M. Cutbush and P. Mollison, The Duffy blood group system, Heredity, vol.4, issue.3, pp.383-392, 1950.
DOI : 10.1038/hdy.1950.31

E. Ikin, A. Mourant, H. Pettenkofer, and G. Blumenthal, Discovery of the Expected H??magglutinin, Anti-Fyb, Nature, vol.13, issue.4286, pp.1077-1085, 1951.
DOI : 10.1038/1681077b0

R. Sanger, R. Race, and J. Jack, The Duffy Blood Groups of New York Negroes: The Phenotype Fy (a???b???), British Journal of Haematology, vol.17, issue.4, pp.370-374, 1955.
DOI : 10.1002/ajpa.1330090202

A. De-brevern, H. Wong, C. Tournamille, C. Y. , 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. De-brevern, L. Autin, C. Y. Bertrand, O. Etchebest, and C. , 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

D. Smolarek, C. Hattab, G. Hassanzadeh-ghassabeh, S. Cochet, C. Gutiérrez et al., A recombinant dromedary antibody fragment (VHH or nanobody) directed against human Duffy Antigen Receptor for Chemokines. Cellular and Molecular Life Sciences, 2010.
URL : https://hal.archives-ouvertes.fr/inserm-00512838

T. Hadley and S. Peiper, From malaria to chemokine receptor: the emerging physiologic role of the Duffy blood group antigen, Blood, vol.89, pp.3077-91, 1997.

C. Tournamille, L. Van-kim, C. Gane, P. Cartron, J. et al., Molecular basis and PCR-DNA typing of the Fya/fyb blood group polymorphism, Human Genetics, vol.95, issue.4, pp.407-417, 1995.
DOI : 10.1007/BF00208965

C. Tournamille, F. A. Wasniowska, K. Gane, P. Lisowska, E. Cartron et al., Structure-function analysis of the extracellular domains of the Duffy antigen/receptor for chemokines: characterization of antibody and chemokine binding sites, British Journal of Haematology, vol.59, issue.6, pp.1014-1037, 2003.
DOI : 10.1016/S0165-2478(98)00121-7

C. Tournamille, Y. Colin, J. Cartron, L. Van-kim, and C. , Disruption of a GATA motif in the Duffy gene promoter abolishes erythroid gene expression in Duffy???negative individuals, Nature Genetics, vol.85, issue.2, pp.224-232, 1995.
DOI : 10.1006/geno.1994.1014

S. Peiper, Z. Wang, K. Neote, A. Martin, H. Showell et al., The Duffy antigen/receptor for chemokines (DARC) is expressed in endothelial cells of Duffy negative individuals who lack the erythrocyte receptor, Journal of Experimental Medicine, vol.181, issue.4, pp.1311-1318, 1995.
DOI : 10.1084/jem.181.4.1311

R. Horuk, A. Martin, J. Hesselgesser, T. Hadley, Z. Lu et al., The Duffy antigen receptor for chemokines: structural analysis and expression in the brain, J Leukoc Biol, vol.59, pp.29-38, 1996.

L. Miller, S. Mason, J. Dvorak, M. Mcginniss, and I. Rothman, Erythrocyte receptors for (Plasmodium knowlesi) malaria: Duffy blood group determinants, Science, vol.189, issue.4202, pp.561-564, 1975.
DOI : 10.1126/science.1145213

L. Miller, S. Mason, D. Clyde, and M. Mcginniss, in Blacks, New England Journal of Medicine, vol.295, issue.6, pp.302-306, 1976.
DOI : 10.1056/NEJM197608052950602

P. Zimmerman, I. Woolley, G. Masinde, S. Miller, D. Mcnamara et al., Emergence of FY*Anull in a Plasmodium vivax-endemic region of Papua New Guinea, Proceedings of the National Academy of Sciences, vol.96, issue.24, pp.13973-13980, 1999.
DOI : 10.1073/pnas.96.24.13973

P. Chootong, F. Ntumngia, K. Vanbuskirk, J. Xainli, J. Cole-tobian et al., Mapping Epitopes of the Plasmodium vivax Duffy Binding Protein with Naturally Acquired Inhibitory Antibodies, Infection and Immunity, vol.78, issue.3, pp.1089-95, 2010.
DOI : 10.1128/IAI.01036-09

J. Rowe, D. Opi, and T. Williams, Blood groups and malaria: fresh insights into pathogenesis and identification of targets for intervention, Current Opinion in Hematology, vol.16, issue.6, pp.480-487, 2009.
DOI : 10.1097/MOH.0b013e3283313de0

C. King, P. Michon, A. Shakri, A. Marcotty, D. Stanisic et al., Naturally acquired Duffy-binding protein-specific binding inhibitory antibodies confer protection from blood-stage Plasmodium vivax infection, Proceedings of the National Academy of Sciences, vol.105, issue.24, pp.8363-8371, 2008.
DOI : 10.1073/pnas.0800371105

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2448842

F. Souza-silva, M. Da-silva-nunes, B. Sanchez, I. Ceravolo, R. Malafronte et al., Naturally Acquired Antibodies to Plasmodium vivax Duffy Binding Protein (DBP) in Rural Brazilian Amazon, American Journal of Tropical Medicine and Hygiene, vol.82, issue.2, pp.185-93, 2010.
DOI : 10.4269/ajtmh.2010.08-0580

L. Storti-melo, W. De-souza-neiras, G. Cassiano, A. Joazeiro, C. Fontes et al., Plasmodium vivax circumsporozoite variants and Duffy blood group genotypes in the Brazilian Amazon region, Transactions of the Royal Society of Tropical Medicine and Hygiene, vol.103, issue.7, pp.672-680, 2009.
DOI : 10.1016/j.trstmh.2008.07.018

D. Menard, C. Barnadas, C. Bouchier, C. Henry-halldin, L. Gray et al., Plasmodium vivax clinical malaria is commonly observed in Duffy-negative Malagasy people, Proceedings of the National Academy of Sciences, vol.107, issue.13, pp.5967-71
DOI : 10.1073/pnas.0912496107

URL : https://hal.archives-ouvertes.fr/pasteur-00741118

M. Avril, M. Hathaway, M. Cartwright, S. Gose, D. Narum et al., Optimizing expression of the pregnancy malaria vaccine candidate, VAR2CSA in Pichia pastoris Functional and immunological characterization of a Duffy binding-like alpha domain from Plasmodium falciparum erythrocyte membrane protein 1 that mediates rosetting, Malar J. Infect Immun, vol.877, pp.3857-63, 2009.

M. Higgins, The Structure of a Chondroitin Sulfate-binding Domain Important in Placental Malaria, Journal of Biological Chemistry, vol.283, issue.32, pp.21842-21848, 2008.
DOI : 10.1074/jbc.C800086200

K. Singh, A. Gittis, P. Nguyen, D. Gowda, L. Miller et al., Structure of the DBL3x domain of pregnancy-associated malaria protein VAR2CSA complexed with chondroitin sulfate A, Nature Structural & Molecular Biology, vol.125, issue.9, pp.932-940, 2008.
DOI : 10.1038/nsmb.1479

S. Singh, R. Hora, H. Belrhali, C. Chitnis, and A. Sharma, Structural basis for Duffy recognition by the malaria parasite Duffy-binding-like domain, Nature, vol.355, issue.7077, pp.741-745, 2006.
DOI : 10.1038/nature04443

N. Tolia, E. Enemark, B. Sim, and L. Joshua-tor, Structural Basis for the EBA-175 Erythrocyte Invasion Pathway of the Malaria Parasite Plasmodium falciparum, Cell, vol.122, issue.2, pp.183-93, 2005.
DOI : 10.1016/j.cell.2005.05.033

H. Shen, R. Schuster, K. Stringer, S. Waltz, and A. Lentsch, The Duffy antigen/receptor for chemokines (DARC) regulates prostate tumor growth, The FASEB Journal, vol.20, issue.1, pp.59-64, 2006.
DOI : 10.1096/fj.05-4764com

M. Pruenster and A. Rot, Throwing light on DARC1005-8. 30. Rot A. Chemokine patterning by glycosaminoglycans and interceptors, Biochem Soc Trans. Front Biosci, vol.3415, pp.645-60, 2006.

E. Borroni, R. Bonecchi, C. Buracchi, B. Savino, A. Mantovani et al., Chemokine Decoy Receptors: New Players in Reproductive Immunology, Immunological Investigations, vol.2, issue.1, pp.483-97, 2008.
DOI : 10.1080/08820130802191318

K. Neote, D. Digregorio, J. Mak, R. Horuk, and T. Schall, Molecular cloning, functional expression, and signaling characteristics of a C-C chemokine receptor, Cell, vol.72, issue.3, pp.415-440, 1993.
DOI : 10.1016/0092-8674(93)90118-A

T. Hadley, Z. Lu, K. Wasniowska, A. Martin, S. Peiper et al., Postcapillary venule endothelial cells in kidney express a multispecific chemokine receptor that is structurally and functionally identical to the erythroid isoform, which is the Duffy blood group antigen., Journal of Clinical Investigation, vol.94, issue.3, pp.985-91, 1994.
DOI : 10.1172/JCI117465

K. Neote, J. Mak, L. Kolakowski, J. Schall, and T. , Functional and biochemical analysis of the cloned Duffy antigen: identity with the red blood cell chemokine receptor, Blood, vol.84, pp.44-52, 1994.

J. Reutershan, B. Harry, D. Chang, G. Bagby, and K. Ley, DARC on RBC limits lung injury by balancing compartmental distribution of CXC chemokines, European Journal of Immunology, vol.282, issue.6, pp.1597-607, 2009.
DOI : 10.1002/eji.200839089

M. Pruenster, L. Mudde, P. Bombosi, S. Dimitrova, M. Zsak et al., The Duffy antigen receptor for chemokines transports chemokines and supports their promigratory activity Duffy antigen receptor for chemokines and CXCL5 are essential for the recruitment of neutrophils in a multicellular model of rheumatoid arthritis synovium The Duffy antigen receptor for chemokines in acute renal failure: A facilitator of renal chemokine presentation, The duffy antigen/receptor for chemokines exists in an oligomeric form in living cells and functionally antagonizes CCR5 signaling through hetero-oligomerization, pp.101-109, 2007.

A. Lachgar, G. Jaureguiberry, L. Buenac, H. Bizzini, B. Zagury et al., Binding of HIV-1 to RBCs involves the Duffy Antigen Receptors for Chemokines (DARC), Biomedicine & Pharmacotherapy, vol.52, issue.10, pp.436-445, 1998.
DOI : 10.1016/S0753-3322(99)80021-3

W. He, S. Neil, H. Kulkarni, E. Wright, B. Agan et al., Duffy Antigen Receptor for Chemokines Mediates trans-Infection of HIV-1 from Red Blood Cells to Target Cells and Affects HIV-AIDS Susceptibility, Cell Host & Microbe, vol.4, issue.1, pp.52-62, 2008.
DOI : 10.1016/j.chom.2008.06.002

Z. Beck, B. Brown, L. Wieczorek, K. Peachman, G. Matyas et al., Human Erythrocytes Selectively Bind and Enrich Infectious HIV-1 Virions, PLoS ONE, vol.4, issue.12, p.8297, 2009.
DOI : 10.1371/journal.pone.0008297.t001

URL : http://doi.org/10.1371/journal.pone.0008297

C. Winkler, P. An, R. Johnson, G. Nelson, and G. Kirk, Expression of Duffy Antigen Receptor for Chemokines (DARC) Has No Effect on HIV-1 Acquisition or Progression to AIDS in African Americans, Cell Host & Microbe, vol.5, issue.5, pp.411-414, 2009.
DOI : 10.1016/j.chom.2009.04.010

B. Julg, S. Reddy, M. Van-der-stok, S. Kulkarni, Y. Qi et al., Lack of Duffy Antigen Receptor for Chemokines: No Influence on HIV Disease Progression in an African Treatment-Naive Population, Cell Host & Microbe, vol.5, issue.5, pp.413-418, 2009.
DOI : 10.1016/j.chom.2009.04.009

N. Walley, B. Julg, S. Dickson, J. Fellay, D. Ge et al., The Duffy Antigen Receptor for Chemokines Null Promoter Variant Does Not Influence HIV-1 Acquisition or Disease Progression, Cell Host & Microbe, vol.5, issue.5, pp.408-418, 2009.
DOI : 10.1016/j.chom.2009.04.011

L. Horton, Y. Yu, S. Zaja-milatovic, R. Strieter, and R. A. , Opposing Roles of Murine Duffy Antigen Receptor for Chemokine and Murine CXC Chemokine Receptor-2 Receptors in Murine Melanoma Tumor Growth, Cancer Research, vol.67, issue.20, pp.9791-9800, 2007.
DOI : 10.1158/0008-5472.CAN-07-0246

M. Zerfaoui, A. Naura, Y. Errami, C. Hans, B. Rezk et al., Effects of PARP-1 deficiency on airway inflammatory cell recruitment in response to LPS or TNF: differential effects on CXCR2 ligands and Duffy antigen receptor for chemokines, Journal of Leukocyte Biology, vol.86, issue.6, pp.1385-92, 2009.
DOI : 10.1189/jlb.0309183

A. Lentsch, The Duffy antigen/receptor for chemokines (DARC) and prostate cancer. A role as clear as black and white?, The FASEB Journal, vol.16, issue.9, pp.1093-1098, 2002.
DOI : 10.1096/fj.02-0066hyp

J. Wang, Z. Ou, Y. Hou, J. Luo, Z. Shen et al., Enhanced expression of Duffy antigen receptor for chemokines by breast cancer cells attenuates growth and metastasis potential, Oncogene, vol.13, issue.54, pp.7201-7212, 2006.
DOI : 10.1038/sj.onc.1209703

L. Van-kim, C. Tournamille, C. Kroviarski, Y. Cartron, J. et al., The 1.35- kb and 7.5-kb Duffy mRNA isoforms are differently regulated in various regions of brain, differ by the length of their 5' untranslated sequence, but encode the same polypeptide, Blood, vol.90, pp.2851-2854, 1997.
URL : https://hal.archives-ouvertes.fr/in2p3-00363188

C. Tournamille, Bases mol??culaires et relations structure-fonction des antig??nes de groupe sanguin Duffy: r??cepteur de chimiokines et de Plasmodium vivax, Transfusion Clinique et Biologique, vol.7, issue.5, pp.497-509, 2000.
DOI : 10.1016/S1246-7820(00)80038-5

C. Tournamille, A. Blancher, L. Van-kim, C. Gane, P. Apoil et al., Sequence, evolution and ligand binding properties of mammalian Duffy antigen/receptor for chemokines, Immunogenetics, vol.55, issue.10, pp.682-94, 2004.
DOI : 10.1007/s00251-003-0633-2

C. Tournamille, L. Van-kim, C. Gane, P. Blanchard, D. Proudfoot et al., Close Association of the First and Fourth Extracellular Domains of the Duffy Antigen/Receptor for Chemokines by a Disulfide Bond Is Required for Ligand Binding, Journal of Biological Chemistry, vol.272, issue.26, pp.16274-80, 1997.
DOI : 10.1074/jbc.272.26.16274

C. Tournamille, L. Van-kim, C. Gane, P. , L. Pennec et al., Arg89Cys substitution results in very low membrane expression of the Duffy antigen/receptor for chemokines in Fy(x) individuals, Blood, vol.92, pp.2147-56, 1998.

M. Czerwinski, J. Kern, M. Grodecka, M. Paprocka, A. Krop-watorek et al., Mutational analysis of the N-glycosylation sites of Duffy antigen/receptor for chemokines, Biochemical and Biophysical Research Communications, vol.356, issue.3, pp.816-837, 2007.
DOI : 10.1016/j.bbrc.2007.03.054

K. Wasniowska, D. Blanchard, D. Janvier, Z. Wang, S. Peiper et al., Identification of the Fy6 epitope recognized by two monoclonal antibodies in the N-terminal extracellular portion of the Duffy antigen receptor for chemokines, Molecular Immunology, vol.33, issue.11-12, pp.917-940, 1996.
DOI : 10.1016/S0161-5890(96)00056-9

B. Sim, C. Chitnis, K. Wasniowska, T. Hadley, and L. Miller, Receptor and ligand domains for invasion of erythrocytes by Plasmodium falciparum, Science, vol.264, issue.5167, pp.1941-1945, 1994.
DOI : 10.1126/science.8009226

C. Tournamille, F. A. Badaut, C. Riottot, M. Longacre, S. Cartron et al., Fine mapping of the Duffy antigen binding site for the Plasmodium vivax Duffy-binding protein, Molecular and Biochemical Parasitology, vol.144, issue.1, pp.100-103, 2005.
DOI : 10.1016/j.molbiopara.2005.04.016

A. De-brevern, Editorial [Hot Topic: In Silico (Guest Editor: Alexandre G. de Brevern)], Infectious Disorders - Drug Targets, vol.9, issue.3, pp.246-253, 2009.
DOI : 10.2174/1871526510909030246

H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat et al., The Protein Data Bank, Nucleic Acids Research, vol.28, issue.1, pp.235-277, 2000.
DOI : 10.1093/nar/28.1.235

G. Tusnady, Z. Dosztanyi, and I. Simon, PDB_TM: selection and membrane localization of transmembrane proteins in the protein data bankD275-8. 63. von Heijne G. Membrane-protein topology, Nucleic Acids Res. Nat Rev Mol Cell Biol, vol.337, pp.909-927, 2005.

K. Mcluskey, A. Roszak, Y. Zhu, and N. Isaacs, Crystal structures of all-alpha type membrane proteins, European Biophysics Journal, vol.391, issue.5, pp.723-55, 2010.
DOI : 10.1007/s00249-009-0546-6

S. Neumann, A. Fuchs, A. Mulkidjanian, and D. Frishman, Current status of membrane protein structure classification, Proteins: Structure, Function, and Bioinformatics, vol.9, issue.Part 6 Part 1, pp.1760-73, 2010.
DOI : 10.1002/prot.22692

S. White, The progress of membrane protein structure determination, Protein Science, vol.185, issue.7, pp.1948-1957, 2004.
DOI : 10.1110/ps.04712004

S. White, Biophysical dissection of membrane proteins, Nature, vol.15, issue.7245, pp.344-350, 2009.
DOI : 10.1038/nature08142

S. Newstead, S. Ferrandon, and S. Iwata, Rationalizing ??-helical membrane protein crystallization, Protein Science, vol.59, issue.3, pp.466-72, 2008.
DOI : 10.1110/ps.073263108

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

S. Harrington and N. Ben-tal, Structural determinants of transmembrane helical proteins 70. de Brevern AG. 3D-structural models of transmembrane proteins Membrane protein structure determination: from structure to function in, Structure. Methods in Molecular Biology collection NJ, vol.17, pp.1092-103, 2009.

N. Fernandez-fuentes, C. Madrid-aliste, B. Rai, J. Fajardo, and A. Fiser, M4T: a comparative protein structure modeling server, Nucleic Acids Research, vol.35, issue.Web Server, pp.363-371, 2007.
DOI : 10.1093/nar/gkm341

J. Kosinski, M. Gajda, I. Cymerman, M. Kurowski, M. Pawlowski et al., FRankenstein becomes a cyborg: The automatic recombination and realignment of fold recognition models in CASP6, Proteins: Structure, Function, and Bioinformatics, vol.13, issue.S7, pp.106-119, 2005.
DOI : 10.1002/prot.20726

K. Palczewski, T. Kumasaka, T. Hori, C. Behnke, H. Motoshima et al., Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor, Science, vol.289, issue.5480, pp.739-784, 2000.
DOI : 10.1126/science.289.5480.739

K. Wasniowska, Y. Petit-leroux, C. Tournamille, L. Van-kim, C. Cartron et al., Structural characterization of the epitope recognized by the new anti-Fy6 monoclonal antibody NaM185-2C3, Transfusion Medicine, vol.4, issue.3, pp.205-216, 2002.
DOI : 10.1016/0161-5890(92)90188-4

M. Cserzo, E. Wallin, I. Simon, G. Von-heijne, and A. Elofsson, Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method 76. von Heijne G. Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule, Protein Eng. J Mol Biol, vol.10225, pp.673-6487, 1992.

M. Claros and G. Von-heijne, TopPred II: an improved software for membrane protein structure predictions, Bioinformatics, vol.10, issue.6, pp.685-691, 1994.
DOI : 10.1093/bioinformatics/10.6.685

G. 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. Tusnady, I. Simon, A. Krogh, B. Larsson, G. Von-heijne et al., The HMMTOP transmembrane topology prediction server Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes, Bioinformatics. J Mol Biol, vol.17305, issue.80, pp.849-50567, 2001.

B. Rost, R. Casadio, P. Fariselli, and C. Sander, Transmembrane helices predicted at 95% accuracy, Protein Science, vol.227, issue.3, pp.521-554, 1995.
DOI : 10.1002/pro.5560040318

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2143072

B. Rost, P. Fariselli, and R. Casadio, Topology prediction for helical transmembrane proteins at 86% accuracy-Topology prediction at 86% accuracy, Protein Science, vol.227, issue.8, pp.1704-1722, 1996.
DOI : 10.1002/pro.5560050824

K. Hofmann and W. Stoffel, TMbase -A database of membrane spanning proteins segments, Biol Chem Hoppe-Seyler, vol.374, pp.166-175, 1993.

T. Hirokawa, S. Boon-chieng, and S. Mitaku, SOSUI: classification and secondary structure prediction system for membrane proteins, Bioinformatics, vol.14, issue.4, pp.378-387, 1998.
DOI : 10.1093/bioinformatics/14.4.378

S. Mitaku and T. Hirokawa, Physicochemical factors for discriminating between soluble and membrane proteins: hydrophobicity of helical segments and protein length, Protein Engineering Design and Selection, vol.12, issue.11, pp.953-960, 1999.
DOI : 10.1093/protein/12.11.953

S. Mitaku, T. Hirokawa, and T. Tsuji, Amphiphilicity index of polar amino acids as an aid in the characterization of amino acid preference at membrane-water interfaces, Bioinformatics, vol.18, issue.4, pp.608-624, 2002.
DOI : 10.1093/bioinformatics/18.4.608

D. Juretic, B. Lee, N. Trinajstic, and R. Williams, Conformational preference functions for predicting helices in membrane proteins, Biopolymers, vol.12, issue.2, pp.255-73, 1993.
DOI : 10.1002/bip.360330208

D. Juretic, L. Zoranic, and D. Zucic, Basic Charge Clusters and Predictions of Membrane Protein Topology, Journal of Chemical Information and Computer Sciences, vol.42, issue.3, pp.620-652, 2002.
DOI : 10.1021/ci010263s

C. Pasquier, S. Hamodrakas, V. Promponas, G. Palaios, J. Hamodrakas et al., An hierarchical artificial neural network system for the classification of transmembrane proteins A novel method for predicting transmembrane segments in proteins based on a statistical analysis of the SwissProt database: the PRED-TMR algorithm, Protein Eng. Protein Eng, vol.1212, pp.631-4381, 1999.

B. Persson and P. Argos, Prediction of Transmembrane Segments in Proteins Utilising Multiple Sequence Alignments, Journal of Molecular Biology, vol.237, issue.2, pp.182-92, 1994.
DOI : 10.1006/jmbi.1994.1220

B. Persson and P. Argos, Topology prediction of membrane proteins, Protein Sci, vol.5, pp.363-71, 1996.

D. Kihara, T. Shimizu, M. Kanehisa, C. Wang, L. Liu et al., Prediction of membrane proteins based on classification of transmembrane segments TM Finder: a prediction program for transmembrane protein segments using a combination of hydrophobicity and nonpolar phase helicity scales, Protein Eng. Protein Sci, vol.1110, pp.961-70212, 1998.

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.1547-55, 2003.
DOI : 10.1110/ps.0305103

D. Jones, W. Taylor, and J. Thornton, A Model Recognition Approach to the Prediction of All-Helical Membrane Protein Structure and Topology, Biochemistry, vol.33, issue.10, pp.3038-3087, 1994.
DOI : 10.1021/bi00176a037

D. Jones, Do transmembrane protein superfolds exist?, FEBS Letters, vol.272, issue.3, pp.281-286, 1998.
DOI : 10.1016/S0014-5793(98)00095-7

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.1908-1925, 2004.
DOI : 10.1110/ps.04625404

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

H. Shen and J. Chou, MemBrain: Improving the Accuracy of Predicting Transmembrane Helices, PLoS ONE, vol.301, issue.6, p.2399, 2008.
DOI : 10.1371/journal.pone.0002399.s004

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.303-312, 2006.
DOI : 10.1093/bioinformatics/bti784

D. 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

J. Pylouster, A. Bornot, C. Etchebest, and A. De-brevern, Influence of assignment on the prediction of transmembrane helices in protein structures. Amino Acids, 2010.
URL : https://hal.archives-ouvertes.fr/inserm-00472869

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

A. 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.271-87, 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

C. Etchebest, C. Benros, S. Hazout, and A. De-brevern, A structural alphabet for local protein structures: Improved prediction methods, Proteins: Structure, Function, and Bioinformatics, vol.20, issue.4, pp.810-837, 2005.
DOI : 10.1002/prot.20458

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

A. Sali and T. Blundell, Definition of general topological equivalence in protein structures, Journal of Molecular Biology, vol.212, issue.2, pp.403-431, 1990.
DOI : 10.1016/0022-2836(90)90134-8

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

M. Marti-renom, A. Stuart, A. Fiser, R. Sanchez, F. Melo et al., Comparative Protein Structure Modeling of Genes and Genomes, Annual Review of Biophysics and Biomolecular Structure, vol.29, issue.1, pp.291-325, 2000.
DOI : 10.1146/annurev.biophys.29.1.291

A. Canutescu, A. Shelenkov, R. Dunbrack, and J. , A graph-theory algorithm for rapid protein side-chain prediction, Protein Science, vol.311, issue.9, pp.2001-2015, 2003.
DOI : 10.1110/ps.03154503

C. Kutzner, D. Van-der-spoel, M. Fechner, E. Lindahl, U. Schmitt et al., Speeding up parallel GROMACS on high-latency networks, Journal of Computational Chemistry, vol.38, issue.12, pp.2075-84, 2007.
DOI : 10.1002/jcc.20703

URL : http://hdl.handle.net/11858/00-001M-0000-0012-E29A-0

D. Van-der-spoel, E. Lindahl, B. Hess, G. Groenhof, A. Mark et al., GROMACS: Fast, flexible, and free, Journal of Computational Chemistry, vol.26, issue.16, pp.1701-1719, 2005.
DOI : 10.1002/jcc.20291

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

S. Wu and Y. Zhang, LOMETS: A local meta-threading-server for protein structure prediction, Nucleic Acids Research, vol.35, issue.10, pp.3375-82, 2007.
DOI : 10.1093/nar/gkm251

S. Wu and Y. Zhang, MUSTER: Improving protein sequence profile-profile alignments by using multiple sources of structure information, Proteins: Structure, Function, and Bioinformatics, vol.53, issue.Suppl 6, pp.547-56, 2008.
DOI : 10.1002/prot.21945

X. Gao, D. Bu, J. Xu, and M. Li, Improving consensus contact prediction via server correlation reduction, BMC Structural Biology, vol.9, issue.1, p.28, 2009.
DOI : 10.1186/1472-6807-9-28

URL : http://doi.org/10.1186/1472-6807-9-28

J. Guo, K. Ellrott, W. Chung, D. Xu, S. Passovets et al., PROSPECT-PSPP: an automatic computational pipeline for protein structure prediction, Nucleic Acids Research, vol.32, issue.Web Server, pp.522-527, 2004.
DOI : 10.1093/nar/gkh414

H. Zhou and J. Skolnick, Protein Structure Prediction by Pro-Sp3-TASSER, Biophysical Journal, vol.96, issue.6, pp.2119-2146, 2009.
DOI : 10.1016/j.bpj.2008.12.3898

URL : http://doi.org/10.1016/j.bpj.2008.12.3898

J. Soding, Protein homology detection by HMM-HMM comparison, Bioinformatics, vol.21, issue.7, pp.951-60, 2005.
DOI : 10.1093/bioinformatics/bti125

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.519.1257

H. Zhou and Y. Zhou, SPARKS 2 and SP3 servers in CASP6, Proteins: Structure, Function, and Bioinformatics, vol.11, issue.S7, pp.152-158, 2005.
DOI : 10.1002/prot.20732

J. Shi, T. Blundell, and K. Mizuguchi, FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties11Edited by B. Honig, Journal of Molecular Biology, vol.310, issue.1, pp.243-57, 2001.
DOI : 10.1006/jmbi.2001.4762

L. Kelley and M. Sternberg, Protein structure prediction on the Web: a case study using the Phyre server, Nature Protocols, vol.5, issue.3, pp.363-71, 2009.
DOI : 10.1093/nar/gkm977

V. Jaakola, M. Griffith, M. Hanson, V. Cherezov, E. Chien et al., The 2.6 Angstrom Crystal Structure of a Human A2A Adenosine Receptor Bound to an Antagonist, Science, vol.322, issue.5905, pp.1211-1218, 2008.
DOI : 10.1126/science.1164772

G. Hoffman, P. Rahl, R. Collins, and R. Cerione, Conserved Structural Motifs in Intracellular Trafficking Pathways, Molecular Cell, vol.12, issue.3, pp.615-640, 2003.
DOI : 10.1016/j.molcel.2003.08.002

F. Dias, F. Vincent, G. Pell, J. Prates, M. Centeno et al., Insights into the Molecular Determinants of Substrate Specificity in Glycoside Hydrolase Family 5 Revealed by the Crystal Structure and Kinetics of Cellvibrio mixtus Mannosidase 5A, Journal of Biological Chemistry, vol.279, issue.24, pp.25517-25543, 2004.
DOI : 10.1074/jbc.M401647200

T. Okada, M. Sugihara, A. Bondar, M. Elstner, P. Entel et al., The Retinal Conformation and its Environment in Rhodopsin in Light of a New 2.2?? Crystal Structure, Journal of Molecular Biology, vol.342, issue.2, pp.571-83, 2004.
DOI : 10.1016/j.jmb.2004.07.044

H. Berendsen, D. Van-der-spoel, R. Van-drunen, and . Gromacs, 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

A. De-brevern, New assessment of a structural alphabet, In Silico Biol, vol.5, pp.283-292, 2005.
URL : https://hal.archives-ouvertes.fr/inserm-00132875

A. 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. De-brevern, C. Benros, R. Gautier, H. Valadie, S. Hazout et al., Local backbone structure prediction of proteins, In Silico Biol, vol.4, pp.381-387, 2004.
URL : https://hal.archives-ouvertes.fr/inserm-00132872

S. Hollup, G. Salensminde, and N. Reuter, WEBnm@: a web application for normal mode analyses of proteins, BMC Bioinformatics, vol.6, issue.1, p.52, 2005.
DOI : 10.1186/1471-2105-6-52

E. Lindahl, C. Azuara, P. Koehl, and M. Delarue, NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis, Nucleic Acids Research, vol.34, issue.Web Server, pp.52-58, 2006.
DOI : 10.1093/nar/gkl082

K. Suhre and Y. Sanejouand, ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement, Nucleic Acids Research, vol.32, issue.Web Server, pp.610-614, 2004.
DOI : 10.1093/nar/gkh368

URL : https://hal.archives-ouvertes.fr/hal-00344557

K. Suhre and Y. Sanejouand, On the potential of normal-mode analysis for solving difficult molecular-replacement problems, Acta Crystallographica Section D Biological Crystallography, vol.60, issue.4, pp.796-805, 2004.
DOI : 10.1107/S0907444904001982

URL : https://hal.archives-ouvertes.fr/hal-00344562

M. Crump, J. Gong, P. Loetscher, K. Rajarathnam, A. Amara et al., Solution structure and basis for functional activity of stromal cell-derived factor-1; dissociation of CXCR4 activation from binding and inhibition of HIV-1, The EMBO Journal, vol.16, issue.23, pp.6996-7007, 1997.
DOI : 10.1093/emboj/16.23.6996

C. Baysal and A. Atilgan, Elucidating the structural mechanisms for biological activity of the chemokine family, Proteins: Structure, Function, and Genetics, vol.264, issue.2, pp.150-60, 2001.
DOI : 10.1002/1097-0134(20010501)43:2<150::AID-PROT1027>3.0.CO;2-M

J. Fernandez-recio, M. Totrov, and R. Abagyan, ICM-DISCO docking by global energy optimization with fully flexible side-chains, Proteins: Structure, Function, and Bioinformatics, vol.10, issue.Suppl 1, pp.113-120, 2003.
DOI : 10.1002/prot.10383

S. Comeau, D. Gatchell, S. Vajda, and C. Camacho, ClusPro: a fully automated algorithm for protein-protein docking, Nucleic Acids Research, vol.32, issue.Web Server, pp.96-105, 2004.
DOI : 10.1093/nar/gkh354

S. Comeau, D. Gatchell, S. Vajda, and C. Camacho, ClusPro: an automated docking and discrimination method for the prediction of protein complexes, Bioinformatics, vol.20, issue.1, pp.45-50, 2004.
DOI : 10.1093/bioinformatics/btg371

C. Hamers-casterman, T. Atarhouch, S. Muyldermans, G. Robinson, C. Hamers et al., Naturally occurring antibodies devoid of light chains, Nature, vol.363, issue.6428, pp.446-454, 1993.
DOI : 10.1038/363446a0

S. Muyldermans, T. Baral, V. Retamozzo, D. Baetselier, P. et al., Camelid immunoglobulins and nanobody technology, Veterinary Immunology and Immunopathology, vol.128, issue.1-3, pp.178-83, 2009.
DOI : 10.1016/j.vetimm.2008.10.299

T. Baral, S. Magez, B. Stijlemans, K. Conrath, B. Vanhollebeke et al., Experimental therapy of African trypanosomiasis with a nanobody-conjugated human trypanolytic factor, Nature Medicine, vol.350, issue.5, pp.580-584, 2006.
DOI : 10.1038/nm1395

R. Abderrazek, I. Hmila, C. Vincke, Z. Benlasfar, M. Pellis et al., Identification of potent nanobodies to neutralize the most poisonous polypeptide from scorpion venom, Biochemical Journal, vol.74, issue.2, pp.263-72, 2009.
DOI : 10.1074/jbc.M806889200

URL : https://hal.archives-ouvertes.fr/pasteur-00859429

M. Dumoulin, A. Last, A. Desmyter, K. Decanniere, D. Canet et al., A camelid antibody fragment inhibits the formation of amyloid fibrils by human lysozyme, Nature, vol.424, issue.6950, pp.783-791, 2003.
DOI : 10.1038/nature01870

S. Altschul, T. Madden, A. Schaffer, J. Zhang, Z. Zhang et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-402, 1997.
DOI : 10.1093/nar/25.17.3389

D. Genst, E. Handelberg, F. Van-meirhaeghe, A. Vynck, S. Loris et al., Chemical Basis for the Affinity Maturation of a Camel Single Domain Antibody, Journal of Biological Chemistry, vol.279, issue.51, pp.53593-601, 2004.
DOI : 10.1074/jbc.M407843200

J. Wootton and S. Federhen, [33] Analysis of compositionally biased regions in sequence databases, Methods Enzymol, vol.266, pp.554-71, 1996.
DOI : 10.1016/S0076-6879(96)66035-2

K. Decanniere, T. Transue, A. Desmyter, D. Maes, S. Muyldermans et al., Degenerate interfaces in antigen-antibody complexes, Journal of Molecular Biology, vol.313, issue.3, pp.473-481, 2001.
DOI : 10.1006/jmbi.2001.5075

J. Thompson, D. Higgins, and T. Gibson, CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-80, 1994.
DOI : 10.1093/nar/22.22.4673

R. Laskowski, M. Macarthur, D. Moss, and J. Thornton, PROCHECK: a program to check the stereochemical quality of protein structures, Journal of Applied Crystallography, vol.26, issue.2, pp.283-91, 1993.
DOI : 10.1107/S0021889892009944