M. Ahram, Z. I. Litou, R. Fang, and G. Tawallbeh, Estimation of membrane proteins in the human proteome, In Silico Biol, vol.6, pp.379-386, 2006.

F. C. Almeida and S. J. Opella, fd coat protein structure in membrane environments: structural dynamics of the loop between the hydrophobic trans-membrane helix and the amphipathic in-plane helix, Journal of Molecular Biology, vol.270, issue.3, pp.481-495, 1997.
DOI : 10.1006/jmbi.1997.1114

S. R. Amirova, J. V. Milchevsky, I. V. Filatov, N. G. Esipova, and V. G. Tumanyan, Study and Prediction of Secondary Structure for Membrane Proteins, Journal of Biomolecular Structure and Dynamics, vol.12, issue.4, pp.421-428, 2007.
DOI : 10.1080/07391102.2007.10507130

M. Arai, M. Ikeda, and T. Shimizu, Comprehensive analysis of transmembrane topologies in prokaryotic genomes, Gene, vol.304, pp.77-86, 2003.
DOI : 10.1016/S0378-1119(02)01181-2

Y. Arinaminpathy, E. Khurana, D. M. Engelman, and M. B. Gerstein, Computational analysis of membrane proteins: the largest class of drug targets, Drug Discovery Today, vol.14, issue.23-24, pp.1130-1135, 2009.
DOI : 10.1016/j.drudis.2009.08.006

P. G. Bagos, T. D. Liakopoulos, and S. J. Hamodrakas, Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins, BMC Bioinformatics, vol.7, issue.1, p.189, 2006.
DOI : 10.1186/1471-2105-7-189

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

O. M. Becker, Y. Marantz, S. Shacham, B. Inbal, A. Heifetz et al., G protein-coupled receptors: In silico drug discovery in 3D, Proceedings of the National Academy of Sciences, vol.101, issue.31, pp.11304-11309, 2004.
DOI : 10.1073/pnas.0401862101

C. Benros, J. Martin, M. Tyagi, and A. G. De-brevern, Description of the local protein structure. I. Classical approaches, Recent Adv, pp.1-33, 2007.
URL : https://hal.archives-ouvertes.fr/inserm-00176471

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

T. Beuming and H. Weinstein, A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins, Bioinformatics, vol.20, issue.12, pp.1822-1835, 2004.
DOI : 10.1093/bioinformatics/bth143

B. Cao, A. Porollo, R. Adamczak, M. Jarrell, and J. Meller, Enhanced recognition of protein transmembrane domains with prediction-based structural profiles, Bioinformatics, vol.22, issue.3, pp.303-309, 2006.
DOI : 10.1093/bioinformatics/bti784

C. P. Chen, A. Kernytsky, R. , and B. , Transmembrane helix predictions revisited, Protein Science, vol.34, issue.Suppl 5, pp.2774-2791, 2002.
DOI : 10.1110/ps.0214502

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2373751

C. P. Chen, R. , and B. , Long membrane helices and short loops predicted less accurately, Protein Science, vol.20, issue.12, pp.2766-2773, 2002.
DOI : 10.1110/ps.0214602

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2373740

C. P. Chen, R. , and B. , State-of-the-art in membrane protein prediction, Appl Bioinformatics, vol.1, pp.21-35, 2002.

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. Caillez, T. L. Blundell, L. , and S. C. , Properties of polyproline II, a secondary structure element implicated in protein-protein interactions, Proteins: Structure, Function, and Bioinformatics, vol.179, issue.4, pp.880-892, 2005.
DOI : 10.1002/prot.20327

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, 2005.
DOI : 10.1186/1471-2105-6-S4-S8

URL : http://doi.org/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

J. M. Cuthbertson, D. A. Doyle, and M. S. Sansom, Transmembrane helix prediction: a comparative evaluation and analysis, Protein Engineering Design and Selection, vol.18, issue.6, pp.295-308, 2005.
DOI : 10.1093/protein/gzi032

A. G. De-brevern, New assessment of Protein Blocks, In Silico Biology, vol.5, pp.283-289, 2005.

A. G. De-brevern, Editorial [Hot Topic: In Silico (Guest Editor: Alexandre G. de Brevern)], Infectious Disorders - Drug Targets, vol.9, issue.3, pp.246-247, 2009.
DOI : 10.2174/1871526510909030246

A. G. De-brevern, L. Autin, Y. Colin, O. Bertrand, and C. Etchebest, In Silico Studies on DARC, silico studies on DARC, pp.289-303, 2009.
DOI : 10.2174/1871526510909030289

URL : https://hal.archives-ouvertes.fr/inserm-00366309

A. G. De-brevern, C. Etchebest, C. Benros, and S. Hazout, ???Pinning strategy???: a novel approach for predicting the backbone structure in terms of protein blocks from sequence, Journal of Biosciences, vol.289, issue.1, pp.51-70, 2007.
DOI : 10.1007/s12038-007-0006-3

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, 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

C. De-graaf and D. And-rognan, Customizing G Protein-Coupled Receptor Models for Structure-Based Virtual Screening, Current Pharmaceutical Design, vol.15, issue.35, pp.4026-4048, 2009.
DOI : 10.2174/138161209789824786

M. R. De-planque, J. A. Kruijtzer, R. M. Liskamp, D. Marsh, D. V. Greathouse et al., Different Membrane Anchoring Positions of Tryptophan and Lysine in Synthetic Transmembrane ??-Helical Peptides, Journal of Biological Chemistry, vol.274, issue.30, pp.20839-20846, 1999.
DOI : 10.1074/jbc.274.30.20839

W. L. Delano, The PyMOL Molecular Graphics System DeLano Scientific, 2002.

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

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

A. Elofsson, V. Heijne, and G. , Membrane Protein Structure: Prediction versus Reality, Annual Review of Biochemistry, vol.76, issue.1, pp.125-140, 2007.
DOI : 10.1146/annurev.biochem.76.052705.163539

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

A. Enosh, S. J. Fleishman, N. Ben-tal, and D. Halperin, Assigning transmembrane segments to helices in intermediate-resolution structures, Bioinformatics, vol.20, issue.Suppl 1, pp.122-129, 2004.
DOI : 10.1093/bioinformatics/bth939

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/20/suppl_1/i122

C. Etchebest, C. Benros, S. Hazout, and A. G. De-brevern, A structural alphabet for local protein structures: Improved prediction methods, Proteins: Structure, Function, and Bioinformatics, vol.20, issue.4, pp.810-827, 2005.
DOI : 10.1002/prot.20458

URL : https://hal.archives-ouvertes.fr/inserm-00143564

S. Faham, D. Yang, E. Bare, S. Yohannan, J. P. Whitelegge et al., Side-chain Contributions to Membrane Protein Structure and Stability, Journal of Molecular Biology, vol.335, issue.1, pp.297-305, 2004.
DOI : 10.1016/j.jmb.2003.10.041

S. J. Fleishman and N. Ben-tal, Progress in structure prediction of ??-helical membrane proteins, Current Opinion in Structural Biology, vol.16, issue.4, pp.496-504, 2006.
DOI : 10.1016/j.sbi.2006.06.003

S. J. Fleishman, V. M. Unger, and N. Ben-tal, Transmembrane protein structures without X-rays, Trends in Biochemical Sciences, vol.31, issue.2, pp.106-113, 2006.
DOI : 10.1016/j.tibs.2005.12.005

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

N. Grigorieff, T. A. Ceska, K. H. Downing, J. M. Baldwin, H. et al., Electron-crystallographic Refinement of the Structure of Bacteriorhodopsin, Journal of Molecular Biology, vol.259, issue.3, pp.393-421, 1996.
DOI : 10.1006/jmbi.1996.0328

M. M. Gromiha and M. Suwa, Discrimination of outer membrane proteins using machine learning algorithms, Proteins: Structure, Function, and Bioinformatics, vol.46, issue.4, pp.1031-1037, 2006.
DOI : 10.1002/prot.20929

S. E. Harrington and N. Ben-tal, Structural Determinants of Transmembrane Helical Proteins, Structure, vol.17, issue.8, pp.1092-1103, 2009.
DOI : 10.1016/j.str.2009.06.009

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

R. Ihaka and R. Gentleman, R: a language for data analysis and graphics, J Comput Graph Stat, vol.5, pp.299-314, 1996.

M. Ikeda, M. Arai, D. M. Lao, and T. Shimizu, Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topologies, In Silico Biol, vol.2, pp.19-33, 2002.

M. Ikeda, M. Arai, T. Okuno, and T. Shimizu, TMPDB: a database of experimentally-characterized transmembrane topologies, Nucleic Acids Research, vol.31, issue.1, pp.406-409, 2003.
DOI : 10.1093/nar/gkg020

E. Jacoby, R. Bouhelal, M. Gerspacher, and K. Seuwen, The 7???TM G-Protein-Coupled Receptor Target Family, ChemMedChem, vol.427, issue.8, pp.761-782, 2006.
DOI : 10.1002/cmdc.200600134

D. T. Jones, Do transmembrane protein superfolds exist?, FEBS Letters, vol.272, issue.3, pp.281-285, 1998.
DOI : 10.1016/S0014-5793(98)00095-7

D. T. Jones, Protein secondary structure prediction based on position-specific scoring matrices, Journal of Molecular Biology, vol.292, issue.2, pp.195-202, 1999.
DOI : 10.1006/jmbi.1999.3091

D. T. Jones, Improving the accuracy of transmembrane protein topology prediction using evolutionary information, Bioinformatics, vol.23, issue.5, pp.538-544, 2007.
DOI : 10.1093/bioinformatics/btl677

A. P. Joseph, A. Bornot, and A. G. De-brevern, Local Structure Alphabets, Protein Structure Prediction (eds. H. Rangwala, and G. Karypis), pp. in press, 2010.
URL : https://hal.archives-ouvertes.fr/inserm-00557300

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

L. Kall, A. Krogh, and E. L. Sonnhammer, A Combined Transmembrane Topology and Signal Peptide Prediction Method, Journal of Molecular Biology, vol.338, issue.5, pp.1027-1036, 2004.
DOI : 10.1016/j.jmb.2004.03.016

L. Kall, A. Krogh, and E. L. Sonnhammer, An HMM posterior decoder for sequence feature prediction that includes homology information, Bioinformatics, vol.21, issue.Suppl 1, pp.251-257, 2005.
DOI : 10.1093/bioinformatics/bti1014

A. Kauko, K. Illergard, and A. Elofsson, Coils in the Membrane Core Are Conserved and Functionally Important, Journal of Molecular Biology, vol.380, issue.1, pp.170-180, 2008.
DOI : 10.1016/j.jmb.2008.04.052

A. Kernytsky, R. , and B. , Static benchmarking of membrane helix predictions, Nucleic Acids Research, vol.31, issue.13, pp.3642-3644, 2003.
DOI : 10.1093/nar/gkg532

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

M. Klammer, D. N. Messina, T. Schmitt, and E. L. Sonnhammer, MetaTM - a consensus method for transmembrane protein topology prediction, BMC Bioinformatics, vol.10, issue.1, p.314, 2009.
DOI : 10.1186/1471-2105-10-314

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, p.501, 2001.

H. Krishnamurthy, C. L. Piscitelli, and E. Gouaux, Unlocking the molecular secrets of sodium-coupled transporters, Nature, vol.30, issue.7245, pp.347-355, 2009.
DOI : 10.1038/nature08143

A. Krogh, B. Larsson, G. Von-heijne, and E. L. Sonnhammer, Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen, Journal of Molecular Biology, vol.305, issue.3, pp.567-580, 2001.
DOI : 10.1006/jmbi.2000.4315

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, 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

J. J. Lacapere, E. Pebay-peyroula, J. M. Neumann, and C. Etchebest, Determining membrane protein structures: still a challenge!, Trends in Biochemical Sciences, vol.32, issue.6, pp.259-270, 2007.
DOI : 10.1016/j.tibs.2007.04.001

URL : https://hal.archives-ouvertes.fr/hal-00258998

Y. Landry and J. P. Gies, Drugs and their molecular targets: an updated overview, Fundamental & Clinical Pharmacology, vol.1171, issue.1, pp.1-18, 2008.
DOI : 10.1016/j.tips.2006.12.006

URL : https://hal.archives-ouvertes.fr/hal-00246545

R. J. Law, C. Capener, M. Baaden, P. J. Bond, J. Campbell et al., Membrane protein structure quality in molecular dynamics simulation, Journal of Molecular Graphics and Modelling, vol.24, issue.2, pp.157-165, 2005.
DOI : 10.1016/j.jmgm.2005.05.006

R. Leinonen, F. G. Diez, D. Binns, W. Fleischmann, R. Lopez et al., UniProt archive, Bioinformatics, vol.20, issue.17, pp.3236-3237, 2004.
DOI : 10.1093/bioinformatics/bth191

URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/20/17/3236

A. L. Lomize, I. D. Pogozheva, M. A. Lomize, and H. I. Mosberg, Positioning of proteins in membranes: A computational approach, Protein Science, vol.77, issue.6, pp.1318-1333, 2006.
DOI : 10.1110/ps.062126106

M. A. Lomize, A. L. Lomize, I. D. Pogozheva, and H. I. Mosberg, OPM: Orientations of Proteins in Membranes database, Bioinformatics, vol.22, issue.5, pp.623-625, 2006.
DOI : 10.1093/bioinformatics/btk023

D. R. Madden, J. C. Gorga, J. L. Strominger, W. , and D. C. , The three-dimensional structure of HLA-B27 at 2.1 ?? resolution suggests a general mechanism for tight peptide binding to MHC, Cell, vol.70, issue.6, pp.1035-1048, 1992.
DOI : 10.1016/0092-8674(92)90252-8

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

P. L. Martelli, P. Fariselli, C. , and R. , An ENSEMBLE machine learning approach for the prediction of all-alpha membrane proteins, Bioinformatics, vol.19, issue.Suppl 1, pp.205-211, 2003.
DOI : 10.1093/bioinformatics/btg1027

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

S. Moller, M. D. Croning, and R. Apweiler, Evaluation of methods for the prediction of membrane spanning regions, Bioinformatics, vol.17, issue.7, pp.646-653, 2001.
DOI : 10.1093/bioinformatics/17.7.646

S. Moller, E. V. Kriventseva, and R. Apweiler, A collection of well characterised integral membrane proteins, Bioinformatics, vol.16, issue.12, pp.1159-1160, 2000.
DOI : 10.1093/bioinformatics/16.12.1159

J. P. Mornon, P. Lehn, C. , and I. , Molecular models of the open and closed states of the whole human CFTR protein, Cellular and Molecular Life Sciences, vol.25, issue.21, pp.3469-3486, 2009.
DOI : 10.1007/s00018-009-0133-0

URL : https://hal.archives-ouvertes.fr/hal-00417499

Z. E. Newby, J. D. O-'connell, F. Gruswitz, F. A. Hays, W. E. Harries et al., A general protocol for the crystallization of membrane proteins for X-ray structural investigation, Nature Protocols, vol.189, issue.5, pp.619-637, 2009.
DOI : 10.1038/nprot.2009.27

S. Newstead, S. Ferrandon, and S. Iwata, Rationalizing ??-helical membrane protein crystallization, Protein Science, vol.59, issue.3, pp.466-472, 2008.
DOI : 10.1110/ps.073263108

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2248303

J. Nilsson, B. Persson, V. Heijne, and G. , Prediction of partial membrane protein topologies using a consensus approach, Protein Science, vol.32, issue.12, pp.2974-2980, 2002.
DOI : 10.1110/ps.0226702

T. Nugent and D. T. Jones, Transmembrane protein topology prediction using support vector machines, BMC Bioinformatics, vol.10, issue.1, p.159, 2009.
DOI : 10.1186/1471-2105-10-159

URL : http://doi.org/10.1186/1471-2105-10-159

A. Oberai, Y. Ihm, S. Kim, and J. U. Bowie, A limited universe of membrane protein families and folds, Protein Science, vol.7, issue.7, pp.1723-1734, 2006.
DOI : 10.1110/ps.062109706

K. Palczewski, T. Kumasaka, T. Hori, C. A. Behnke, H. Motoshima et al., Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor, Science, vol.289, issue.5480, pp.739-745, 2000.
DOI : 10.1126/science.289.5480.739

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

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. R. Rabiner, A tutorial on hidden Markov models and selected applications in speech recognition, Proceedings of the IEEE, vol.77, issue.2, pp.257-286, 1989.
DOI : 10.1109/5.18626

H. Rangwala, C. Kauffman, and G. Karypis, svmPRAT: SVM-based Protein Residue Annotation Toolkit, BMC Bioinformatics, vol.10, issue.1, p.439, 2009.
DOI : 10.1186/1471-2105-10-439

URL : http://doi.org/10.1186/1471-2105-10-439

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

R. P. Riek, I. Rigoutsos, J. Novotny, G. , and R. M. , Non-??-helical elements modulate polytopic membrane protein architecture11Edited by G. Von Heijne, Journal of Molecular Biology, vol.306, issue.2, pp.349-362, 2001.
DOI : 10.1006/jmbi.2000.4402

I. Rigoutsos, P. Riek, R. M. Graham, and J. Novotny, Structural details (kinks and non-?? conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors, Nucleic Acids Research, vol.31, issue.15, pp.4625-4631, 2003.
DOI : 10.1093/nar/gkg639

A. Rosenhouse-dantsker and D. E. Logothetis, New Roles for a Key Glycine and Its Neighboring Residue in Potassium Channel Gating, Biophysical Journal, vol.91, issue.8, pp.2860-2873, 2006.
DOI : 10.1529/biophysj.105.080242

B. Rost, P. Fariselli, C. , and R. , Topology prediction for helical transmembrane proteins at 86% accuracy-Topology prediction at 86% accuracy, Protein Science, vol.227, issue.8, pp.1704-1718, 1996.
DOI : 10.1002/pro.5560050824

B. Rost, C. Sander, and R. Schneider, Redefining the goals of protein secondary structure prediction, Journal of Molecular Biology, vol.235, issue.1, pp.13-26, 1994.
DOI : 10.1016/S0022-2836(05)80007-5

R. Choudhury, A. Novic, and M. , Data-driven model for the prediction of protein transmembrane regions, SAR and QSAR in Environmental Research, vol.4, issue.7-8, pp.741-754, 2009.
DOI : 10.1186/1471-2105-7-189

S. Jr and J. W. , A nonlinear mapping for data structure analysis, IEEE Transactions on Computers, vol.18, pp.401-409, 1969.

C. A. Sarkar, I. Dodevski, M. Kenig, S. Dudli, A. Mohr et al., Directed evolution of a G protein-coupled receptor for expression, stability, and binding selectivity, Proceedings of the National Academy of Sciences, vol.105, issue.39, pp.14808-14813, 2008.
DOI : 10.1073/pnas.0803103105

S. Shacham, Y. Marantz, S. Bar-haim, O. Kalid, D. Warshaviak et al., PREDICT modeling and in-silico screening for G-protein coupled receptors, Proteins: Structure, Function, and Bioinformatics, vol.21, issue.2-3, pp.51-86, 2004.
DOI : 10.1002/prot.20195

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

T. J. Stevens and I. T. Arkin, Are membrane proteins ?inside-out? proteins?, Proteins: Structure, Function, and Genetics, vol.366, issue.1, pp.135-143, 1999.
DOI : 10.1002/(SICI)1097-0134(19990701)36:1<135::AID-PROT11>3.0.CO;2-I

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

W. R. Taylor, D. T. Jones, and N. M. Green, A method for ??-helical integral membrane protein fold prediction, Proteins: Structure, Function, and Genetics, vol.225, issue.3, pp.281-294, 1994.
DOI : 10.1002/prot.340180309

A. Thomas, O. Bouffioux, D. Geeurickx, and R. Brasseur, Pex, analytical tools for PDB files. I. GF-Pex: Basic file to describe a protein, Proteins: Structure, Function, and Genetics, vol.302, issue.1, pp.28-36, 2001.
DOI : 10.1002/1097-0134(20010401)43:1<28::AID-PROT1014>3.0.CO;2-M

G. E. Tusnady, Z. Dosztanyi, and I. Simon, Transmembrane proteins in the Protein Data Bank: identification and classification, Bioinformatics, vol.20, issue.17, pp.2964-2972, 2004.
DOI : 10.1093/bioinformatics/bth340

G. E. Tusnady, Z. Dosztanyi, and I. Simon, PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bank, Nucleic Acids Research, vol.33, issue.Database issue, pp.275-278, 2005.
DOI : 10.1093/nar/gki002

G. E. Tusnady, Z. Dosztanyi, and I. Simon, TMDET: web server for detecting transmembrane regions of proteins by using their 3D coordinates, Bioinformatics, vol.21, issue.7, pp.1276-1277, 2005.
DOI : 10.1093/bioinformatics/bti121

G. E. Tusnady and I. Simon, Principles governing amino acid composition of integral membrane proteins: application to topology prediction, Journal of Molecular Biology, vol.283, issue.2, pp.489-506, 1998.
DOI : 10.1006/jmbi.1998.2107

G. E. Tusnady and I. Simon, The HMMTOP transmembrane topology prediction server, Bioinformatics, vol.17, issue.9, pp.849-850, 2001.
DOI : 10.1093/bioinformatics/17.9.849

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.1869-1881, 2009.
DOI : 10.1002/pro.198

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

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

M. Tyagi, V. S. Gowri, N. Srinivasan, A. G. De-brevern, and B. Offmann, A substitution matrix for structural alphabet based on structural alignment of homologous proteins and its applications, Proteins: Structure, Function, and Bioinformatics, vol.272, issue.1, pp.32-39, 2006.
DOI : 10.1002/prot.21087

URL : https://hal.archives-ouvertes.fr/inserm-00133760

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

I. Ubarretxena-belandia and D. M. Engelman, Helical membrane proteins: diversity of functions in the context of simple architecture, Current Opinion in Structural Biology, vol.11, issue.3, pp.370-376, 2001.
DOI : 10.1016/S0959-440X(00)00217-7

. Uniprot_consortium, The Universal Protein Resource (UniProt) in 2010, Nucleic Acids Research, vol.38, issue.Database, pp.142-148, 2010.
DOI : 10.1093/nar/gkp846

N. Vaidehi, W. B. Floriano, R. Trabanino, S. E. Hall, P. Freddolino et al., Prediction of structure and function of G proteincoupled receptors, Proc Natl Acad Sci, vol.3, issue.99, pp.12622-12627, 2002.

H. Viklund and A. Elofsson, Best ??-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information, Protein Science, vol.12, issue.7, pp.1908-1917, 2004.
DOI : 10.1110/ps.04625404

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2279939

G. Von-heijne, Membrane-protein topology, Nature Reviews Molecular Cell Biology, vol.13, issue.12, pp.909-918, 2006.
DOI : 10.1038/nrm2063

G. Von-heijne and Y. Gavel, Topogenic signals in integral membrane proteins, European Journal of Biochemistry, vol.1, issue.4, pp.671-678, 1988.
DOI : 10.1146/annurev.biochem.55.1.511

E. Wallin, V. Heijne, and G. , Genome-wide analysis of integral membrane proteins from eubacterial, archaean, and eukaryotic organisms, Protein Science, vol.271, issue.4, pp.1029-1038, 1998.
DOI : 10.1002/pro.5560070420

S. H. White, The progress of membrane protein structure determination, Protein Science, vol.185, issue.7, pp.1948-1949, 2004.
DOI : 10.1110/ps.04712004

S. H. White, Biophysical dissection of membrane proteins, Nature, vol.15, issue.7245, pp.344-346, 2009.
DOI : 10.1038/nature08142

S. H. White, A. S. Ladokhin, S. Jayasinghe, and K. Hristova, How Membranes Shape Protein Structure, Journal of Biological Chemistry, vol.276, issue.35, pp.32395-32398, 2001.
DOI : 10.1074/jbc.R100008200

S. H. White, V. Heijne, and G. , Transmembrane helices before, during, and after insertion, Current Opinion in Structural Biology, vol.15, issue.4, pp.378-386, 2005.
DOI : 10.1016/j.sbi.2005.07.004

S. H. White and W. C. Wimley, MEMBRANE PROTEIN FOLDING AND STABILITY: Physical Principles, Annual Review of Biophysics and Biomolecular Structure, vol.28, issue.1, pp.319-365, 1999.
DOI : 10.1146/annurev.biophys.28.1.319

V. Yarov-yarovoy, J. Schonbrun, and D. Baker, Multipass membrane protein structure prediction using Rosetta, Proteins: Structure, Function, and Bioinformatics, vol.289, issue.5480, pp.1010-1025, 2006.
DOI : 10.1002/prot.20817

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1479309

S. Yohannan, S. Faham, D. Yang, J. P. Whitelegge, and J. U. Bowie, The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors, Proceedings of the National Academy of Sciences, vol.101, issue.4, pp.959-963, 2004.
DOI : 10.1073/pnas.0306077101

S. Yohannan, D. Yang, S. Faham, G. Boulting, J. Whitelegge et al., Proline Substitutions are not Easily Accommodated in a Membrane Protein, Journal of Molecular Biology, vol.341, issue.1, pp.1-6, 2004.
DOI : 10.1016/j.jmb.2004.06.025

A. Zemla, C. Venclovas, K. Fidelis, R. , and B. , 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

Y. Zhang, M. E. Devries, and J. Skolnick, Structure Modeling of All Identified G Protein???Coupled Receptors in the Human Genome, PLoS Computational Biology, vol.20, issue.2, p.13, 2006.
DOI : 0376-5067(1995)020[0374:RBGFA]2.0.CO;2

G. Zhao and E. London, An amino acid ???transmembrane tendency??? scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: Relationship to biological hydrophobicity, Protein Science, vol.225, issue.8, pp.1987-2001, 2006.
DOI : 10.1110/ps.062286306

H. Zhou and Y. Zhou, Predicting the topology of transmembrane helical proteins using mean burial propensity and a hidden-Markov-model-based method, Protein Science, vol.49, issue.7, pp.1547-1555, 2003.
DOI : 10.1110/ps.0305103

D. Zucic and D. Juretic, Precise annotation of transmembrane segments with Garlic -a free molecular visualization program, Croatica Chemica Acta, vol.77, pp.397-401, 2004.