B. Al-lazikani, A. M. Lesk, and C. Chothia, Standard conformations for the canonical structures of immunoglobulins, Journal of Molecular Biology, vol.273, issue.4, pp.927-948, 1997.
DOI : 10.1006/jmbi.1997.1354

J. Almagro, Identification of differences in the specificity-determining residues of antibodies that recognize antigens of different size: implications for the rational design of antibody repertoires, Journal of Molecular Recognition, vol.17, issue.2, pp.132-143, 2004.
DOI : 10.1002/jmr.659

R. Bahadur, P. Chakrabarti, F. Rodier, and J. Janin, A Dissection of Specific and Non-specific Protein???Protein Interfaces, Journal of Molecular Biology, vol.336, issue.4, pp.943-955, 2004.
DOI : 10.1016/j.jmb.2003.12.073

F. D. Batista and M. S. Neuberger, Affinity Dependence of the B Cell Response to Antigen: A Threshold, a Ceiling, and the Importance of Off-Rate, Immunity, vol.8, issue.6, pp.751-759, 1998.
DOI : 10.1016/S1074-7613(00)80580-4

T. N. Bhat, G. A. Bentley, G. Boulot, M. I. Greene, D. Tello et al., Bound water molecules and conformational stabilization help mediate an antigen-antibody association., Proceedings of the National Academy of Sciences, vol.91, issue.3, pp.1089-1093, 1994.
DOI : 10.1073/pnas.91.3.1089

G. Biau and L. Devroye, Lectures on the nearest neighbor method, 2015.
DOI : 10.1007/978-3-319-25388-6
URL : https://hal.archives-ouvertes.fr/hal-01361816

B. Bouvier, R. Grunberg, M. Nilgès, and F. Cazals, Shelling the Voronoi interface of protein-protein complexes reveals patterns of residue conservation, dynamics, and composition, Proteins: Structure, Function, and Bioinformatics, vol.2, issue.3, pp.677-692, 2009.
DOI : 10.1002/prot.22381
URL : https://hal.archives-ouvertes.fr/hal-00796032

F. Cazals, Revisiting the Voronoi Description of Protein-Protein Interfaces: Algorithms, International Conference on Pattern Recognition in Bioinformatics, pp.419-430, 2010.
DOI : 10.1007/978-3-642-16001-1_36
URL : https://hal.archives-ouvertes.fr/hal-00796062

F. Cazals, F. Proust, R. Bahadur, and J. Janin, Revisiting the Voronoi description of protein-protein interfaces, Protein Science, vol.15, issue.9, pp.2082-2092, 2006.
DOI : 10.1110/ps.062245906
URL : https://hal.archives-ouvertes.fr/hal-00796062

A. Chailyan, P. Marcatili, D. Cirillo, and A. Tramontano, Structural repertoire of immunoglobulin ?? light chains, Proteins: Structure, Function, and Bioinformatics, vol.264, issue.Web Server issu, pp.1513-1524, 2011.
DOI : 10.1002/prot.22979

A. Chailyan, P. Marcatili, and A. Tramontano, The association of heavy and light chain variable domains in antibodies: implications for antigen specificity, FEBS Journal, vol.346, issue.16, pp.2782858-2866, 2011.
DOI : 10.1111/j.1742-4658.2011.08207.x

C. A. Chia-en, W. Chen, and M. K. Gilson, Ligand configurational entropy and protein binding, pp.1534-1539, 2007.

Y. Choi and C. M. Deane, Predicting antibody complementarity determining region structures without classification, Molecular BioSystems, vol.52, issue.1, pp.3327-3334, 2011.
DOI : 10.1128/mBio.00345-10

C. Chothia and A. M. Lesk, Canonical structures for the hypervariable regions of immunoglobulins, Journal of Molecular Biology, vol.196, issue.4, 1987.
DOI : 10.1016/0022-2836(87)90412-8

C. Chothia, A. M. Lesk, A. Tramontano, M. Levitt, S. J. Smith-gill et al., Conformations of immunoglobulin hypervariable regions, Nature, vol.342, issue.6252, pp.342877-883, 1989.
DOI : 10.1038/342877a0

A. V. Collis, A. P. Brouwer, and A. C. Martin, Analysis of the Antigen Combining Site: Correlations Between Length and Sequence Composition of the Hypervariable Loops and the Nature of the Antigen, Journal of Molecular Biology, vol.325, issue.2, pp.337-354, 2003.
DOI : 10.1016/S0022-2836(02)01222-6

L. J. Cooper, A. R. Shikhman, D. Glass, D. Kangisser, M. W. Cunningham et al., Role of heavy chain constant domains in antibody-antigen interaction. apparent specificity differences among streptococcal IgG antibodies expressing identical variable domains, The Journal of Immunology, vol.150, issue.6, pp.2231-2242, 1993.

L. J. Cooper, D. Robertson, R. Granzow, and N. S. Greenspan, Variable domain-identical antibodies exhibit IgG subclass-related differences in affinity and kinetic constants as determined by surface plasmon resonance, Molecular Immunology, vol.31, issue.8, pp.31577-584, 1994.
DOI : 10.1016/0161-5890(94)90165-1

J. Dunitz, Win some, lose some: enthalpy-entropy compensation in weak intermolecular interactions, Chemistry & Biology, vol.2, issue.11, pp.709-712, 1995.
DOI : 10.1016/1074-5521(95)90097-7

F. Ehrenmann, Q. Kaas, and M. Lefranc, IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF, Nucleic Acids Research, vol.38, issue.Database, pp.301-307, 2010.
DOI : 10.1093/nar/gkp946

W. J. Finlay and J. C. Almagro, Natural and man-made V-gene repertoires for antibody discovery, Frontiers in Immunology, vol.3, 2012.
DOI : 10.3389/fimmu.2012.00342

S. J. Fleishman, T. A. Whitehead, D. C. Ekiert, C. Dreyfus, J. E. Corn et al., Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin, Science, vol.332, issue.6031, pp.332816-821, 2011.
DOI : 10.1126/science.1202617

M. Gerstein, F. M. Richards-]-l, L. Guddat, Z. Shan, K. N. Fan et al., Protein geometry: volumes, areas, and distances The international tables for crystallography Intramolecular signaling upon complexation, The FASEB journal, vol.9, issue.221, pp.531-539101, 1995.

L. Györfi and A. Krzyzak, A distribution-free theory of nonparametric regression, 2002.
DOI : 10.1007/b97848

J. Janin, A minimal model of protein-protein binding affinities, Protein Science, vol.2, issue.12, pp.1813-1817, 2014.
DOI : 10.1002/pro.2560

J. Janin, R. P. Bahadur, and P. Chakrabarti, Protein???protein interaction and quaternary structure, Quarterly Reviews of Biophysics, vol.31, issue.02, pp.133-180, 2008.
DOI : 10.1073/pnas.93.19.10167

S. Jones and J. Thornton, Principles of protein-protein interactions., Proceedings of the National Academy of Sciences, vol.93, issue.1, pp.13-20, 1996.
DOI : 10.1073/pnas.93.1.13

P. L. Kastritis, I. H. Moal, H. Hwang, Z. Weng, P. A. Bates et al., A structure-based benchmark for protein-protein binding affinity, Protein Science, vol.3, issue.3, pp.482-491, 2011.
DOI : 10.1002/pro.580

P. L. Kastritis, J. P. Rodrigues, G. E. Folkers, R. Boelens, and A. M. Bonvin, Proteins Feel More Than They See: Fine-Tuning of Binding Affinity by Properties of the Non-Interacting Surface, Journal of Molecular Biology, vol.426, issue.14, pp.2632-2652, 2014.
DOI : 10.1016/j.jmb.2014.04.017

O. V. Koliasnikov, M. O. Kiral, V. G. Grigorenko, and A. M. Egorov, ANTIBODY CDR H3 MODELING RULES: EXTENSION FOR THE CASE OF ABSENCE OF ARG H94 AND ASP H101, Journal of Bioinformatics and Computational Biology, vol.04, issue.02, pp.415-424, 2006.
DOI : 10.1142/S0219720006001874

D. Kuroda, H. Shirai, M. Kobori, and H. Nakamura, Structural classification of CDR-H3 revisited: A lesson in antibody modeling, Proteins: Structure, Function, and Bioinformatics, vol.23, issue.Database issue, pp.608-620, 2008.
DOI : 10.1002/prot.22087

D. Kuroda, H. Shirai, M. Kobori, and H. Nakamura, Systematic classification of CDR-L3 in antibodies: Implications of the light chain subtypes and the VL-VH interface, Proteins: Structure, Function, and Bioinformatics, vol.94, issue.Database issue, pp.139-146, 2009.
DOI : 10.1002/prot.22230

N. F. Landolfi, A. B. Thakur, H. Fu, M. Vásquez, C. Queen et al., The Integrity of the Ball-and-Socket Joint Between V and C Domains Is Essential for Complete Activity of a Humanized Antibody, The Journal of Immunology, vol.166, issue.3, pp.1748-1754, 2001.
DOI : 10.4049/jimmunol.166.3.1748

M. Lee, P. Lloyd, X. Zhang, J. M. Schallhorn, K. Sugimoto et al., Shapes of Antibody Binding Sites:?? Qualitative and Quantitative Analyses Based on a Geomorphic Classification Scheme, The Journal of Organic Chemistry, vol.71, issue.14, pp.715082-5092, 2006.
DOI : 10.1021/jo052659z

M. Lefranc and G. Lefranc, The immunoglobulin FactsBook, 2001.

M. Lefranc, C. Pommié, M. Ruiz, V. Giudicelli, E. Foulquier et al., IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains, Developmental & Comparative Immunology, vol.27, issue.1, pp.55-77, 2003.
DOI : 10.1016/S0145-305X(02)00039-3

M. F. Lensink and S. J. Wodak, Docking, scoring, and affinity prediction in CAPRI, Proteins: Structure, Function, and Bioinformatics, vol.22, issue.12, pp.2082-2095, 2013.
DOI : 10.1002/prot.24428

A. Lesk and C. Chothia, Elbow motion in the immunoglobulins involves a molecular balland-socket joint, Nature, vol.8, issue.335, pp.188-90, 1988.

S. M. Lippow, K. D. Wittrup, and B. Tidor, Computational design of antibody-affinity improvement beyond in vivo maturation, Nature Biotechnology, vol.103, issue.10, pp.1171-1176, 2007.
DOI : 10.1038/nbt1336

L. Lo-conte, C. Chothia, and J. Janin, The atomic structure of protein-protein recognition sites11Edited by A. R. Fersht, Journal of Molecular Biology, vol.285, issue.5, pp.2177-2198, 1999.
DOI : 10.1006/jmbi.1998.2439

S. Loriot and F. Cazals, Modeling macro-molecular interfaces with Intervor, Bioinformatics, vol.26, issue.7, pp.964-965, 2010.
DOI : 10.1093/bioinformatics/btq052
URL : https://hal.archives-ouvertes.fr/hal-00849822

R. M. Maccallum, A. C. Martin, and J. M. Thornton, Antibody-antigen Interactions: Contact Analysis and Binding Site Topography, Journal of Molecular Biology, vol.262, issue.5, pp.732-745, 1996.
DOI : 10.1006/jmbi.1996.0548

N. Malod-dognin, A. Bansal, and F. Cazals, Characterizing the morphology of protein binding patches, Proteins: Structure, Function, and Bioinformatics, vol.42, issue.suppl 2, pp.2652-2665, 2012.
DOI : 10.1002/prot.24144
URL : https://hal.archives-ouvertes.fr/hal-00849793

V. Manivel, N. C. Sahoo, D. M. Salunke, and K. V. Rao, Maturation of an Antibody Response Is Governed by Modulations in Flexibility of the Antigen-Combining Site, Immunity, vol.13, issue.5, pp.611-620, 2000.
DOI : 10.1016/S1074-7613(00)00061-3

S. Marillet, P. Boudinot, and F. Cazals, High-resolution crystal structures leverage protein binding affinity predictions, Proteins: Structure, Function, and Bioinformatics, vol.32, issue.1, pp.9-20, 2015.
DOI : 10.1002/prot.24946
URL : https://hal.archives-ouvertes.fr/hal-01159641

N. Mccloskey, . Turner, . Steffner, D. Owens, and . Goldblatt, Human constant regions influence the antibody binding characteristics of mouse-human chimeric IgG subclasses, Immunology, vol.153, issue.2, pp.169-173, 1996.
DOI : 10.1111/j.1365-2567.1996.tb00001.x

G. Meng, N. Arkus, M. P. Brenner, and V. N. Manoharan, The Free-Energy Landscape of Clusters of Attractive Hard Spheres, Science, vol.327, issue.5965, pp.327560-563, 2010.
DOI : 10.1126/science.1181263

V. Morea, A. Tramontano, M. Rustici, C. Chothia, and A. M. Lesk, Conformations of the third hypervariable region in the VH domain of immunoglobulins, Journal of Molecular Biology, vol.275, issue.2, pp.269-294, 1998.
DOI : 10.1006/jmbi.1997.1442

T. Deepak, K. Nair, Z. Singh, . Siddiqui, P. Bishnu et al., Epitope recognition by diverse antibodies suggests conformational convergence in an antibody response, The Journal of Immunology, vol.168, issue.5, pp.2371-2382, 2002.

B. North, A. Lehmann, and R. L. Dunbrack, A New Clustering of Antibody CDR Loop Conformations, Journal of Molecular Biology, vol.406, issue.2, pp.228-256, 2011.
DOI : 10.1016/j.jmb.2010.10.030

F. Pedregosa, G. Varoquaux, A. Gramfort, V. Michel, B. Thirion et al., Scikit-learn: Machine learning in Python, Journal of Machine Learning Research, vol.12, pp.2825-2830, 2011.
URL : https://hal.archives-ouvertes.fr/hal-00650905

O. Pritsch, G. Hudry-clergeon, M. Buckle, Y. Pétillot, J. Bouvet et al., Can immunoglobulin CH1 constant region domain modulate antigen binding affinity of antibodies Can isotype switch modulate antigen-binding affinity and influence clonal selection? European journal of immunology, Journal of Clinical Investigation, issue.1012, pp.982235-303387, 1996.

G. Raghunathan, J. Smart, J. Williams, and J. Almagro, Antigen-binding site anatomy and somatic mutations in antibodies that recognize different types of antigens, Journal of Molecular Recognition, vol.145, issue.3, pp.103-113, 2012.
DOI : 10.1002/jmr.2158

D. Rajamani, S. Thiel, S. Vajda, and C. J. Camacho, Anchor residues in protein-protein interactions, Proceedings of the National Academy of Sciences, vol.101, issue.31, pp.11287-11292, 2004.
DOI : 10.1073/pnas.0401942101

A. Schmidt, H. Xu, A. Khan, T. O. Donnell, S. Khurana et al., Preconfiguration of the antigen-binding site during affinity maturation of a broadly neutralizing influenza virus antibody, Proceedings of the National Academy of Sciences, vol.110, issue.1, pp.264-269, 2013.
DOI : 10.1073/pnas.1218256109

H. Shirai, A. Kidera, and H. Nakamura, Structural classification of CDR-H3 in antibodies, FEBS Letters, vol.92, issue.1-2, pp.1-8, 1996.
DOI : 10.1016/S0014-5793(96)01252-5

J. Shirai, A. Kidera, and H. Nakamura, H3-rules: identification of CDR-H3 structures in antibodies, FEBS Letters, vol.16, issue.1-2, pp.188-197, 1999.
DOI : 10.1016/S0014-5793(99)00821-2

R. L. Stanfield, A. Zemla, I. Wilson, and B. Rupp, Antibody Elbow Angles are Influenced by their Light Chain Class, Journal of Molecular Biology, vol.357, issue.5, pp.1566-1574, 2006.
DOI : 10.1016/j.jmb.2006.01.023

E. J. Sundberg and R. A. Mariuzza, Molecular recognition in antibody-antigen complexes Advances in protein chemistry, pp.119-160, 2002.

M. Torres, N. Fernández-fuentes, A. Fiser, and A. Casadevall, The Immunoglobulin Heavy Chain Constant Region Affects Kinetic and Thermodynamic Parameters of Antibody Variable Region Interactions with Antigen, Journal of Biological Chemistry, vol.282, issue.18, pp.13917-13927, 2007.
DOI : 10.1074/jbc.M700661200

A. Vangone and A. Bonvin, Contacts-based prediction of binding affinity in protein?protein complexes. eLife, p.7454, 2015.

E. Vargas-madrazo, F. Lara-ochoa, and J. C. Almagro, Canonical Structure Repertoire of the Antigen-binding Site of Immunoglobulins Suggests Strong Geometrical Restrictions Associated to the Mechanism of Immune Recognition, Journal of Molecular Biology, vol.254, issue.3, pp.497-504, 1995.
DOI : 10.1006/jmbi.1995.0633

J. Xu and M. M. Davis, Diversity in the CDR3 Region of VH Is Sufficient for Most Antibody Specificities, Immunity, vol.13, issue.1, pp.37-45, 2000.
DOI : 10.1016/S1074-7613(00)00006-6

C. Li, . Xue, P. João, . Rodrigues, L. Panagiotis et al., Prodigy: a web server for predicting the binding affinity of protein-protein complexes, Bioinformatics, pp.514-2016