer, The number of turns in globular proteins, Nature, vol.155, issue.5622, pp.769-770, 1977.
DOI : 10.1038/260729a0

S. S. Zimmermann and H. A. Scheraga, Influence of local interactions on protein structure. I. Conformational energy studies ofN-acetyl-N?-methylamides of pro-X and X-pro dipeptides, Biopolymers, vol.97, issue.4, pp.811-843, 1977.
DOI : 10.1002/bip.1977.360160408

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. Wilmot and J. M. Thornton, Analysis and prediction of the different types of ?turn in proteins, J Mol Biol, vol.5, pp.221-232, 1988.

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

S. G. Ball and . Hughes, ??-turn topography, Tetrahedron, vol.49, issue.17, pp.3467-3478
DOI : 10.1016/S0040-4020(01)90207-8

X. Ashish, A. Grover, and R. Kishore, Characterization of a novel type VII ??-turn conformation for a bio-active tetrapeptide rigin, European Journal of Biochemistry, vol.44, issue.5, pp.1455-1463, 2000.
DOI : 10.1046/j.1432-1327.2000.01144.x

K. C. Chou, Prediction of Tight Turns and Their Types in Proteins, Analytical Biochemistry, vol.286, issue.1, pp.1-16, 2000.
DOI : 10.1006/abio.2000.4757

V. Pavone, G. Gaeta, A. Lombardi, F. Nastri, O. Maglio et al., 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

H. Kaur and G. P. Raghava, Prediction of ??-turns in proteins using PSI-BLAST profiles and secondary structure information, Proteins: Structure, Function, and Bioinformatics, vol.114, issue.1, pp.83-90, 2004.
DOI : 10.1002/prot.10569

E. J. Milner-white, B. M. Ross, R. Ismail, K. Belhadj-mostefa, and R. Poet, One type of gamma-turn, rather than the other gives rise to chain-reversal in proteins, Journal of Molecular Biology, vol.204, issue.3, pp.777-782, 1988.
DOI : 10.1016/0022-2836(88)90368-3

K. R. Rajashankar and S. Ramakumar, ?-turns in proteins and peptides: HAL author manuscript inserm-00134564, 1996.

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

K. Guruprasad, M. S. Prasad, and G. R. 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

J. F. Leszczynski and G. D. Rose, Loops in globular proteins: a novel category of secondary structure, Science, vol.234, issue.4778, pp.849-855, 1986.
DOI : 10.1126/science.3775366

J. S. Fetrow, Omega loops: nonregular secondary structures significant in protein function and stability, FASEB J, vol.9, pp.708-717, 1995.

M. Pal and S. Dasgupta, The nature of the turn in omega loops of proteins, Proteins: Structure, Function, and Bioinformatics, vol.99, issue.4, pp.606-616, 2003.
DOI : 10.1002/prot.10376

J. S. Fetrow, T. S. Cardillo, and F. Sherman, Deletions and replacements of omega loops in yeast iso-1-cytochromec, Proteins: Structure, Function, and Genetics, vol.237, issue.4, pp.372-381, 1989.
DOI : 10.1002/prot.340060404

M. M. Krishna, Y. Lin, J. N. Rumbley, and S. W. Englander, Cooperative Omega Loops in Cytochrome c: Role in Folding and Function, Journal of Molecular Biology, vol.331, issue.1, pp.29-36, 2003.
DOI : 10.1016/S0022-2836(03)00697-1

B. L. Sibanda and J. M. Thornton, ??-Hairpin families in globular proteins, Nature, vol.19, issue.6024, pp.170-174, 1985.
DOI : 10.1038/316170a0

E. J. Milner-white and R. Poet, -hairpins in proteins, Biochemical Journal, vol.240, issue.1, pp.289-292, 1986.
DOI : 10.1042/bj2400289

URL : https://hal.archives-ouvertes.fr/hal-01299213

B. L. Sibanda, T. L. Blundell, and J. M. Thornton, Conformation of beta-hairpins in HAL author manuscript inserm-00134564, 1989.

B. L. Sibanda and J. M. Thornton, [5] Conformation of ?? hairpins in protein structures: Classification and diversity in homologous structures, Methods Enzymol, vol.202, pp.59-82, 1991.
DOI : 10.1016/0076-6879(91)02007-V

B. L. Sibanda and J. M. Thornton, Accommodating Sequence Changes in ??-Hairpins in Proteins, Journal of Molecular Biology, vol.229, issue.2, pp.428-447, 1993.
DOI : 10.1006/jmbi.1993.1044

K. Gunasekaran, C. Ramakrishan, and P. Balaram, Beta-hairpins in proteins revisited: lessons for de novo design, Protein Engineering Design and Selection, vol.10, issue.10, pp.1131-1141, 1997.
DOI : 10.1093/protein/10.10.1131

T. Blandl, A. G. Cochran, and N. J. Skelton, Turn stability in ??-hairpin peptides: Investigation of peptides containing 3:5 type I G1 bulge turns, Protein Science, vol.3, issue.2, pp.237-247, 2003.
DOI : 10.1110/ps.0228603

J. Kim, S. R. Brych, J. Lee, T. M. Logan, and M. Blaber, Identification of a Key Structural Element for Protein Folding Within ??-Hairpin Turns, Journal of Molecular Biology, vol.328, issue.4, pp.951-961, 2003.
DOI : 10.1016/S0022-2836(03)00321-8

A. V. Efimov, A novel super-secondary structure of proteins and the relation between the structure and the amino acid sequence, FEBS Letters, vol.10, issue.1, pp.33-38, 1984.
DOI : 10.1016/0014-5793(84)80039-3

P. A. Rice, A. Goldman, and T. A. Steitz, A helix-turn-strand structural motif common in ??-?? proteins, Proteins: Structure, Function, and Genetics, vol.85, issue.4, pp.334-340, 1990.
DOI : 10.1002/prot.340080407

J. Tang, M. N. James, I. N. Hsu, J. A. Jenkins, and T. L. Blundell, Structural evidence for gene duplication in the evolution of the acid proteases, Nature, vol.248, issue.5646, pp.618-622, 1978.
DOI : 10.1038/267808a0

R. T. Wintjens, M. J. Rooman, and S. J. Wodak, Automatic Classification and Analysis of ????-Turn Motifs in Proteins, Journal of Molecular Biology, vol.255, issue.1, pp.235-253, 1996.
DOI : 10.1006/jmbi.1996.0020

R. T. Wintjens, M. J. Rooman, . Wodak, and . Sj, 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

N. S. Boutonnet, A. V. Kajava, and M. J. Rooman, Structural classification of HAL author manuscript inserm-00134564, 1998.

J. Kwasigroch, J. Chomilier, and J. Mornon, A Global Taxonomy of Loops in Globular Proteins, Journal of Molecular Biology, vol.259, issue.4, pp.855-872, 1996.
DOI : 10.1006/jmbi.1996.0363

V. Geetha and P. J. Munson, Linkers of secondary structures in proteins, Protein Science, vol.44, issue.12, pp.2538-2547, 1997.
DOI : 10.1002/pro.5560061206

A. Tramontano, C. Chothia, and A. M. Lesk, Structural determinants of the conformations of medium-sized loops in proteins, Proteins: Structure, Function, and Genetics, vol.14, issue.4, pp.382-394, 1989.
DOI : 10.1002/prot.340060405

L. E. Donate, S. D. Rufino, L. H. Canard, and T. L. Blundell, Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: A database for modeling and prediction, Protein Science, vol.6, issue.12, pp.2600-2616, 1996.
DOI : 10.1002/pro.5560051223

W. Li, Z. Liu, and L. Lai, Protein loops on structurally similar scaffolds: Database and conformational analysis, Biopolymers, vol.229, issue.6, pp.481-495, 1999.
DOI : 10.1002/(SICI)1097-0282(199905)49:6<481::AID-BIP6>3.0.CO;2-V

C. S. Ring, D. G. Kneller, R. Langridge, and F. E. Cohen, Taxonomy and conformational analysis of loops in proteins, Journal of Molecular Biology, vol.224, issue.3, pp.685-699, 1992.
DOI : 10.1016/0022-2836(92)90553-V

T. Fechteler, U. Dengler, and D. Schomburg, Prediction of protein threedimensional structures in insertion and deletion regions: a procedure for searching data bases of representative protein fragments using geometric scoring criteria, J Mol Biol, vol.267, pp.114-131, 1995.

S. D. Rufino, L. E. Donate, L. H. Canard, and T. L. Blundell, Predicting the conformational class of short and medium size loops connecting regular secondary structures: application to comparative modelling, Journal of Molecular Biology, vol.267, issue.2, pp.352-367, 1997.
DOI : 10.1006/jmbi.1996.0851

H. W. Vlijmen and M. Karplus, PDB-based protein loop prediction: parameters for selection and methods for optimization, Journal of Molecular Biology, vol.267, issue.4, pp.975-1001, 1997.
DOI : 10.1006/jmbi.1996.0857

J. Wojick, J. Mornon, and J. Chomilier, New efficient statistical sequence- HAL author manuscript inserm-00134564, 1999.

A. Fiser, R. K. Do, and A. Sali, Modeling of loops in protein structures, Protein Science, vol.14, issue.9, pp.1753-1773, 2000.
DOI : 10.1110/ps.9.9.1753

K. Fidelis, P. S. Stern, D. Bacon, and J. Moult, Comparison of systematic search and database methods for constructing segments of protein structure, "Protein Engineering, Design and Selection", vol.7, issue.8, pp.953-960, 1994.
DOI : 10.1093/protein/7.8.953

B. Oliva, P. A. Bates, E. Querol, F. X. Aviles, and M. J. Sternberg, An automated classification of the structure of protein loops, Journal of Molecular Biology, vol.266, issue.4, pp.814-830, 1997.
DOI : 10.1006/jmbi.1996.0819

E. Michalsky, A. Goede, and R. Preissner, Loops In Proteins (LIP)--a comprehensive loop database for homology modelling, Protein Engineering Design and Selection, vol.16, issue.12, pp.979-985, 2003.
DOI : 10.1093/protein/gzg119

M. Bansal, S. Kumar, and R. Velavan, HELANAL: A Program to Characterize Helix Geometry in Proteins, Journal of Biomolecular Structure and Dynamics, vol.31, issue.5, pp.811-819, 2000.
DOI : 10.1107/S0021889891004399

M. Levitt and G. Greer, Automatic identification of secondary structure in globular proteins, Journal of Molecular Biology, vol.114, issue.2, pp.181-293, 1977.
DOI : 10.1016/0022-2836(77)90207-8

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

F. C. Bernstein, T. F. Koetzle, G. J. Williams, M. Jr, E. F. Brice et al., The protein data bank: A computer-based archival file for macromolecular structures, Journal of Molecular Biology, vol.112, issue.3, pp.535-540, 1977.
DOI : 10.1016/S0022-2836(77)80200-3

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

D. Frishman and P. Argos, Knowledge-based protein secondary structure assignment, Proteins: Structure, Function, and Genetics, vol.206, issue.4, pp.566-579, 1995.
DOI : 10.1002/prot.340230412

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.132.9420

C. A. Andersen, A. G. Palmer, S. Brunak, and B. Rost, Continuum secondary HAL author manuscript inserm-00134564, 2002.

C. A. Andersen and B. Rost, Secondary structure assignement in Structural, pp.341-364, 2002.

P. Carter, C. A. Andersen, and B. Rost, DSSPcont: continuous secondary structure assignments for proteins, Nucleic Acids Research, vol.31, issue.13, pp.3293-3295, 2003.
DOI : 10.1093/nar/gkg626

F. M. Ridchards and C. E. Kundrot, Identification of structural motifs from protein coordinate data: Secondary structure and first-level supersecondary structure, Proteins: Structure, Function, and Genetics, vol.72, issue.2, pp.71-84, 1988.
DOI : 10.1002/prot.340030202

H. Sklenar, C. Etchebest, and R. Lavery, Describing protein structure: A general algorithm yielding complete helicoidal parameters and a unique overall axis, Proteins: Structure, Function, and Genetics, vol.6, issue.1, pp.46-60, 1989.
DOI : 10.1002/prot.340060105

URL : https://hal.archives-ouvertes.fr/hal-00313453

G. Labesse, N. Colloc-'h, J. Pothier, and J. Mornon, PSEA: a new efficient assignment of secondary structure from C? trace of proteins, Comput Appl Biosci, vol.13, pp.291-295, 1997.

S. M. King and W. Johnson, Assigning secondary structure from protein coordinate data, Proteins: Structure, Function, and Genetics, vol.234, issue.3, pp.313-320, 1999.
DOI : 10.1002/(SICI)1097-0134(19990515)35:3<313::AID-PROT5>3.0.CO;2-1

D. J. Barlow and J. M. Thornton, Helix geometry in proteins, Journal of Molecular Biology, vol.201, issue.3, pp.601-619, 1988.
DOI : 10.1016/0022-2836(88)90641-9

M. Bansal, S. Kumar, and R. Velavan, HELANAL: A Program to Characterize Helix Geometry in Proteins, Journal of Biomolecular Structure and Dynamics, vol.31, issue.5, pp.811-820, 2000.
DOI : 10.1107/S0021889891004399

S. Woodcock, J. P. Mornon, and B. Henrissat, Detection of secondary structure elements in proteins by hydrophobic cluster analysis, "Protein Engineering, Design and Selection", vol.5, issue.7, pp.629-635, 1992.
DOI : 10.1093/protein/5.7.629

A. G. De-brevern, A. C. Camproux, S. Hazout, C. Etchebest, and P. Tuffery, Beyond the secondary structures : the structural alphabets Research signpost, pp.319-331, 2001.

R. Karchin, Evaluating local structure alphabets for protein structure prediction, Ph.D. Computer Science, 2003.

R. Unger, D. Harel, S. Wherland, and J. L. Sussman, A 3D building blocks approach to analyzing and predicting structure of proteins, Proteins: Structure, Function, and Genetics, vol.5, issue.4, pp.355-373, 1989.
DOI : 10.1002/prot.340050410

S. J. Prestelski, W. Jr, A. L. Liebman, and M. N. , Generation of a substructure library for the description and classification of protein secondary structure. I. Overview of the methods and results, Proteins: Structure, Function, and Genetics, vol.14, issue.4, pp.430-439, 1992.
DOI : 10.1002/prot.340140404

R. Unger and J. L. Sussman, The importance of short structural motifs in protein structure analysis, Journal of Computer-Aided Molecular Design, vol.6, issue.4, pp.457-472, 1993.
DOI : 10.1007/BF02337561

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

B. H. Park and M. Levitt, The complexity and accuracy of discrete state models of protein structure, Journal of Molecular Biology, vol.249, issue.2, pp.493-507, 1995.
DOI : 10.1006/jmbi.1995.0311

R. Kolodny, P. Koehl, L. Guibas, and M. Levitt, Small Libraries of Protein Fragments Model Native Protein Structures Accurately, Journal of Molecular Biology, vol.323, issue.2, pp.297-307, 2002.
DOI : 10.1016/S0022-2836(02)00942-7

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

M. J. Rooman, J. Rodriguez, and S. J. Wodak, Automatic definition of recurrent local structure motifs in proteins, Journal of Molecular Biology, vol.213, issue.2, pp.327-336, 1990.
DOI : 10.1016/S0022-2836(05)80194-9

J. S. Fetrow, M. J. Palumbo, and G. Berg, Patterns, structures, and amino acid frequencies in structural building blocks, a protein secondary structure classification scheme, Proteins: Structure, Function, and Genetics, vol.19, issue.2, pp.249-271, 1997.
DOI : 10.1002/(SICI)1097-0134(199702)27:2<249::AID-PROT11>3.0.CO;2-M

C. Bystroff and D. Baker, Prediction of local structure in proteins using a library of sequence-structure motifs, Journal of Molecular Biology, vol.281, issue.3, pp.565-577, 1998.
DOI : 10.1006/jmbi.1998.1943

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. C. Camproux, P. Tuffery, L. Buffat, C. Andre, J. F. Boisvieux et al., Analyzing patterns between regular secondary structures using short structural building blocks defined by a hidden Markov model, Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), vol.101, issue.1-3, pp.33-40, 1999.
DOI : 10.1007/s002140050402

A. C. Camproux, A. G. De-brevern, S. Hazout, and P. Tuffery, Exploring the use of a structural alphabet for structural prediction of protein loops, Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), vol.106, issue.1-2, pp.28-35, 2001.
DOI : 10.1007/s002140100261

URL : https://hal.archives-ouvertes.fr/inserm-00134555

A. G. De-brevern and S. Hazout, Compacting local protein folds with a "hybrid protein model", Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta), vol.106, issue.1-2, pp.36-47, 2001.
DOI : 10.1007/s002140000227

A. G. De-brevern and S. Hazout, Hybrid Protein Model (HPM) : une nouvelle approche pour caractériser les relations séquence-structure dans les protéines, Premières Journées Ouvertes de Biologie, Informatique et Mathématiques. Recueil des Actes, pp.105-112, 2000.

A. G. De-brevern, H. Valadié, S. Hazout, and C. Etchebest, Extension of a local backbone description using a structural alphabet: A new approach to the sequence-structure relationship, Protein Science, vol.40, issue.(1/2), pp.2871-2886, 2002.
DOI : 10.1110/ps.0220502

URL : https://hal.archives-ouvertes.fr/inserm-00143374

A. G. De-brevern and S. Hazout, Compactage d'une base de données protéiques recodées dans un alphabet structural, Secondes Journées Ouvertes de Biologie, Informatique et Mathématiques. Recueil des Actes, pp.85-92, 2001.

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

C. Benros, S. Hazout, and A. G. De-brevern, Hybrid Protein Model": a new clustering approach for 3D local structures, Proceedings of Workshop on Bioinformatics ISMIS. Chapter 5, pp.1-6, 2002.
URL : https://hal.archives-ouvertes.fr/inserm-00134559

C. Benros, A. G. De-brevern, and S. Hazout, Hybrid protein model (HPM): a method for building a library of overlapping local structural prototypes. Sensitivity study and improvements of the training, 2003 IEEE XIII Workshop on Neural Networks for Signal Processing (IEEE Cat. No.03TH8718), pp.53-70, 2003.
DOI : 10.1109/NNSP.2003.1318004

URL : https://hal.archives-ouvertes.fr/inserm-00133639

R. Bonneau, J. Tsai, I. Ruczinski, D. Chivian, C. Rohl et al., Rosetta in CASP4: Progress in ab initio protein structure prediction, Proteins: Structure, Function, and Genetics, vol.20, issue.S5, pp.119-126, 2001.
DOI : 10.1002/prot.1170

R. Bonneau and D. Baker, Ab Initio Protein Structure Prediction: Progress and Prospects, Annual Review of Biophysics and Biomolecular Structure, vol.30, issue.1, pp.173-189, 2001.
DOI : 10.1146/annurev.biophys.30.1.173

R. Karchin, M. Cline, Y. Mandel-gutfreund, and K. Karplus, 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. M. Thornton, B. L. Sibanda, M. S. Edwards, and D. J. Barlow, Analysis, design and modification of loop regions in proteins, BioEssays, vol.188, issue.2-3, pp.63-69, 1988.
DOI : 10.1002/bies.950080205

D. R. Westhead, T. W. Slidel, T. P. Flores, and J. M. Thornton, Protein structural topology: automated analysis, diagrammatic representation and database HAL author manuscript inserm-00134564, 1999.
DOI : 10.1110/ps.8.4.897

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2144300

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

C. A. Orengo, A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells et al., CATH ??? a hierarchic classification of protein domain structures, Structure, vol.5, issue.8, pp.1093-1108, 1997.
DOI : 10.1016/S0969-2126(97)00260-8

R. Day, D. A. Beck, R. S. Armen, and V. Daggett, A consensus view of fold space: combining SCOP, 2004.

J. E. Bray, A. E. Todd, F. M. Pearl, J. M. Thornton, and C. A. Orengo, The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues, Protein Engineering Design and Selection, vol.13, issue.3, pp.153-165, 2000.
DOI : 10.1093/protein/13.3.153

F. M. Pearl, D. Lee, J. E. Bray, I. Sillitoe, A. E. Todd et al., Assigning genomic sequences to CATH, Nucleic Acids Research, vol.28, issue.1, pp.277-282, 2000.
DOI : 10.1093/nar/28.1.277

URL : http://doi.org/10.1093/nar/28.1.277

A. D. Michie, C. A. Orengo, and J. Thornton, Analysis of Domain Structural Class Using an Automated Class Assignment Protocol, Journal of Molecular Biology, vol.262, issue.2, pp.168-185, 1996.
DOI : 10.1006/jmbi.1996.0506

T. Noguchi, H. Matsuda, and Y. Akiyama, PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB), Nucleic Acids Research, vol.29, issue.1, pp.219-220, 2001.
DOI : 10.1093/nar/29.1.219

U. Hobohm, F. Scharf, R. Schneider, and C. Sander, Selection of representative protein data sets, Protein Science, vol.11, issue.3, pp.409-417, 1992.
DOI : 10.1002/pro.5560010313

U. Hobohm and C. Sander, Enlarged representative set of protein structures, Protein Science, vol.2, issue.3, 1994.
DOI : 10.1002/pro.5560030317

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

S. E. Brenner, P. Koehl, and M. Levitt, The ASTRAL compendium for protein structure and sequence analysis, Nucleic Acids Research, vol.28, issue.1, pp.254-256, 2000.
DOI : 10.1093/nar/28.1.254

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, 3rd edition, 2001.

L. R. Rabiner, A tutorial on Hidden Markov Models and selected applications in speech recognition, Proc. of the IEEE, pp.257-285, 1989.

K. V. Mardia, T. Kent, and J. M. Bibby, Multivariate Analysis, 1979.

S. Jr, A non-linear mapping for data structure analysis, IEEE Transactions on Computers C, vol.18, pp.401-409, 1969.

D. K. Agrafiotis, A new method for analyzing protein sequence relationships based on Sammon maps, Protein Science, vol.18, issue.2, pp.287-293, 1997.
DOI : 10.1002/pro.5560060203

M. A. Andrade, G. Casari, C. Sander, and A. Valencia, Classification of protein families and detection of the determinant residues with an improved self-organizing map, Biological Cybernetics, vol.76, issue.6, 1997.
DOI : 10.1007/s004220050357

C. Bystroff, V. Thorsson, and D. Baker, HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins, Journal of Molecular Biology, vol.301, issue.1, pp.173-190, 2000.
DOI : 10.1006/jmbi.2000.3837

R. Koradi, M. Billeter, and K. Wuthrich, MOLMOL: A program for display and analysis of macromolecular structures, Journal of Molecular Graphics, vol.14, issue.1, pp.29-32, 1996.
DOI : 10.1016/0263-7855(96)00009-4