L. Pauling, R. Corey, and H. Branson, The structure of proteins: Two hydrogen-bonded helical configurations of the polypeptide chain, Proceedings of the National Academy of Sciences, vol.203, issue.4, pp.205-211, 1951.
DOI : 10.1073/pnas.37.4.205

L. Pauling and R. Corey, The Pleated Sheet, A New Layer Configuration of Polypeptide Chains, Proc Natl Acad SciU S A 1951, pp.251-256
DOI : 10.1073/pnas.37.5.251

J. Gibrat, T. Madej, and S. Bryant, Surprising similarities in structure comparison, Current Opinion in Structural Biology, vol.6, issue.3, pp.377-385, 1996.
DOI : 10.1016/S0959-440X(96)80058-3

A. Murzin, S. 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.536-576, 1995.
DOI : 10.1016/S0022-2836(05)80134-2

C. Orengo, A. Michie, S. Jones, D. Jones, M. 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. Sayle and E. Milner-white, RASMOL: biomolecular graphics for all, Trends in Biochemical Sciences, vol.20, issue.9, p.374, 1995.
DOI : 10.1016/S0968-0004(00)89080-5

W. Humphrey, A. Dalke, and K. Schulten, VMD: Visual molecular dynamics, Journal of Molecular Graphics, vol.14, issue.1, pp.33-38, 1996.
DOI : 10.1016/0263-7855(96)00018-5

A. Sali and T. Blundell, Comparative Protein Modelling by Satisfaction of Spatial Restraints, Journal of Molecular Biology, vol.234, issue.3, pp.779-815, 1993.
DOI : 10.1006/jmbi.1993.1626

P. Bradley, D. Chivian, J. Meiler, K. Misura, C. Rohl et al., Rosetta predictions in CASP5: Successes, failures, and prospects for complete automation, Proteins: Structure, Function, and Genetics, vol.16, issue.S6, pp.53457-468, 2003.
DOI : 10.1002/prot.10552

G. Pollastri, D. Przybylski, B. Rost, and P. Baldi, Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles, Proteins: Structure, Function, and Genetics, vol.47, issue.2, pp.228-235, 2002.
DOI : 10.1002/prot.10082

T. Petersen, C. Lundegaard, M. Nielsen, H. Bohr, J. Bohr et al., Prediction of protein secondary structure at 80% accuracy, Proteins: Structure, Function, and Genetics, vol.9, issue.1, pp.17-20, 2000.
DOI : 10.1002/1097-0134(20001001)41:1<17::AID-PROT40>3.0.CO;2-F

D. Jones, Protein secondary structure prediction based on position-specific scoring matrices, Journal of Molecular Biology, vol.292, issue.2
DOI : 10.1006/jmbi.1999.3091

D. Frishman and P. Argos, The future of protein secondary structure prediction accuracy, Folding and Design, vol.2, issue.3, pp.159-62, 1997.
DOI : 10.1016/S1359-0278(97)00022-9

B. Rost, Review: Protein Secondary Structure Prediction Continues to Rise, Journal of Structural Biology, vol.134, issue.2-3, pp.204-218, 2001.
DOI : 10.1006/jsbi.2001.4336

G. Schulz, C. Barry, J. Friedman, P. Chou, G. Fasman et al., Comparison of predicted and experimentally determined secondary structure of adenyl kinase, Nature, vol.70, issue.5462, pp.250140-250142, 1974.
DOI : 10.1038/250140a0

B. Robson and J. Garnier, Introduction to Proteins and Protein Engineering Amsterdam, 1986.

D. Barlow and J. 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

S. Kumar and M. Bansal, Structural and sequence characteristics of long alpha helices in globular proteins, Biophysical Journal, vol.71, issue.3, pp.1574-1586, 1996.
DOI : 10.1016/S0006-3495(96)79360-8

S. Kumar and M. Bansal, Geometrical and Sequence Characteristics of ??-Helices in Globular Proteins, Biophysical Journal, vol.75, issue.4, pp.1935-1944, 1998.
DOI : 10.1016/S0006-3495(98)77634-9

M. Levitt and J. Greer, Automatic identification of secondary structure in globular proteins, Journal of Molecular Biology, vol.114, issue.2, pp.181-239, 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.2577-637, 1983.
DOI : 10.1002/bip.360221211

H. Berendsen, D. Van-der-spoel, and R. Van-drunen, GROMACS: A message-passing parallel molecular dynamics implementation, Computer Physics Communications, vol.91, issue.1-3, pp.43-56, 1995.
DOI : 10.1016/0010-4655(95)00042-E

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

M. 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

F. Richards and C. 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, P-SEA: a new efficient assignment of secondary structure from C?? trace of proteins, Bioinformatics, vol.13, issue.3, pp.291-296, 1997.
DOI : 10.1093/bioinformatics/13.3.291

S. King and W. Johnson, Assigning secondary structure from protein coordinate data, Proteins, vol.3, issue.35, pp.313-320, 1999.

F. Dupuis, J. Sadoc, and J. Mornon, Protein secondary structure assignment through Vorono?? tessellation, Proteins: Structure, Function, and Bioinformatics, vol.13, issue.3, pp.519-528, 2004.
DOI : 10.1002/prot.10566
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.138.3512

H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. 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

N. Colloc-'h, C. Etchebest, E. Thoreau, B. Henrissat, and J. Mornon, Comparison of three algorithms for the assignment of secondary structure in proteins: the advantages of a consensus assignment, "Protein Engineering, Design and Selection", vol.6, issue.4, pp.377-382, 1993.
DOI : 10.1093/protein/6.4.377
URL : https://hal.archives-ouvertes.fr/hal-00310605

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

L. Fourrier, C. Benros, and A. 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

C. Andersen, B. Rost, P. Bourne, and W. H. Hoboken, Automated Secondary Structure Assignment, pp.341-363

S. 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

U. Hobohm, M. 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

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

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. Zemla, C. Venclovas, K. Fidelis, and B. Rost, A modified definition of Sov, a segment-based measure for protein secondary structure prediction assessment, Proteins: Structure, Function, and Genetics, vol.1, issue.2, pp.220-223, 1999.
DOI : 10.1002/(SICI)1097-0134(19990201)34:2<220::AID-PROT7>3.0.CO;2-K

P. Kraulis, MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures, Journal of Applied Crystallography, vol.24, issue.5, pp.946-950, 1991.
DOI : 10.1107/S0021889891004399