C. A. Andersen, A. G. Palmer, S. Brunak, R. , and B. , Continuum Secondary Structure Captures Protein Flexibility, Structure, vol.10, issue.2, pp.175-184, 2002.
DOI : 10.1016/S0969-2126(02)00700-1

URL : http://doi.org/10.1016/s0969-2126(02)00700-1

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

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2143812

D. Bang, A. V. Gribenko, V. Tereshko, A. A. Kossiakoff, S. B. Kent et al., Dissecting the energetics of protein ??-helix C-cap termination through chemical protein synthesis, Nature Chemical Biology, vol.96, issue.3, pp.139-143, 2006.
DOI : 10.1038/nchembio766

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

C. Benros, A. G. De-brevern, C. Etchebest, and S. Hazout, Assessing a novel approach for predicting local 3D protein structures from sequence, Proteins: Structure, Function, and Bioinformatics, vol.30, issue.23, pp.865-880, 2006.
DOI : 10.1002/prot.20815

URL : https://hal.archives-ouvertes.fr/inserm-00133180

C. Benros, A. G. De-brevern, and S. Hazout, Analyzing the sequence???structure relationship of a library of local structural prototypes, Journal of Theoretical Biology, vol.256, issue.2, pp.215-226, 2009.
DOI : 10.1016/j.jtbi.2008.08.032

URL : https://hal.archives-ouvertes.fr/inserm-00318954

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, E. F. Meyer, . Jr et al., The protein data bank: A computer-based archival file for macromolecular structures, Journal of Molecular Biology, vol.112, issue.3, pp.535-542, 1977.
DOI : 10.1016/S0022-2836(77)80200-3

W. Boomsma and T. Hamelryck, Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space, BMC Bioinformatics, vol.6, issue.1, p.159, 2005.
DOI : 10.1186/1471-2105-6-159

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

A. Bornot, C. Etchebest, and A. G. De-brevern, A new prediction strategy for long local protein structures using an original description, Proteins: Structure, Function, and Bioinformatics, vol.19, issue.1/2, 2009.
DOI : 10.1002/prot.22370

URL : https://hal.archives-ouvertes.fr/inserm-00348740

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

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

M. V. Cubellis, F. Cailliez, L. , and S. C. , Secondary structure assignment that accurately reflects physical and evolutionary characteristics, BMC Bioinformatics, vol.6, issue.Suppl 4, p.8, 2005.
DOI : 10.1186/1471-2105-6-S4-S8

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, New assessment of a structural alphabet, In Silico Biol, vol.5, pp.283-289, 2005.
URL : https://hal.archives-ouvertes.fr/inserm-00132875

A. G. De-brevern, C. Benros, R. Gautier, H. Valadie, S. Hazout et al., Local backbone structure prediction of proteins, In Silico Biol, vol.4, pp.381-386, 2004.
URL : https://hal.archives-ouvertes.fr/inserm-00132872

A. G. De-brevern, C. Benros, and S. Hazout, Structural Alphabet: From a Local Point of View to a Global Description of Protein 3D Structures, pp.127-169, 2005.
URL : https://hal.archives-ouvertes.fr/inserm-00134564

A. G. De-brevern, A. Camproux, S. Hazout, C. Etchebest, P. G. Tuffery et al., Protein structural alphabets: beyond the secondary structure descriptionPinning strategy": a novel approach for predicting the backbone structure in terms of protein blocks from sequence, In Recent Research Developments in Protein Engineering. (ed. S. Sangadai) Research Signpost J Biosci, vol.32, pp.319-331, 2001.

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 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

A. G. De-brevern, H. Valadie, 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, H. Wong, C. Tournamille, Y. Colin, L. Van-kim et al., A structural model of a seven-transmembrane helix receptor: The Duffy antigen/receptor for chemokine (DARC), Biochimica et Biophysica Acta (BBA) - General Subjects, vol.1724, issue.3, pp.288-306, 2005.
DOI : 10.1016/j.bbagen.2005.05.016

URL : https://hal.archives-ouvertes.fr/inserm-00143373

A. J. Doig and R. L. Baldwin, N- and C-capping preferences for all 20 amino acids in ??-helical peptides, Protein Science, vol.33, issue.7, pp.1325-1336, 1995.
DOI : 10.1002/pro.5560040708

N. V. Dovidchenko, N. S. Bogatyreva, and O. V. Galzitskaya, PREDICTION OF LOOP REGIONS IN PROTEIN SEQUENCE, Journal of Bioinformatics and Computational Biology, vol.06, issue.05, pp.1035-1047, 2008.
DOI : 10.1142/S0219720008003758

F. Dupuis, J. F. Sadoc, R. Jullien, B. Angelov, and J. P. And-mornon, Voro3D: 3D Voronoi tessellations applied to protein structures, Voro3D: 3D Voronoi tessellations applied to protein structures, pp.1715-1716, 2005.
DOI : 10.1093/bioinformatics/bth365

URL : https://hal.archives-ouvertes.fr/hal-00021968

F. Dupuis, J. F. Sadoc, and J. P. And-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

M. S. Edwards, J. E. Sternberg, T. , and J. M. , Structural and sequence patterns in the loops of ?????? units, "Protein Engineering, Design and Selection", vol.1, issue.3, pp.173-181, 1987.
DOI : 10.1093/protein/1.3.173

A. V. Efimov, Structure of ??-??-hairpins with short connections, "Protein Engineering, Design and Selection", vol.4, issue.3, pp.245-250, 1991.
DOI : 10.1093/protein/4.3.245

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

A. V. Efimov, Structural trees for proteins containing ??-motifs, Biochemistry (Moscow), vol.73, issue.1, pp.23-28, 2008.
DOI : 10.1134/S0006297908010033

J. Espadaler, E. Querol, F. X. Aviles, and B. Oliva, Identification of function-associated loop motifs and application to protein function prediction, Bioinformatics, vol.22, issue.18, pp.2237-2243, 2006.
DOI : 10.1093/bioinformatics/btl382

C. Etchebest, C. Benros, A. Bornot, A. C. Camproux, and A. G. De-brevern, A reduced amino acid alphabet for understanding and designing protein adaptation to mutation, European Biophysics Journal, vol.92, issue.8, pp.1059-1069, 2007.
DOI : 10.1007/s00249-007-0188-5

URL : https://hal.archives-ouvertes.fr/inserm-00155390

G. Faure, A. Bornot, and A. G. De-brevern, Analysis of protein contacts into Protein Units, Biochimie, vol.91, issue.7, 2009.
DOI : 10.1016/j.biochi.2009.04.008

URL : https://hal.archives-ouvertes.fr/inserm-00375095

N. Fernandez-fuentes and A. Fiser, Saturating representation of loop conformational fragments in structure databanks, BMC Structural Biology, vol.6, issue.1, p.15, 2006.
DOI : 10.1186/1472-6807-6-15

N. Fernandez-fuentes, A. Hermoso, J. Espadaler, E. Querol, F. X. Aviles et al., Classification of common functional loops of kinase super-families, Proteins: Structure, Function, and Bioinformatics, vol.5, issue.7, pp.539-555, 2004.
DOI : 10.1002/prot.20136

N. Fernandez-fuentes, B. Oliva, and A. Fiser, A supersecondary structure library and search algorithm for modeling loops in protein structures, Nucleic Acids Research, vol.34, issue.7, pp.2085-2097, 2006.
DOI : 10.1093/nar/gkl156

N. Fernandez-fuentes, J. Zhai, and A. Fiser, ArchPRED: a template based loop structure prediction server, Nucleic Acids Research, vol.34, issue.Web Server, pp.173-176, 2006.
DOI : 10.1093/nar/gkl113

N. C. Fitzkee, P. J. Fleming, H. Gong, N. Panasik, . Jr et al., Are proteins made from a limited parts list?, Trends in Biochemical Sciences, vol.30, issue.2, pp.73-80, 2005.
DOI : 10.1016/j.tibs.2004.12.005

N. C. Fitzkee, P. J. Fleming, R. , and G. D. , 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

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

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

D. Frishman, A. , and P. , 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

P. F. Fuchs, A. , and A. J. , 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

S. Hosseini, M. Sadeghi, H. Pezeshk, C. Eslahchi, and M. Habibi, PROSIGN: A method for protein secondary structure assignment based on three-dimensional coordinates of consecutive C?? atoms, Computational Biology and Chemistry, vol.32, issue.6, pp.406-411, 2008.
DOI : 10.1016/j.compbiolchem.2008.07.027

X. Hu, H. Wang, H. Ke, and B. Kuhlman, High-resolution design of a protein loop, Proceedings of the National Academy of Sciences, vol.104, issue.45, pp.17668-17673, 2007.
DOI : 10.1073/pnas.0707977104

Z. Huang, C. F. Wong, W. , and R. A. , Flexible protein???flexible ligand docking with disrupted velocity simulated annealing, Proteins: Structure, Function, and Bioinformatics, vol.2, issue.1, 2007.
DOI : 10.1002/prot.21781

E. G. Hutchinson, T. , and J. M. , HERA???A program to draw schematic diagrams of protein secondary structures, Proteins: Structure, Function, and Genetics, vol.250, issue.3, pp.203-212, 1990.
DOI : 10.1002/prot.340080303

E. G. Hutchinson, T. , and J. M. , The Greek key motif: extraction, classification and analysis, "Protein Engineering, Design and Selection", vol.6, issue.3, pp.233-245, 1993.
DOI : 10.1093/protein/6.3.233

E. G. Hutchinson, T. , and J. M. , 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

E. G. Hutchinson, T. , and J. M. , 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

H. Jiang and C. Blouin, Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions, BMC Bioinformatics, vol.8, issue.1, p.444, 2007.
DOI : 10.1186/1471-2105-8-444

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

V. Kanagasabai, J. Arunachalam, P. A. Prasad, and N. Gautham, Exploring the conformational space of protein loops using a mean field technique with MOLS sampling, Proteins: Structure, Function, and Bioinformatics, vol.7, issue.4, pp.908-921, 2007.
DOI : 10.1002/prot.21333

S. M. King, J. , and W. C. , 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

E. Kruus, P. Thumfort, C. Tang, and N. S. Wingreen, Gibbs sampling and helix-cap motifs, Nucleic Acids Research, vol.33, issue.16, pp.5343-5353, 2005.
DOI : 10.1093/nar/gki842

URL : http://doi.org/10.1093/nar/gki842

S. Kullback and R. A. Leibler, On Information and Sufficiency, The Annals of Mathematical Statistics, vol.22, issue.1, pp.79-86, 1951.
DOI : 10.1214/aoms/1177729694

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

G. Labesse, N. Colloc-'h, J. Pothier, and J. P. 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

A. M. Lesk, Introduction to Bioinformatics Importance of anchor group positioning in protein loop prediction, Proteins, vol.37, pp.56-64, 1999.

M. Levitt, G. , and J. , 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

T. Madej, A. R. Panchenko, J. Chen, and S. H. Bryant, Protein homologous cores and loops: important clues to evolutionary relationships between structurally similar proteins, BMC Structural Biology, vol.7, issue.1, p.23, 2007.
DOI : 10.1186/1472-6807-7-23

URL : http://doi.org/10.1186/1472-6807-7-23

I. Majumdar, S. S. Krishna, and N. V. Grishin, PALSSE: A program to delineate linear secondary structural elements from protein structures, BMC Bioinformatics, vol.6, issue.1, p.202, 2005.
DOI : 10.1186/1471-2105-6-202

Y. Mandel-gutfreund and L. M. Gregoret, On the Significance of Alternating Patterns of Polar and Non-polar Residues in Beta-strands, Journal of Molecular Biology, vol.323, issue.3, pp.453-461, 2002.
DOI : 10.1016/S0022-2836(02)00973-7

Y. Mandel-gutfreund, S. M. Zaremba, and L. M. Gregoret, Contributions of residue pairing to ??-sheet formation:conservation and covariation of amino acid residue pairs on antiparallel ??-strands, Journal of Molecular Biology, vol.305, issue.5, pp.1145-1159, 2001.
DOI : 10.1006/jmbi.2000.4364

J. Martin, G. Letellier, A. Marin, J. Taly, A. G. De-brevern et al., 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

I. Michalopoulos, G. M. Torrance, D. R. Gilbert, and D. R. Westhead, TOPS: an enhanced database of protein structural topology, Nucleic Acids Research, vol.32, issue.90001, pp.251-254, 2004.
DOI : 10.1093/nar/gkh060

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

S. Miyazaki, Y. Kuroda, Y. , and S. , Characterization and prediction of linker sequences of multi-domain proteins by a neural network, Journal of Structural and Functional Genomics, vol.2, issue.1, pp.37-51, 2002.
DOI : 10.1023/A:1014418700858

M. Monnigmann and C. A. Floudas, Protein loop structure prediction with flexible stem geometries, Proteins: Structure, Function, and Bioinformatics, vol.96, issue.4, pp.748-762, 2005.
DOI : 10.1002/prot.20669

S. B. Nabuurs, M. Wagener, and J. De-vlieg, A Flexible Approach to Induced Fit Docking, Journal of Medicinal Chemistry, vol.50, issue.26, 2007.
DOI : 10.1021/jm070593p

M. A. Olson, M. Feig, and C. L. Brooks, Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions, Journal of Computational Chemistry, vol.67, issue.5, 2007.
DOI : 10.1002/jcc.20827

A. R. Panchenko and T. Madej, Analysis of protein homology by assessing the (dis)similarity in protein loop regions, Proteins: Structure, Function, and Bioinformatics, vol.289, issue.144, pp.539-547, 2004.
DOI : 10.1002/prot.20237

A. R. Panchenko and T. Madej, Structural similarity of loops in protein families: toward the understanding of protein evolution, BMC Evolutionary Biology, vol.5, issue.1, p.10, 2005.
DOI : 10.1186/1471-2148-5-10

A. R. Panchenko, Y. I. Wolf, L. A. Panchenko, and T. Madej, Evolutionary plasticity of protein families: Coupling between sequence and structure variation, Proteins: Structure, Function, and Bioinformatics, vol.301, issue.Suppl 1, pp.535-544, 2005.
DOI : 10.1002/prot.20644

M. Parisien and F. Major, A new catalog of protein ??-sheets, Proteins: Structure, Function, and Bioinformatics, vol.5, issue.3, pp.545-558, 2005.
DOI : 10.1002/prot.20677

L. Pauling, C. , and R. B. , 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, 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

P. A. Prasad, V. Kanagasabai, J. Arunachalam, and N. Gautham, Exploring conformational space using a mean field technique with MOLS sampling, Journal of Biosciences, vol.32, issue.S1, pp.909-920, 2007.
DOI : 10.1007/s12038-007-0091-3

L. G. Presta, R. , and G. D. , Helix signals in proteins, Science, vol.240, issue.4859, pp.1632-1641, 1988.
DOI : 10.1126/science.2837824

C. S. Rapp, T. Strauss, A. Nederveen, and G. Fuentes, Prediction of protein loop geometries in solution, Proteins: Structure, Function, and Bioinformatics, vol.43, issue.Suppl 3, pp.69-74, 2007.
DOI : 10.1002/prot.21503

M. T. Reetz, J. D. Carballeira, and A. Vogel, Iterative Saturation Mutagenesis on the Basis of B Factors as a Strategy for Increasing Protein Thermostability, Angewandte Chemie International Edition, vol.41, issue.7, pp.7745-7751, 2006.
DOI : 10.1002/anie.200602795

N. Rekha and N. Srinivasan, Structural basis of regulation and substrate specificity of protein kinase CK2 deduced from the modeling of proteinprotein interactions, BMC Structural Biology, vol.3, issue.1, p.4, 2003.
DOI : 10.1186/1472-6807-3-4

F. M. Richards 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

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. 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

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

C. A. Rohl, C. E. Strauss, D. Chivian, and D. Baker, Modeling structurally variable regions in homologous proteins with rosetta, Proteins: Structure, Function, and Bioinformatics, vol.24, issue.Suppl 5, pp.656-677, 2004.
DOI : 10.1002/prot.10629

G. D. Rose, Lifting the lid on helix-capping, Nature Chemical Biology, vol.120, issue.3, pp.123-124, 2006.
DOI : 10.1038/nchembio0306-123

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

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

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

G. Sheikhnejad, A. Brank, J. K. Christman, A. Goddard, E. Alvarez et al., Mechanism of inhibition of DNA (cytosine C5)-methyltransferases by oligodeoxyribonucleotides containing 5,6-dihydro-5-azacytosine11Edited by R. Huber, Journal of Molecular Biology, vol.285, issue.5, pp.2021-2034, 1999.
DOI : 10.1006/jmbi.1998.2426

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

D. Smith, SSTRUC: A program to calculate a secondary structural summary, Department of Crystal-lography, 1989.

C. S. Soto, M. Fasnacht, J. Zhu, L. Forrest, and B. Honig, Loop modeling: Sampling, filtering, and scoring, Proteins: Structure, Function, and Bioinformatics, vol.4, issue.3, 2007.
DOI : 10.1002/prot.21612

N. Srinivasan, B. Bax, T. L. Blundell, P. , and P. J. , Structural aspects of the functional modules in human protein kinase-C?? deduced from comparative analyses, Proteins: Structure, Function, and Genetics, vol.11, issue.2, pp.217-235, 1996.
DOI : 10.1002/(SICI)1097-0134(199610)26:2<217::AID-PROT11>3.0.CO;2-S

R. Srinivasan, R. , and G. D. , A physical basis for protein secondary structure, Proceedings of the National Academy of Sciences, vol.96, issue.25, pp.14258-14263, 1999.
DOI : 10.1073/pnas.96.25.14258

T. O. Street, N. C. Fitzkee, L. L. Perskie, R. , and G. D. , Physical-chemical determinants of turn conformations in globular proteins, Protein Science, vol.289, issue.8, pp.1720-1727, 2007.
DOI : 10.1110/ps.072898507

T. Taylor, M. Rivera, G. Wilson, and I. Vaisman, New method for protein secondary structure assignment based on a simple topological descriptor, Proteins: Structure, Function, and Bioinformatics, vol.7, issue.1, pp.513-524, 2005.
DOI : 10.1002/prot.20471

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

M. Tyagi, P. Sharma, C. S. Swamy, F. Cadet, N. Srinivasan et al., 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

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

G. Wang, R. L. Dunbrack, and . Jr, PISCES: recent improvements to a PDB sequence culling server, Nucleic Acids Research, vol.33, issue.Web Server, pp.94-98, 2005.
DOI : 10.1093/nar/gki402

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

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

G. Wohlfahrt, V. Hangoc, and D. Schomburg, Positioning of anchor groups in protein loop prediction: The importance of solvent accessibility and secondary structure elements, Proteins: Structure, Function, and Genetics, vol.9, issue.3, pp.370-378, 2002.
DOI : 10.1002/prot.10098

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

Y. Wolf, T. Madej, V. Babenko, B. Shoemaker, and A. R. Panchenko, Longterm trends in evolution of indels in protein sequences, BMC Evolutionary Biology, vol.7, issue.1, p.19, 2007.
DOI : 10.1186/1471-2148-7-19

S. Wong and M. P. Jacobson, Conformational selection in silico: Loop latching motions and ligand binding in enzymes, Proteins, 2007.

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

W. Zhang, A. K. Dunker, and Y. Zhou, Assessing secondary structure assignment of protein structures by using pairwise sequence-alignment benchmarks, Proteins: Structure, Function, and Bioinformatics, vol.68, issue.1, pp.61-67, 2007.
DOI : 10.1002/prot.21654

W. Zhang, A. K. Dunker, and Y. Zhou, Assessing secondary structure assignment of protein structures by using pairwise sequence-alignment benchmarks, Proteins: Structure, Function, and Bioinformatics, vol.68, issue.1, pp.61-67, 2008.
DOI : 10.1002/prot.21654