A multivariate approach to investigate docking parameters' effects on docking performance, J Chem Inf Model, vol.47, issue.4, pp.1673-1687, 2007. ,
Michela Spagnuolo, and Bianca Falcidieno. 3d shape matching through topological structures, Discrete Geometry for Computer Imagery, pp.194-203, 2004. ,
Molecular recognition by induced fit: how fit is the concept?, News Physiol Sci, vol.16, pp.171-173, 2001. ,
The Poisson Index: a new probabilistic model for protein ligand binding site similarity, Bioinformatics, vol.23, issue.22, pp.3001-3008, 2007. ,
DOI : 10.1093/bioinformatics/btm470
Multi-Instance Kernels, Proceedings of the Nineteenth International Conference on Machine Learning, pp.179-186, 2002. ,
SitesBase: a database for structure-based protein-ligand binding site comparisons, Nucleic Acids Research, vol.34, issue.90001, pp.231-234, 2006. ,
DOI : 10.1093/nar/gkj062
A method for localizing ligand binding pockets in protein structures, Proteins, vol.62, issue.2, pp.479-488, 2006. ,
Chemical Information in 3D Space, Journal of Chemical Information and Computer Sciences, vol.36, issue.5, pp.1030-1037, 1996. ,
DOI : 10.1021/ci960343+
Convolution Kernels on Discrete Structures, 1999. ,
Three-dimensional shape searching: state-of-the-art review and future trends, Computer-Aided Design, vol.37, issue.5, pp.509-530, 2005. ,
DOI : 10.1016/j.cad.2004.07.002
A kernel between sets of vectors, International Conference on Machine Learning (ICML), 2003. ,
Shape Variation in Protein Binding Pockets and their Ligands, Journal of Molecular Biology, vol.368, issue.1, pp.283-301, 2007. ,
DOI : 10.1016/j.jmb.2007.01.086
Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites, Bioinformatics, vol.21, issue.9, pp.1908-1916, 2005. ,
DOI : 10.1093/bioinformatics/bti315
Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations, BMC Bioinformatics, vol.9, issue.1, p.427, 2008. ,
DOI : 10.1186/1471-2105-9-427
URL : https://hal.archives-ouvertes.fr/inria-00338202
Prediction of protein-ligand interactions . docking and scoring: successes and gaps, J Med Chem, vol.49, issue.20, pp.5851-5855, 2006. ,
Gaussian docking functions, Biopolymers, vol.68, issue.1, pp.76-90, 2003. ,
Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons, Bioinformatics, vol.21, issue.10, pp.2347-2355, 2005. ,
DOI : 10.1093/bioinformatics/bti337
Oechem, version 1.3.4, openeye scientific software. website, 2005. ,
Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites, Bioinformatics, vol.24, issue.16, pp.24-105, 2008. ,
DOI : 10.1093/bioinformatics/btn263
Efficient 3D shape matching and retrieval using a concrete radialized spherical projection representation, Pattern Recognition, vol.40, issue.9, pp.2437-2452, 2007. ,
DOI : 10.1016/j.patcog.2006.12.026
URL : https://hal.archives-ouvertes.fr/hal-00758964
A Fast Flexible Docking Method using an Incremental Construction Algorithm, Journal of Molecular Biology, vol.261, issue.3, pp.470-489, 1996. ,
DOI : 10.1006/jmbi.1996.0477
MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions, Nucleic Acids Research, vol.36, issue.Web Server, pp.260-264, 2008. ,
DOI : 10.1093/nar/gkn185
A simple and fuzzy method to align and compare druggable ligand-binding sites, Proteins: Structure, Function, and Bioinformatics, vol.8, issue.Suppl 4, pp.1755-1778, 2008. ,
DOI : 10.1002/prot.21858
URL : https://hal.archives-ouvertes.fr/hal-00620777
Kernel principal component analysis, Advances in Kernel Methods -Support Vector Learning, pp.327-352, 1999. ,
DOI : 10.1007/BFb0020217
The gromos biomolecular simulation program package, J. Phys. Chem. A, vol.103, pp.3596-3607, 1999. ,
3D Model Retrieval with Spherical Harmonics and Moments, Proceedings of the 23rd DAGM-Symposium on Pattern Recognition, pp.392-397, 2001. ,
DOI : 10.1007/3-540-45404-7_52
A Critical Assessment of Docking Programs and Scoring Functions, Journal of Medicinal Chemistry, vol.49, issue.20, pp.495912-5931, 2006. ,
DOI : 10.1021/jm050362n
Multiple Graph Alignment for the Structural Analysis of Protein Active Sites, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.4, issue.2, pp.310-320, 2007. ,
DOI : 10.1109/TCBB.2007.358301
Implementation of nearest-neighbor searching in an online chemical structure search system, Journal of Chemical Information and Modeling, vol.26, issue.1, pp.36-41, 1986. ,
DOI : 10.1021/ci00049a008
Iterative point matching for registration of free-form curves and surfaces, Institut National de Recherche en Informatique et en Automatique (INRIA), 1992. ,
DOI : 10.1007/BF01427149