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

J. Janin, K. Henrick, J. Moult, T. Eyck, L. Sternberg et al., CAPRI: A Critical Assessment of PRedicted Interactions, Proteins: Structure, Function, and Genetics, vol.11, issue.1, pp.2-9, 2003.
DOI : 10.1002/prot.10381

R. Méndez, R. Leplae, L. Maria, and S. Wodak, Assessment of blind predictions of protein-protein interactions: Current status of docking methods, Proteins: Structure, Function, and Bioinformatics, vol.4, issue.Suppl 1, pp.51-67, 2003.
DOI : 10.1002/prot.10393

Y. Inbar, H. Benyamini, R. Nussinov, and H. Wolfson, Prediction of Multimolecular Assemblies by Multiple Docking, Journal of Molecular Biology, vol.349, issue.2, pp.435-447, 2005.
DOI : 10.1016/j.jmb.2005.03.039

D. Schneidman-duhovny, R. Nussinov, and H. Wolfson, Automatic prediction of protein interactions with large scale motion, Proteins: Structure, Function, and Bioinformatics, vol.60, issue.4, pp.764-773, 2007.
DOI : 10.1002/prot.21759

C. Wang, P. Bradley, and D. Baker, Protein???Protein Docking with Backbone Flexibility, Journal of Molecular Biology, vol.373, issue.2, pp.503-519, 2007.
DOI : 10.1016/j.jmb.2007.07.050

C. Dominguez, R. Boelens, and A. Bonvin, HADDOCK:?? A Protein???Protein Docking Approach Based on Biochemical or Biophysical Information, Journal of the American Chemical Society, vol.125, issue.7, pp.1731-1737, 2003.
DOI : 10.1021/ja026939x

A. Bonvin, Flexible protein???protein docking, Current Opinion in Structural Biology, vol.16, issue.2, pp.194-200, 2006.
DOI : 10.1016/j.sbi.2006.02.002

A. May and M. Zacharias, Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking, Proteins: Structure, Function, and Bioinformatics, vol.15, issue.3, pp.794-809, 2007.
DOI : 10.1002/prot.21579

K. Bastard, A. Thureau, R. Lavery, and C. Prévost, Docking macromolecules with flexible segments, Journal of Computational Chemistry, vol.221, issue.15, pp.1910-1920, 2003.
DOI : 10.1002/jcc.10329

URL : https://hal.archives-ouvertes.fr/hal-00313401

K. Bastard, C. Prévost, and M. Zacharias, Accounting for loop flexibility during protein-protein docking, Proteins: Structure, Function, and Bioinformatics, vol.14, issue.Suppl 6, pp.956-969, 2006.
DOI : 10.1002/prot.20770

M. Zacharias, Protein-protein docking with a reduced protein model accounting for side-chain flexibility, Protein Science, vol.238, issue.6, pp.1271-1282, 2003.
DOI : 10.1110/ps.0239303

P. Poulain, A. Saladin, B. Hartmann, and C. Prévost, Insights on protein-DNA recognition by coarse grain modelling, Journal of Computational Chemistry, vol.24, issue.15, pp.2582-2592, 2008.
DOI : 10.1002/jcc.21014

URL : https://hal.archives-ouvertes.fr/inserm-00320808

K. Hinsen, The molecular modeling toolkit: A new approach to molecular simulations, Journal of Computational Chemistry, vol.91, issue.2, pp.79-85, 2000.
DOI : 10.1002/(SICI)1096-987X(20000130)21:2<79::AID-JCC1>3.0.CO;2-B

A. Chowdry, K. Reynolds, M. Hanes, M. Voorhies, N. Pokala et al., An object-oriented library for computational protein design, Journal of Computational Chemistry, vol.15, issue.14, pp.2378-2388, 2007.
DOI : 10.1002/jcc.20727

S. Meyers, Effective C++: 55 Specific Ways to Improve Your Programs and Designs 3rd edition, 2005.

J. Seward and N. Nethercote, Using Valgrind to detect undefined value errors with bit-precision, Proceedings of the USENIX'05

M. Fourment and M. Gillings, A comparison of common programming languages used in bioinformatics, BMC Bioinformatics, vol.9, issue.1, p.82, 2008.
DOI : 10.1186/1471-2105-9-82

R. Yakovenko, Py++, an object-oriented framework for creating a code generator for Boost.Python library

M. Sippl and H. Stegbuchner, Superposition of three-dimensional objects: A fast and numerically stable algorithm for the calculation of the matrix of optimal rotation, Computers & Chemistry, vol.15, issue.1, pp.73-78, 1991.
DOI : 10.1016/0097-8485(91)80026-I

J. Nocedal, Updating quasi-Newton matrices with limited storage, Mathematics of Computation, vol.35, issue.151, pp.773-782, 1980.
DOI : 10.1090/S0025-5718-1980-0572855-7

D. Liu and J. Nocedal, On the limited memory BFGS method for large scale optimization, Mathematical Programming, vol.32, issue.2, pp.503-528, 1989.
DOI : 10.1007/BF01589116

M. Zacharias, ATTRACT: Protein-protein docking in CAPRI using a reduced protein model, Proteins: Structure, Function, and Bioinformatics, vol.97, issue.2, pp.252-256, 2005.
DOI : 10.1002/prot.20566

F. Van-keulen, R. Haftka, and N. Kim, Review of options for structural design sensitivity analysis. Part 1: Linear systems, Computer Methods in Applied Mechanics and Engineering, vol.194, issue.30-33, pp.3213-3243, 2005.
DOI : 10.1016/j.cma.2005.02.002

J. Martins, P. Sturdza, and J. Alonso, The complex-step derivative approximation, ACM Transactions on Mathematical Software, vol.29, issue.3, pp.245-262, 2003.
DOI : 10.1145/838250.838251

URL : https://hal.archives-ouvertes.fr/hal-01483287

D. Van-heesch, Doxygen: Source code documentation generator tool, 2008.

A. Shrake and J. Rupley, Environment and exposure to solvent of protein atoms. Lysozyme and insulin, Journal of Molecular Biology, vol.79, issue.2, pp.351-371, 1973.
DOI : 10.1016/0022-2836(73)90011-9

D. Thain, T. Tannenbaum, and M. Livny, Distributed computing in practice: the Condor experience. Concurrency ? Practice and Experience, pp.323-356, 2005.

C. Gaboriaud, J. Juanhuix, A. Gruez, M. Lacroix, C. Darnault et al., The Crystal Structure of the Globular Head of Complement Protein C1q Provides a Basis for Its Versatile Recognition Properties, Journal of Biological Chemistry, vol.278, issue.47, pp.46974-46982, 2003.
DOI : 10.1074/jbc.M307764200

T. Cheng, T. Blundell, and J. Fernandez-recio, pyDock: Electrostatics and desolvation for effective scoring of rigid-body protein-protein docking, Proteins: Structure, Function, and Bioinformatics, vol.101, issue.2, pp.503-515, 2007.
DOI : 10.1002/prot.21419

S. De-vries, A. Van-dijk, M. Krzeminski, M. Van-dijk, A. Thureau et al., HADDOCK versus HADDOCK: Publish with Bio Med Central and every scientist can read your work free of chargeBioMed Central will be the most significant development for disseminating the results of biomedical researc h in our lifetime Sir Paul Nurse, Cancer Research UK Your research papers will be: available free of charge to the entire biomedical community peer reviewed and published immediately upon acceptance cited in PubMed and archived on PubMed Central yours ? you keep the copyright Submit your manuscript here, asp BioMedcentral BMC Structural Biology, vol.99, pp.27-1472, 2009.