U. Rester, From virtuality to reality ? Virtual screening in lead discovery and lead optimization: a medicinal chemistry perspective, Curr Opin Drug Discov Devel, vol.11, issue.4, pp.559-68, 2008.

G. Sittampalam, S. Kahl, and W. Janzen, High-throughput screening: advances in assay technologies, Current Opinion in Chemical Biology, vol.1, issue.3, pp.384-91, 1997.
DOI : 10.1016/S1367-5931(97)80078-6

T. Blundell, H. Jhoti, and C. Abell, HIGH-THROUGHPUT CRYSTALLOGRAPHY FOR LEAD DISCOVERY IN DRUG DESIGN, Nature Reviews Drug Discovery, vol.1, issue.1, pp.45-54, 2002.
DOI : 10.1038/nrd706

A. Nefzi, C. Dooley, J. Ostresh, and R. Houghten, Combinatorial chemistry: From peptides and peptidomimetics to small organic and heterocyclic compounds, Bioorganic & Medicinal Chemistry Letters, vol.8, issue.17, pp.2273-2281, 1998.
DOI : 10.1016/S0960-894X(98)00412-0

O. Sperandio, M. Miteva, F. Delfaud, and B. Villoutreix, Receptorbased computational screening of compound databases: the main docking-scoring engines, Curr Protein Pept Sci, vol.7, issue.5, pp.369-93, 2006.

B. Stockwell, Chemical genetics: ligand-based discovery of gene function, Nature Reviews Genetics, vol.1, issue.2, pp.116-141, 2000.
DOI : 10.1038/35038557

E. Esposito, A. Hopfinger, and J. Madura, Methods for Applying the Quantitative Structure-Activity Relationship Paradigm, Methods Mol Biol, vol.275, pp.131-214, 2004.
DOI : 10.1385/1-59259-802-1:131

T. Girke and L. Cheng, ChemMine. A Compound Mining Database for Chemical Genomics, PLANT PHYSIOLOGY, vol.138, issue.2, pp.573-580, 2005.
DOI : 10.1104/pp.105.062687

C. Lemmen, T. Lengauer, and G. Klebe, S:?? A Method for Fast Flexible Ligand Superposition, Journal of Medicinal Chemistry, vol.41, issue.23, pp.414502-414522, 1998.
DOI : 10.1021/jm981037l

O. Sperandio, O. Andrieu, M. Miteva, M. Vo, M. Souaille et al., MED-SuMoLig: a new ligand-based screening tool for efficient scaffolds hopping, J Chem Inf Model, issue.3, pp.471097-110, 2007.

T. Cheeseright, M. Mackey, J. Melville, and J. Vinter, FieldScreen: Virtual Screening Using Molecular Fields. Application to the DUD Data Set, Journal of Chemical Information and Modeling, vol.48, issue.11, pp.482108-482125, 2008.
DOI : 10.1021/ci800110p

S. Khedkar, A. Malde, E. Coutinho, and S. Srivastava, Pharmacophore Modeling in Drug Discovery and Development: An Overview, Medicinal Chemistry, vol.3, issue.2, pp.187-97, 2007.
DOI : 10.2174/157340607780059521

A. Jain, Ligand-Based Structural Hypotheses for Virtual Screening, Journal of Medicinal Chemistry, vol.47, issue.4, pp.947-61, 2004.
DOI : 10.1021/jm030520f

V. Escalier, J. Pothier, H. Soldano, and A. Viari, Pairwise and Multiple Identification of Three-Dimensional Common Substructures in Proteins, Journal of Computational Biology, vol.5, issue.1, pp.41-56, 1998.
DOI : 10.1089/cmb.1998.5.41

R. Sheridan, G. Mcgaughey, and W. Cornell, Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results, Journal of Computer-Aided Molecular Design, vol.11, issue.3-4, pp.3-4257, 2008.
DOI : 10.1007/s10822-008-9168-9

P. Willett, Searching Techniques for Databases of Two- and Three-Dimensional Chemical Structures, Journal of Medicinal Chemistry, vol.48, issue.13, pp.4183-99, 2005.
DOI : 10.1021/jm0582165

R. Knegtel and M. Wagener, Efficacy and selectivity in flexible database docking, Proteins: Structure, Function, and Genetics, vol.1, issue.3, pp.334-379, 1999.
DOI : 10.1002/(SICI)1097-0134(19991115)37:3<334::AID-PROT3>3.0.CO;2-9

A. Knox, M. Meegan, G. Carta, and D. Lloyd, Considerations in Compound Database Preparation???Hidden??? Impact on Virtual Screening Results, Journal of Chemical Information and Modeling, vol.45, issue.6, pp.1908-1927, 2005.
DOI : 10.1021/ci050185z

G. Mcgaughey, R. Sheridan, C. Bayly, J. Culberson, C. Kreatsoulas et al., Comparison of Topological, Shape, and Docking Methods in Virtual Screening, Journal of Chemical Information and Modeling, vol.47, issue.4, pp.1504-1523, 2007.
DOI : 10.1021/ci700052x

S. Maignan, J. Guilloteau, Y. Choi-sledeski, M. Becker, W. Ewing et al., Molecular Structures of Human Factor Xa Complexed with Ketopiperazine Inhibitors:?? Preference for a Neutral Group in the S1 Pocket, Journal of Medicinal Chemistry, vol.46, issue.5, pp.46685-90, 2003.
DOI : 10.1021/jm0203837

S. Reich, M. Melnick, J. Davies, K. Appelt, K. Lewis et al., Protein structurebased design of potent orally bioavailable, nonpeptide inhibitors of human immunodeficiency virus protease, Proc Natl Acad Sci, issue.8, pp.923298-302, 1995.

V. Stoll, K. Stewart, C. Maring, S. Muchmore, V. Giranda et al., Influenza Neuraminidase Inhibitors:?? Structure-Based Design of a Novel Inhibitor Series, Biochemistry, vol.42, issue.3, pp.42718-42745, 2003.
DOI : 10.1021/bi0205449

M. Stubbs, S. Reyda, F. Dullweber, M. Möller, G. Klebe et al., Wurziger H: pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design, Chembiochem, vol.3, pp.2-3246, 2002.

M. Miteva, S. Violas, M. Montes, D. Gomez, P. Tuffery et al., FAF-Drugs: free ADME/tox filtering of compound collections, Nucleic Acids Research, vol.34, issue.Web Server, pp.738-782, 2006.
DOI : 10.1093/nar/gkl065

URL : https://hal.archives-ouvertes.fr/inserm-00106930

M. Verdonk and M. Hartshorn, Structure-guided fragment screening for lead discovery, Curr Opin Drug Discov Devel, vol.7, issue.4, pp.404-414, 2004.

M. Miller, R. Sheridan, and S. Kearsley, SQ:?? A Program for Rapidly Producing Pharmacophorically Relevent Molecular Superpositions, Journal of Medicinal Chemistry, vol.42, issue.9, pp.1505-1519, 1999.
DOI : 10.1021/jm9806143

R. Guha, M. Howard, G. Hutchison, P. Murray-rust, H. Rzepa et al., The Blue Obelisk???Interoperability in Chemical Informatics, Journal of Chemical Information and Modeling, vol.46, issue.3
DOI : 10.1021/ci050400b