R. D. Smith, J. B. Dunbar, P. M. Ung, E. X. Esposito, C. Y. Yang et al., CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions, Journal of Chemical Information and Modeling, vol.51, issue.9, p.2115, 2011.
DOI : 10.1021/ci200269q

T. D. Crawford, C. O. Ndubaku, H. Chen, J. W. Boggs, B. J. Bravo et al., Discovery of Selective 4-Amino-pyridopyrimidine Inhibitors of MAP4K4 Using Fragment-Based Lead Identification and Optimization, Journal of Medicinal Chemistry, vol.57, issue.8, pp.3484-500155, 1021.
DOI : 10.1021/jm500155b

N. Homeyer and H. Gohlke, FEW: A workflow tool for free energy calculations of ligand binding, Journal of Computational Chemistry, vol.130, issue.11, p.965, 2013.
DOI : 10.1002/jcc.23218

L. Wang, Y. Wu, Y. Deng, B. Kim, L. Pierce et al., Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force Field, Journal of the American Chemical Society, vol.137, issue.7, p.2695, 2015.
DOI : 10.1021/ja512751q

L. Wang, B. Berne, and R. A. Friesner, On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities, Proceedings of the National Academy of Sciences, vol.109, issue.6, p.1937, 2012.
DOI : 10.1073/pnas.1114017109

P. Popov and S. Grudinin, Knowledge of Native Protein???Protein Interfaces Is Sufficient To Construct Predictive Models for the Selection of Binding Candidates, Journal of Chemical Information and Modeling, vol.55, issue.10, p.2242, 2015.
DOI : 10.1021/acs.jcim.5b00372
URL : https://hal.archives-ouvertes.fr/hal-01229886

V. N. Maiorov and G. M. Grippen, Contact potential that recognizes the correct folding of globular proteins, Journal of Molecular Biology, vol.227, issue.3, p.876, 1992.
DOI : 10.1016/0022-2836(92)90228-C

J. Qiu and R. Elber, Atomically detailed potentials to recognize native and approximate protein structures, Proteins: Structure, Function, and Bioinformatics, vol.269, issue.4, p.44, 2005.
DOI : 10.1002/prot.20585

R. Rajgaria, S. Mcallister, and C. Floudas, distance dependent force field based on a high quality decoy set, Proteins: Structure, Function, and Bioinformatics, vol.54, issue.3, p.726, 2006.
DOI : 10.1002/prot.21149

D. Tobi and I. Bahar, Optimal design of protein docking potentials: Efficiency and limitations, Proteins: Structure, Function, and Bioinformatics, vol.280, issue.4, p.970, 2006.
DOI : 10.1002/prot.20859

D. Ravikant and R. Elber, PIE??????Efficient filters and coarse grained potentials for unbound protein??????protein docking, Proteins: Structure, Function, and Bioinformatics, vol.61, issue.2, p.400, 2010.
DOI : 10.1002/prot.22550

M. H. Chae, F. Krull, S. Lorenzen, and E. W. Knapp, Predicting protein complex geometries with a neural network, Proteins: Structure, Function, and Bioinformatics, vol.1, issue.4, p.1026, 2010.
DOI : 10.1002/prot.22626

G. Neudert and G. Klebe, fconv: format conversion, manipulation and feature computation of molecular data, Bioinformatics, vol.27, issue.7, p.1021, 2011.
DOI : 10.1093/bioinformatics/btr055

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

F. Cazals, H. Kanhere, and S. Loriot, Computing the volume of a union of balls, ACM Transactions on Mathematical Software, vol.38, issue.1, p.1, 2011.
DOI : 10.1145/2049662.2049665
URL : https://hal.archives-ouvertes.fr/hal-00849809

G. Meng, N. Arkus, M. Brenner, and V. Manoharan, The Free-Energy Landscape of Clusters of Attractive Hard Spheres, Science, vol.327, issue.5965, p.560, 2010.
DOI : 10.1126/science.1181263

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

P. Kastritis, J. Rodrigues, G. Folkers, R. Boelens, and A. , 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, p.2632, 2014.
DOI : 10.1016/j.jmb.2014.04.017

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, p.677, 2009.
DOI : 10.1002/prot.22381
URL : https://hal.archives-ouvertes.fr/hal-00796032

R. Wang, X. Fang, Y. Lu, C. Y. Yang, and S. Wang, The PDBbind Database:?? Methodologies and Updates, Journal of Medicinal Chemistry, vol.48, issue.12, p.4111, 2005.
DOI : 10.1021/jm048957q

R. Wang, X. Fang, Y. Lu, and S. Wang, The PDBbind Database:?? Collection of Binding Affinities for Protein???Ligand Complexes with Known Three-Dimensional Structures, Journal of Medicinal Chemistry, vol.47, issue.12, p.2977, 2004.
DOI : 10.1021/jm030580l

D. Barber, Bayesian reasoning and machine learning
DOI : 10.1017/CBO9780511804779

M. Kadukova and S. Grudinin, Knodle: A Support Vector Machines-Based Automatic Perception of Organic Molecules from 3D Coordinates, Journal of Chemical Information and Modeling, vol.56, issue.8, p.1410, 2016.
DOI : 10.1021/acs.jcim.5b00512
URL : https://hal.archives-ouvertes.fr/hal-01381010

D. Seeliger and B. L. De-groot, Ligand docking and binding site analysis with PyMOL and Autodock/Vina, Journal of Computer-Aided Molecular Design, vol.9, issue.1, p.417, 2010.
DOI : 10.1007/s10822-010-9352-6

N. M. O-'boyle, M. Banck, C. A. James, C. Morley, T. Vandermeersch et al., Open Babel: An open chemical toolbox, Journal of Cheminformatics, vol.3, issue.1, p.33, 2011.
DOI : 10.1093/nar/gkp324

A. Heifets and R. Lilien, LigAlign: Flexible ligand-based active site alignment and analysis, Journal of Molecular Graphics and Modelling, vol.29, issue.1, p.93, 2010.
DOI : 10.1016/j.jmgm.2010.05.005

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