, Background and presentation of the question, p.101

. .. Algorithm,

.. .. Conclusion,

. .. Work-done, 115 protein and see how each of them interact with the different predicted interfaces of

E. Dequeker, A. Laine, and . Carbone, INTerface Builder: A Fast Protein-Protein Interface Reconstruction Tool, J Chem Inf Model, vol.57, issue.11, pp.2613-2617, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01617113

C. Dequeker, E. Laine, and A. Carbone, Multiple binding sites of protein-protein interactions predicted by combining sequence analysis and molecular docking, 2018.

C. Dequeker, E. Laine, and A. Carbone, Protein partners discrimination reached with coarse-grain docking and binding sites predictions, 2018.

C. Posters, E. Dequeker, A. Laine, and . Carbone, Large scale analysis of protein interactions, Journées Ouvertes de Biologie Informatique & Mathématiques (JOBIM 2018), 2018.

C. Dequeker, E. Laine, and A. Carbone, Large scale analysis of protein interactions, Journée de Biologie Structurale, 2017.

C. Dequeker, R. Raucci, E. Laine, and A. Carbone, Large scale analysis of protein interactions, 15th European Conference on Computational Biology (ECCB 2016), 2016.

F. Corsi, C. Dequeker, E. Laine, F. Nadalin, R. Raucci et al., Large scale analysis of protein interactions, 2016.

C. Dequeker, E. Laine, and A. Carbone, Proteins and their multiple interaction sites, UPMC Young Researchers' Meeting: Modeling Complex Biological Systems, 2017.

C. Dequeker, E. Laine, and A. Carbone, Approaches and scorings for partner discrimination. MAPPING meeting, 2017.

C. Dequeker, E. Laine, and A. Carbone, Approaches and scorings for partner discrimination. Internal Seminar at the Laboratory of Computational and Quantitative Biology (LCQB), 2017.

P. Aloy and R. B. Russell, Structural systems biology: modelling protein interactions, Nature Reviews Molecular Cell Biology, vol.7, issue.3, pp.188-197, 2006.

M. R. Arkin, Y. Tang, and J. A. Wells, Small-molecule inhibitors of proteinprotein interactions: Progressing toward the reality, Chem. Biol, vol.21, issue.9, pp.1102-1114, 2014.

A. Armon, D. Graur, and N. Ben-tal, ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information11Edited by F, Cohen. J. Mol. Biol, vol.307, issue.1, pp.447-463, 2001.

T. T. Aumentado-armstrong, B. Istrate, and R. A. Murgita, Algorithmic approaches to protein-protein interaction site prediction, 2015.

A. Selim-aytuna, A. Gursoy, and O. Keskin, Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces, Bioinformatics, vol.21, issue.12, pp.2850-2855, 2005.

R. Prasad-bahadur, P. Chakrabarti, F. Rodier, and J. Janin, Dissecting subunit interfaces in homodimeric proteins, Proteins Struct. Funct. Bioinf, vol.53, issue.3, pp.708-719, 2003.

K. Bastard, C. Prevost, and M. Zacharias, Accounting for loop flexibility during protein-protein docking, Proteins, vol.62, issue.4, pp.956-969, 2006.

J. Calem, S. Bendell, T. Liu, B. Aumentado-armstrong, P. T. Istrate et al., Transient protein-protein interface prediction: datasets, features, algorithms, and the RAD-T predictor, BMC Bioinf, vol.15, issue.1, p.82, 2014.

H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat et al., The Protein Data Bank, Nucleic Acids Res, vol.28, issue.1, pp.235-242, 2000.

S. Betzi, A. Restouin, S. Opi, S. T. Arold, I. Parrot et al., Protein protein interaction inhibition (2P2I) combining high throughput and virtual screening: Application to the HIV-1 Nef protein, Proc. Natl. Acad. Sci. U.S.A, vol.104, issue.49, pp.19256-19261, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00473817

A. A. Bogan and K. S. Thorn, Anatomy of hot spots in protein interfaces, J. Mol. Biol, vol.280, issue.1, pp.1-9, 1998.

J. Andrew, R. Bordner, and . Abagyan, Statistical analysis and prediction of protein-protein interfaces, Proteins Struct. Funct. Bioinf, vol.60, issue.3, pp.353-366, 2005.

J. R. Bradford, C. J. Needham, A. J. Bulpitt, and D. R. Westhead, Insights into Protein-Protein Interfaces using a Bayesian Network Prediction Method, J. Mol. Biol, vol.362, issue.2, pp.365-386, 2006.

J. R. Bradford and D. R. Westhead, Improved prediction of protein-protein binding sites using a support vector machines approach, Bioinformatics, vol.21, issue.8, pp.1487-1494, 2005.

F. Cazals, F. Proust, R. P. Bahadur, and J. Janin, Revisiting the Voronoi Description of Protein-Protein Interfaces, Protein Sci, vol.15, issue.9, pp.2082-2092, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00796062

N. Ceres, M. Pasi, and R. Lavery, A protein solvation model based on residue burial, Journal of Chemical Theory and Computation, vol.8, issue.6, pp.2141-2144, 2012.

P. Chakrabarti and J. Janin, Dissecting protein-protein recognition sites, vol.47, pp.334-343, 2002.

H. Chen and H. Zhou, Prediction of interface residues in protein-protein complexes by a consensus neural network method: Test against NMR data, Proteins Struct. Funct. Bioinf, vol.61, issue.1, pp.21-35, 2005.

R. Chen and Z. Weng, Docking unbound proteins using shape complementarity, desolvation, and electrostatics, Proteins, vol.47, issue.3, pp.281-294, 2002.

Y. Chen, J. Xu, B. Yang, Y. Zhao, and W. He, A novel method for prediction of protein interaction sites based on integrated RBF neural networks, Comput. Biol. Med, vol.42, issue.4, pp.402-407, 2012.

G. Cheng, B. Qian, R. Samudrala, and D. Baker, Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design, Nucleic Acids Res, vol.33, issue.18, pp.5861-5867, 2005.

C. Loredana-lo-conte, J. Chothia, and . Janin, The atomic structure of protein-protein recognition sites11Edited by A. R. Fersht, J. Mol. Biol, vol.285, issue.5, pp.2177-2198, 1999.

C. Darwin, On the origin of species, p.1859

A. Sjoerd-j-de-vries and . Bonvin, Cport: a consensus interface predictor and its performance in prediction-driven docking with haddock, PloS one, vol.6, issue.3, p.17695, 2011.

C. Dequeker, E. Laine, and A. Carbone, INTerface Builder: A Fast Protein-Protein Interface Reconstruction Tool, J Chem Inf Model, vol.57, issue.11, pp.2613-2617, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01617113

C. Dominguez, R. Boelens, and A. M. Bonvin, HADDOCK: A Protein-Protein Docking Approach Based on Biochemical or Biophysical Information, J. Am. Chem. Soc, vol.125, issue.7, pp.1731-1737, 2003.

Q. Dong, X. Wang, L. Lin, and Y. Guan, Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins, BMC Bioinf, vol.8, issue.1, p.147, 2007.

A. H. Elcock and J. Andrew-mccammon, Identification of protein oligomerization states by analysis of interface conservation, Proc. Natl. Acad. Sci. U.S.A, vol.98, issue.6, pp.2990-2994, 2001.

S. Engelen, L. A. Trojan, S. Sacquin-mora, R. Lavery, and A. Carbone, Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling, PLoS Comput. Biol, vol.5, issue.1, p.1000267, 2009.
URL : https://hal.archives-ouvertes.fr/inserm-00705756

R. Esmaielbeiki, K. Krawczyk, B. Knapp, J. Nebel, and C. M. Deane, Progress and challenges in predicting protein interfaces, Briefings Bioinf, vol.17, issue.1, pp.117-131, 2016.

R. Esmaielbeiki and J. Nebel, Scoring docking conformations using predicted protein interfaces, BMC Bioinf, vol.15, issue.1, p.171, 2014.

P. Fariselli, F. Pazos, A. Valencia, and R. Casadio, Prediction of protein-protein interaction sites in heterocomplexes with neural networks, Eur. J. Biochem, vol.269, issue.5, pp.1356-1361, 2002.

J. Fernandez-recio, M. Totrov, and R. Abagyan, Identification of proteinprotein interaction sites from docking energy landscapes, J. Mol. Biol, vol.335, issue.3, pp.843-865, 2004.

X. Gallet, B. Charloteaux, A. Thomas, and R. Brasseur, A fast method to predict protein interaction sites from sequences, J. Mol. Biol, vol.302, issue.4, pp.917-926, 2000.

A. W. Ghoorah, M. D. Devignes, M. Smail-tabbone, and D. W. Ritchie, Protein Docking Using Case-Based Reasoning, Proteins, vol.81, issue.12, pp.2150-2158, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00880341

F. Glaser, D. M. Steinberg, I. A. Vakser, and N. Ben, Residue frequencies and pairing preferences at protein-protein interfaces, Proteins, vol.43, issue.2, pp.89-102, 2001.

S. Grosdidier and J. Fernández-recio, Identification of hot-spot residues in protein-protein interactions by computational docking, BMC bioinformatics, vol.9, issue.1, p.447, 2008.

L. Hakes, J. W. Pinney, D. L. Robertson, and S. C. Lovell, Protein-protein interaction networks and biology-what's the connection?, Nat. Biotechnol, vol.26, issue.1, pp.69-72, 2008.

L. H. Hartwell, J. J. Hopfield, S. Leibler, and A. W. Murray, From molecular to modular cell biology, Nature, vol.402, pp.47-52, 1999.

A. L. Hopkins, Network pharmacology: the next paradigm in drug discovery, Nat. Chem. Biol, vol.4, issue.11, p.682, 2008.

S. J. Hubbard and J. M. Thornton, Naccess. Computer Program, Department of Biochemistry and Molecular Biology, 1993.

E. L. Huttlin, L. Ting, R. J. Bruckner, F. Gebreab, M. P. Gygi et al., The Bio-Plex Network: A Systematic Exploration of the Human Interactome, Cell, vol.162, issue.2, pp.425-440, 2015.

H. Hwang, T. Vreven, J. Janin, and Z. Weng, Protein-protein docking benchmark version 4.0, Proteins, vol.78, issue.15, pp.3111-3114, 2010.

H. Hwang, T. Vreven, G. Brian, J. Pierce, Z. Hung et al., Performance of zdock and zrank in capri rounds 13-19, Proteins: Structure, Function, and Bioinformatics, vol.78, issue.15, pp.3104-3110, 2010.

H. Hwang, T. Vreven, and Z. Weng, Binding interface prediction by combining protein-protein docking results, Proteins: Structure, Function, and Bioinformatics, vol.82, issue.1, pp.57-66, 2014.

C. and A. Innis, siteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins, Nucleic Acids Res, vol.35, issue.2, pp.489-494, 2007.

S. Jones, A. Marin, and J. M. Thornton, Protein domain interfaces: characterization and comparison with oligomeric protein interfaces, Protein Eng, vol.13, issue.2, pp.77-82, 2000.

S. Jones and J. M. Thornton, Principles of protein-protein interactions, vol.93, pp.13-20, 1996.

S. Jones and J. M. Thornton, Review Principles of protein-protein interactions, Proc. Natl. Acad. Sci. USA, p.8, 1996.

S. Jones and J. M. Thornton, Prediction of protein-protein interaction sites using patch analysis, J. Mol. Biol, vol.272, issue.1, pp.133-143, 1997.

L. Panagiotis, A. M. Kastritis, and . Bonvin, Are Scoring Functions in Protein-Protein Docking Ready To Predict Interactomes? Clues from a Novel Binding Affinity Benchmark, J. Proteome Res, vol.9, issue.5, pp.2216-2225, 2010.

L. Panagiotis, I. H. Kastritis, H. Moal, Z. Hwang, P. A. Weng et al., A structure-based benchmark for protein-protein binding affinity, Protein Sci, vol.20, issue.3, pp.482-491, 2011.

R. Krause, P. Christian-von-mering, T. Bork, and . Dandekar, Shared components of protein complexes-versatile building blocks or biochemical artefacts?, Bioessays, vol.26, issue.12, pp.1333-1343, 2004.

E. Krissinel and K. Henrick, Inference of macromolecular assemblies from crystalline state, Journal of Molecular Biology, vol.372, issue.3, pp.774-797, 2007.

N. Lagarde, A. Carbone, and S. Sacquin-mora, Hidden partners: Using cross-docking calculations to predict binding sites for proteins with multiple interactions. Proteins, xx(xx):xx-xx, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02104315

E. Laine and A. Carbone, Protein Social Behavior Makes a Stronger Signal for Partner Identification than Surface Geometry, Proteins, vol.85, issue.1, pp.137-154, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01400887

E. Laine and A. Carbone, Local geometry and evolutionary conservation of protein surfaces reveal the multiple recognition patches in proteinprotein interactions, PLOS Computational Biology, vol.11, issue.12, pp.1-32, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01274084

M. A. Larkin, G. Blackshields, N. P. Brown, R. Chenna, P. A. Mcgettigan et al., Clustal W and Clustal X version 2.0, Bioinformatics, vol.23, issue.21, pp.2947-2948, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00206210

T. A. Larsen, A. J. Olson, and D. S. Goodsell, Morphology of protein-protein interfaces, Structure, vol.6, issue.4, pp.421-427, 1998.

M. F. Lensink and S. J. Wodak, Docking and scoring protein interactions: CAPRI, Proteins, vol.78, issue.15, pp.3073-3084, 2009.

F. Marc, S. J. Lensink, and . Wodak, Blind predictions of protein interfaces by docking calculations in capri, Proteins: Structure, Function, and Bioinformatics, vol.78, issue.15, pp.3085-3095, 2010.

E. D. Levy, A Simple Definition of Structural Regions in Proteins and Its Use in Analyzing Interface Evolution, J. Mol. Biol, vol.403, issue.4, pp.660-670, 2010.

B. Li, K. Feng, L. Chen, T. Huang, and Y. Cai, Prediction of Protein-Protein Interaction Sites by Random Forest Algorithm with mRMR and IFS, PLoS One, vol.7, issue.8, p.43927, 2012.

H. Li, Y. Zhou, and Z. Zhang, Competition-cooperation relationship networks characterize the competition and cooperation between proteins, Sci. Rep, vol.5, p.11619, 2015.

N. Li, Z. Sun, and F. Jiang, Prediction of protein-protein binding site by using core interface residue and support vector machine, BMC Bioinf, vol.9, issue.1, p.553, 2008.

O. Lichtarge, H. R. Bourne, and F. E. Cohen, An evolutionary trace method defines binding surfaces common to protein families, J. Mol. Biol, vol.257, issue.2, pp.342-358, 1996.

A. Lopes, S. Sacquin-mora, V. Dimitrova, E. Laine, Y. Ponty et al., Protein-Protein Interactions in a Crowded Environment: an Analysis via Cross-Docking Simulations and Evolutionary Information, PLoS Comput. Biol, vol.9, issue.12, p.1003369, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00875116

C. Simon, D. L. Lovell, and . Robertson, An Integrated View of Molecular Coevolution in Protein-Protein Interactions, Mol. Biol. Evol, vol.27, issue.11, pp.2567-2575, 2010.

B. Ma, T. Elkayam, H. Wolfson, and R. Nussinov, Protein-protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces, vol.100, pp.5772-5777, 2003.

S. Maheshwari and M. Brylinski, Across-proteome modeling of dimer structures for the bottom-up assembly of protein-protein interaction networks, BMC Bioinf, vol.18, p.257, 2017.

J. Martin and R. Lavery, Arbitrary protein-protein docking targets biologically relevant interfaces, BMC Biophys, vol.5, issue.7, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00965885

J. Martin and R. Lavery, Arbitrary protein-protein docking targets biologically relevant interfaces, BMC biophysics, vol.5, issue.1, p.7, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00965885

S. R. Mcguffee and A. H. Elcock, Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm, PLoS Comput. Biol, vol.6, issue.3, p.1000694, 2010.

M. Mezei, A new method for mapping macromolecular topography. Journal of Molecular Graphics and Modelling, vol.21, pp.463-472, 2003.

I. Mihalek, I. Res, and O. Lichtarge, A family of evolution-entropy hybrid methods for ranking protein residues by importance, J. Mol. Biol, vol.336, issue.5, pp.1265-1282, 2004.

J. Mintseris, K. Wiehe, B. Pierce, R. Anderson, R. Chen et al., Protein-Protein Docking Benchmark 2.0: an Update, Proteins, vol.60, issue.2, pp.214-216, 2005.

J. Mintseris and Z. Weng, Structure, function, and evolution of transient and obligate protein-protein interactions, vol.102, pp.10930-10935, 2005.

B. K. Mishra, A review of computer simulation of tumbling mills by the discrete element method: Part i-contact mechanics, Int. J. Min. Proc, vol.71, pp.73-95, 2003.

F. Nadalin and A. Carbone, Protein-protein interaction specificity is captured by contact preferences and interface composition, Bioinformatics, vol.34, issue.3, pp.459-468, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01596388

S. S. Negi and W. Braun, Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces, J Mol Model, vol.13, issue.11, pp.1157-1167, 2007.

H. Neuvirth, R. Raz, and G. Schreiber, ProMate: a structure based prediction program to identify the location of protein-protein binding sites, J. Mol. Biol, vol.338, issue.1, pp.181-199, 2004.

H. Neuvirth, R. Raz, and G. Schreiber, ProMate: A Structure Based Prediction Program to Identify the Location of Protein-Protein Binding Sites, J. Mol. Biol, vol.338, issue.1, pp.181-199, 2004.

I. M. Nooren, NEW EMBO MEMBER'S REVIEW: Diversity of proteinprotein interactions, The EMBO Journal, vol.22, issue.14, pp.3486-3492, 2003.

Y. Ofran and B. Rost, ISIS: interaction sites identified from sequence, Bioinformatics, vol.23, issue.2, pp.13-16, 2007.

F. Pazos, M. Helmer-citterich, G. Ausiello, and A. Valencia, Correlated mutations contain information about protein-protein interaction 11Edited by, A. R. Fersht. J. Mol. Biol, vol.271, issue.4, pp.511-523, 1997.

J. R. Perkins, I. Diboun, H. Benoit, J. G. Dessailly, C. Lees et al., Transient Protein-Protein Interactions: Structural, Functional, and Network Properties, vol.18, pp.1233-1243, 2010.

B. G. Pierce, K. Wiehe, H. Hwang, B. H. Kim, T. Vreven et al., Interactive Docking Prediction of Protein-Protein Complexes and Symmetric Multimers, Bioinformatics, vol.30, issue.12, pp.1771-1773, 2014.

T. Pupko, R. E. Bell, I. Mayrose, F. Glaser, and N. Ben-tal, Rate4Site: an algorithmic tool for the identification of functional regions, Bioinformatics, vol.18, issue.1, pp.71-77, 2002.

Z. Qiu and X. Wang, Prediction of protein-protein interaction sites using patch-based residue characterization, J. Theor. Biol, vol.293, pp.143-150, 2012.

D. Reichmann, O. Rahat, M. Cohen, H. Neuvirth, and G. Schreiber, The molecular architecture of protein-protein binding sites. Current Opinion in Structural Biology, vol.17, pp.67-76, 2007.

H. Ripoche, E. Laine, N. Ceres, and A. Carbone, JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures, Nucleic Acids Res, vol.45, issue.7, p.4278, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01417190

W. David, G. J. Ritchie, and . Kemp, Protein docking using spherical polar Fourier correlations, Proteins Struct. Funct. Bioinf, vol.39, issue.2, pp.178-194, 2000.

T. Rolland, M. Ta?an, B. Charloteaux, S. J. Pevzner, Q. Zhong et al., Cell, vol.159, issue.5, pp.1212-1226, 2014.

A. Russel, On the Tendency of Varieties to Depart Indefinitely From the Original Type. Paper on natural selection sent by Wallace to Darwin, p.1858

S. Sacquin-mora, A. Carbone, and R. Lavery, Identification of Protein Interaction Partners and Protein-Protein Interaction Sites, J. Mol. Biol, vol.382, issue.5, pp.1276-1289, 2008.

S. Sacquin-mora, E. Laforet, and R. Lavery, Locating the active sites of enzymes using mechanical properties, Proteins, vol.67, issue.2, pp.350-359, 2007.

S. Sacquin-mora and R. Lavery, Investigating the local flexibility of functional residues in hemoproteins, Biophys. J, vol.90, issue.8, pp.2706-2717, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00313391

C. E. Schindler, J. Sjoerd, M. De-vries, and . Zacharias, iATTRACT: Simultaneous global and local interface optimization for protein-protein docking refinement, Proteins Struct. Funct. Bioinf, vol.83, issue.2, pp.248-258, 2015.

J. Segura, P. F. Jones, and N. Fernandez-fuentes, Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams, BMC Bioinf, vol.12, issue.1, p.352, 2011.

J. Segura, P. F. Jones, and N. Fernandez-fuentes, A holistic in silico approach to predict functional sites in protein structures, Bioinformatics, vol.28, issue.14, pp.1845-1850, 2012.

J. A. Studier and K. J. Keppler, A note on the neighbor-joining algorithm of Saitou and Nei, Mol. Biol. Evol, vol.5, issue.6, pp.729-731, 1988.

C. Hong, T. Iwai, and P. Greil, Fast particle pair detection algorithm for particle simulations, Int. J. Mod. Phys. C, vol.10, issue.05, 1999.

S. Tonddast-navaei and J. Skolnick, Are protein-protein interfaces special regions on a protein's surface?, J Chem Phys, vol.143, issue.24, p.243149, 2015.

A. Tovchigrechko and I. A. Vakser, GRAMM-X Public Web Server For Protein-Protein Docking, Nucleic Acids Res, vol.34, pp.310-314, 2006.

C. J. Tsai, S. L. Lin, H. J. Wolfson, and R. Nussinov, Studies of proteinprotein interfaces: a statistical analysis of the hydrophobic effect, Protein Sci, vol.6, issue.1, pp.53-64, 1997.

M. Tyagi, R. Ratna, D. Thangudu, S. H. Zhang, T. Bryant et al., Homology Inference of Protein-Protein Interactions via Conserved Binding Sites, PLoS One, vol.7, issue.1, p.28896, 2012.

L. Vamparys, B. Laurent, A. Carbone, and S. Sacquin-mora, Great interactions: How binding incorrect partners can teach us about protein recognition and function, Proteins, vol.84, issue.10, pp.1408-1421, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01347160

T. Vreven, I. H. Moal, A. Vangone, B. G. Pierce, P. L. Kastritis et al., Updates to the Integrated Protein-Protein Interaction Benchmarks: Docking Benchmark Version 5 and Affinity Benchmark Version 2, J. Mol. Biol, vol.427, issue.19, pp.3031-3041, 2015.

C. Wang, P. Bradley, and D. Baker, Protein-protein docking with backbone flexibility, J. Mol. Biol, vol.373, issue.2, pp.503-519, 2007.

M. Nicholas-wass, G. Fuentes, C. Pons, F. Pazos, and A. Valencia, Towards the prediction of protein interaction partners using physical docking, Mol. Syst. Biol, vol.7, issue.1, p.469, 2011.

J. A. Wells and C. L. Mcclendon, Reaching for high-hanging fruit in drug discovery at protein-protein interfaces, Nature, vol.450, issue.7172, pp.1001-1009, 2007.

C. Li, D. Xue, . Dobbs, M. J. Alexandre, V. Bonvin et al., Computational prediction of protein interfaces: A review of data driven methods, FEBS Letters, vol.589, issue.23, pp.3516-3526, 2015.

C. Li, D. Xue, V. Dobbs, and . Honavar, HomPPI: a class of sequence homology based protein-protein interface prediction methods, BMC Bioinf, vol.12, issue.1, p.244, 2011.

C. Yan, D. Dobbs, and V. Honavar, A two-stage classifier for identification of protein-protein interface residues, Bioinformatics, vol.20, pp.371-378, 2004.

M. Zacharias, Protein-protein docking with a reduced protein model accounting for side-chain flexibility, Protein Sci, vol.12, issue.6, pp.1271-1282, 2003.

M. Zacharias, Attract: protein-protein docking in capri using a reduced protein model, Proteins: Structure, Function, and Bioinformatics, vol.60, issue.2, pp.252-256, 2005.

H. Zellner, M. Staudigel, T. Trenner, M. Bittkowski, V. Wolowski et al., Prescont: Predicting protein-protein interfaces utilizing four residue properties, Proteins Struct. Funct. Bioinf, vol.80, issue.1, pp.154-168, 2011.

L. Zhao and J. Chmielewski, Inhibiting protein-protein interactions using designed molecules, Curr. Opin. Struct. Biol, vol.15, issue.1, pp.31-34, 2005.

X. Huan, Y. Zhou, and . Shan, Prediction of protein interaction sites from sequence profile and residue neighbor list, Proteins Struct. Funct. Bioinf, vol.44, issue.3, pp.336-343, 2001.