D. Ritchie, Recent Progress and Future Directions in Protein-Protein Docking, Current Protein & Peptide Science, vol.9, issue.1, pp.1-15, 2008.
DOI : 10.2174/138920308783565741

URL : https://hal.archives-ouvertes.fr/inria-00434268

N. Andrusier, E. Mashiach, R. Nussinov, and H. Wolfson, Principles of flexible protein-protein docking, Proteins: Structure, Function, and Bioinformatics, vol.13, issue.Web Server issu, pp.271-289, 2008.
DOI : 10.1002/prot.22170

S. Vajda and D. Kozakov, Convergence and combination of methods in protein???protein docking, Current Opinion in Structural Biology, vol.19, issue.2, pp.164-170, 2009.
DOI : 10.1016/j.sbi.2009.02.008

G. Smith and M. Sternberg, Prediction of protein???protein interactions by docking methods, Current Opinion in Structural Biology, vol.12, issue.1, pp.38-73, 2002.
DOI : 10.1016/S0959-440X(02)00285-3

E. Katchalski-katzir, Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques., Proceedings of the National Academy of Sciences, vol.89, issue.6, pp.2195-2199, 1992.
DOI : 10.1073/pnas.89.6.2195

H. Gabb, R. Jackson, and M. Sternberg, Modelling protein docking using shape complementarity, electrostatics and biochemical information, Journal of Molecular Biology, vol.272, issue.1, pp.106-120, 1997.
DOI : 10.1006/jmbi.1997.1203

R. Chen, L. Li, and Z. Weng, ZDOCK: An initial-stage protein-docking algorithm, Proteins: Structure, Function, and Genetics, vol.162, issue.1, pp.80-87, 2003.
DOI : 10.1002/prot.10389

D. Kozakov, R. Brenke, S. Comeau, and S. Vajda, PIPER: An FFT-based protein docking program with pairwise potentials, Proteins: Structure, Function, and Bioinformatics, vol.100, issue.2, pp.392-406, 2006.
DOI : 10.1002/prot.21117

J. Mintseris, Integrating statistical pair potentials into protein complex prediction, Proteins: Structure, Function, and Bioinformatics, vol.52, issue.3, pp.511-520, 2007.
DOI : 10.1002/prot.21502

J. Mandell, Protein docking using continuum electrostatics and geometric fit, Protein Engineering Design and Selection, vol.14, issue.2, pp.105-113, 2001.
DOI : 10.1093/protein/14.2.105

I. Vakser, Low-resolution docking: Prediction of complexes for underdetermined structures, Biopolymers, vol.69, issue.3, pp.455-464, 1996.
DOI : 10.1002/(SICI)1097-0282(199609)39:3<455::AID-BIP16>3.0.CO;2-A

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, pp.400-419, 2010.
DOI : 10.1002/prot.22550

R. Crowther, The Molecular Replacement Method, pp.173-178, 1972.

D. Ritchie and G. Kemp, Protein docking using spherical polar Fourier correlations, Proteins: Structure, Function, and Genetics, vol.3, issue.2, pp.178-194, 2000.
DOI : 10.1002/(SICI)1097-0134(20000501)39:2<178::AID-PROT8>3.0.CO;2-6

URL : https://hal.archives-ouvertes.fr/inria-00434273

D. Ritchie, D. Kozakov, and S. Vajda, Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions, Bioinformatics, vol.24, issue.17, pp.1865-1873, 2008.
DOI : 10.1093/bioinformatics/btn334

URL : https://hal.archives-ouvertes.fr/inria-00434264

J. Kovacs, P. Chacón, Y. Cong, E. Metwally, and W. Wriggers, Fast rotational matching of rigid bodies by fast Fourier transform acceleration of five degrees of freedom, Acta Crystallographica Section D Biological Crystallography, vol.59, issue.8, pp.1371-1376, 2003.
DOI : 10.1107/S0907444903011247

J. Garzon, FRODOCK: a new approach for fast rotational protein-protein docking, Bioinformatics, vol.25, issue.19, pp.2544-2551, 2009.
DOI : 10.1093/bioinformatics/btp447

D. Ritchie and V. Venkatraman, Ultra-fast FFT protein docking on graphics processors, Bioinformatics, vol.26, issue.19, pp.2398-2405, 2010.
DOI : 10.1093/bioinformatics/btq444

URL : https://hal.archives-ouvertes.fr/inria-00537988

P. Kostelec and D. Rockmore, FFTs on the Rotation Group, Journal of Fourier Analysis and Applications, vol.63, issue.6, pp.145-179, 2008.
DOI : 10.1007/s00041-008-9013-5

D. Kozakov, How good is automated protein docking?, Proteins: Structure, Function, and Bioinformatics, vol.70, issue.12, pp.2159-2166, 2013.
DOI : 10.1002/prot.24403

J. Gray, Protein???Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations, Journal of Molecular Biology, vol.331, issue.1, pp.281-299, 2003.
DOI : 10.1016/S0022-2836(03)00670-3

J. Driscoll and D. Healy, Computing Fourier Transforms and Convolutions on the 2-Sphere, Advances in Applied Mathematics, vol.15, issue.2, pp.202-250, 1994.
DOI : 10.1006/aama.1994.1008

D. Ritchie, High-order analytic translation matrix elements for real-space six-dimensional polar Fourier correlations, Journal of Applied Crystallography, vol.38, issue.5, pp.808-818, 2005.
DOI : 10.1107/S002188980502474X

URL : https://hal.archives-ouvertes.fr/inria-00434270

H. Hwang, T. Vreven, J. Janin, and Z. Weng, Protein-protein docking benchmark version 4.0, Proteins: Structure, Function, and Bioinformatics, vol.20, issue.Web Server issu, pp.3111-3114, 2010.
DOI : 10.1002/prot.22830

M. Frigo and S. Johnson, The Design and Implementation of FFTW3, Proceedings of the IEEE, vol.93, issue.2, pp.216-231, 2005.
DOI : 10.1109/JPROC.2004.840301

G. Chuang, D. Kozakov, R. Brenke, S. Comeau, and S. Vajda, DARS (Decoys As the Reference State) Potentials for Protein-Protein Docking, Biophysical Journal, vol.95, issue.9, pp.4217-4227, 2008.
DOI : 10.1529/biophysj.108.135814

A. Murzin, S. Brenner, T. Hubbard, and C. Chothia, SCOP: A structural classification of proteins database for the investigation of sequences and structures, Journal of Molecular Biology, vol.247, issue.4, pp.536-540, 1995.
DOI : 10.1016/S0022-2836(05)80134-2

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

H. Hwang, T. Vreven, and Z. Weng, Binding interface prediction by combining protein-protein docking results, Proteins: Structure, Function, and Bioinformatics, vol.125, issue.1, pp.57-66, 2014.
DOI : 10.1002/prot.24354

J. Fernández-recio, M. Totrov, and R. Abagyan, Identification of Protein???Protein Interaction Sites from Docking Energy Landscapes, Journal of Molecular Biology, vol.335, issue.3, pp.843-865, 2004.
DOI : 10.1016/j.jmb.2003.10.069

N. Eswar, Comparative protein structure modeling using MODELLER, Current Protocols in Bioinformatics, pp.5-6, 2006.

L. Biedenharn and J. Louck, Angular Momentum in Quantum Physics, 1981.
DOI : 10.1017/CBO9780511759888

D. Potts, J. Prestin, and A. Vollrath, A fast algorithm for nonequispaced Fourier transforms on the rotation group, Numerical Algorithms, vol.71, issue.276, pp.355-384, 2009.
DOI : 10.1007/s11075-009-9277-0

L. Rabiner, On the use of symmetry in FFT computation, IEEE Transactions on Acoustics, Speech, and Signal Processing, vol.27, issue.3, pp.233-239, 1979.
DOI : 10.1109/TASSP.1979.1163235