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

D. Baker and A. Sali, Protein Structure Prediction and Structural Genomics, Science, vol.294, issue.5540, pp.93-96, 2001.
DOI : 10.1126/science.1065659

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.82.1058

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

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

F. C. Bernstein, T. F. Koetzle, G. J. Williams, J. Meyer, 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

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. 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

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

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

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

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

A. C. Camproux, P. Tuffery, J. P. Chevrolat, J. F. Boisvieux, and S. Hazout, Hidden Markov model approach for identifying the modular framework of the protein backbone, Protein Engineering Design and Selection, vol.12, issue.12, pp.1063-1073, 1999.
DOI : 10.1093/protein/12.12.1063

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

J. M. Chandonia and M. Karplus, New methods for accurate prediction of protein secondary structure, Proteins: Structure, Function, and Genetics, vol.10, issue.3, pp.293-306, 1999.
DOI : 10.1002/(SICI)1097-0134(19990515)35:3<293::AID-PROT3>3.0.CO;2-L

K. C. Chou, Prediction and classification of ??-turn types, Biopolymers, vol.89, issue.7, pp.837-853, 1997.
DOI : 10.1002/(SICI)1097-0282(199712)42:7<837::AID-BIP9>3.0.CO;2-U

N. Colloc-'h, C. Etchebest, E. Thoreau, B. Henrissat, and J. And-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

J. A. Cuff and G. J. Barton, Evaluation and improvement of multiple sequence methods for protein secondary structure prediction, Proteins: Structure, Function, and Genetics, vol.266, issue.4, pp.508-519, 1999.
DOI : 10.1002/(SICI)1097-0134(19990301)34:4<508::AID-PROT10>3.0.CO;2-4

A. G. De-brevern and S. Hazout, Hybrid Protein Model (HPM): a method to compact protein 3D-structure information and physicochemical properties, Proceedings Seventh International Symposium on String Processing and Information Retrieval. SPIRE 2000, pp.49-54, 2000.
DOI : 10.1109/SPIRE.2000.878179

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. G. De-brevern, A. C. Camproux, S. Hazout, C. Etchebest, and P. Tuffery, Beyond the secondary structures: The structural alphabets, Recent Advances In Protein Engineering, pp.319-331, 2001.

D. Jr and L. , Omega loops: Nonregular secondary structures significant in protein function and stability, FASEB J, vol.9, pp.708-717, 1995.

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

A. Fiser and A. Sali, MODELLER: Generation and refinement of homology models, Methods Enzymol, 2001.

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

U. Hobohm and C. Sander, Enlarged representative set of protein structures, Protein Science, vol.2, issue.3, pp.522-524, 1994.
DOI : 10.1002/pro.5560030317

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

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

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

L. Jaroszewski, L. Rychlewski, B. Zhang, and A. Godzik, Fold prediction by a hierarchy of sequence, threading, and modeling methods, Protein Science, vol.12, issue.6, pp.1431-1440, 1998.
DOI : 10.1002/pro.5560070620

D. T. Jones, M. Tress, K. Bryson, H. , and C. , Successful recognition of protein folds using threading methods biased by sequence similarity and predicted secondary structure, Proteins, vol.3, pp.104-111, 1999.

L. A. Kelley, R. M. Maccallum, and M. J. Sternberg, Enhanced genome annotation using structural profiles in the program 3D-PSSM, Journal of Molecular Biology, vol.299, issue.2, pp.499-520, 2000.
DOI : 10.1006/jmbi.2000.3741

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

R. Koradi, M. Billeter, and K. Wüthrich, MOLMOL: A program for display and analysis of macromolecular structures, Journal of Molecular Graphics, vol.14, issue.1, pp.51-55, 1996.
DOI : 10.1016/0263-7855(96)00009-4

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

J. Kwasigroch, J. Chomilier, and J. And-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

G. Labesse, N. Colloc-'h, J. Pothier, and J. And-mornon, P-SEA: a new efficient assignment of secondary structure from C?? trace of proteins, Bioinformatics, vol.13, issue.3, pp.291-295, 1997.
DOI : 10.1093/bioinformatics/13.3.291

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. Meller and R. Elber, Linear programming optimization and a double statistical filter for protein threading protocols, Proteins: Structure, Function, and Genetics, vol.247, issue.3, pp.241-261, 2001.
DOI : 10.1002/prot.1145

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

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

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

C. A. Orengo, J. E. Bray, T. Hubbard, L. Loconte, and I. Sillitoe, Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction, Proteins: Structure, Function, and Genetics, vol.5, issue.S3, pp.149-170, 1999.
DOI : 10.1002/(SICI)1097-0134(1999)37:3+<149::AID-PROT20>3.0.CO;2-H

M. Ouali and R. D. King, Cascaded multiple classifiers for secondary structure prediction, Protein Science, vol.195, issue.2, pp.1162-1176, 2000.
DOI : 10.1110/ps.9.6.1162

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

T. N. 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

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

L. R. Rabiner, A tutorial on hidden Markov models and selected applications in speech recognition, Proceedings of the IEEE, vol.77, issue.2, pp.257-285, 1989.
DOI : 10.1109/5.18626

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

J. S. Richardson, E. D. Getzoff, and D. C. Richardson, The beta bulge: a common small unit of nonrepetitive protein structure., Proc. Natl. Acad. Sci, pp.2574-2578, 1978.
DOI : 10.1073/pnas.75.6.2574

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

C. A. Rohl and A. J. Doig, Models for the 3 10 -helix/coil, -helix-coil and -helix/3 10 -helix/coil transitions in isolated peptides, Protein Sci, vol.5, pp.1689-1696, 1996.

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

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

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

B. Rost and C. Sander, Prediction of Protein Secondary Structure at Better than 70% Accuracy, Journal of Molecular Biology, vol.232, issue.2, pp.584-599, 1993.
DOI : 10.1006/jmbi.1993.1413

A. A. Salamov and V. V. Solovyev, Protein secondary structure prediction using local alignments, Journal of Molecular Biology, vol.268, issue.1, pp.31-36, 1997.
DOI : 10.1006/jmbi.1997.0958

A. Sali and T. L. 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

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. 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

K. T. Simons, C. Kooperberg, E. Huang, and D. Baker, Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions, Journal of Molecular Biology, vol.268, issue.1, pp.209-225, 1997.
DOI : 10.1006/jmbi.1997.0959

K. Simons, R. Bonneau, I. Ruczinski, and D. Baker, Ab initio protein structure prediction of CASP III targets using ROSETTA, Proteins: Structure, Function, and Genetics, vol.277, issue.S3, pp.171-176, 1999.
DOI : 10.1002/(SICI)1097-0134(1999)37:3+<171::AID-PROT21>3.0.CO;2-Z

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

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

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

J. Wojick, J. Mornon, and J. Chomilier, New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification, J. Mol. Biol, vol.289, pp.1469-1490, 1999.

Y. Xu and D. Xu, Protein threading using PROSPECT: Design and evaluation, Proteins: Structure, Function, and Genetics, vol.14, issue.3, pp.343-354, 2000.
DOI : 10.1002/1097-0134(20000815)40:3<343::AID-PROT10>3.0.CO;2-S