Une nouvelle méthode performante de classification des surfaces protéiques d'interaction: MED-SMA BIBLIOGRAPHIE [1] Liolios The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata, Nucleic Acids Res, vol.36, pp.475-484, 2008. ,
The SWISS-PROT protein sequence database: its relevance to human molecular medical research, J Mol Med, vol.75, issue.2, pp.312-318, 1997. ,
Challenges of structural genomics: Expectations and Outcomes, pp.36-41, 2003. ,
Protein Structure Initiative: getting into gear, Nature Structural & Molecular Biology, vol.14, issue.6, pp.459-460, 2007. ,
DOI : 10.1038/nsmb0607-459
The Protein Data Bank, Nucleic Acids Research, vol.28, issue.1, pp.235-277, 2000. ,
DOI : 10.1093/nar/28.1.235
Process for identifying similar 3D substructures onto 3D atomic structures and its applications. 02291407.1. CNRS Un système bioinformatique de recherche de similitudes fonctionnelles dans les structures 3D de protéines A new bioinformatic approach to detect common 3D sites in protein structures, Proteins, vol.52, pp.137-182, 2002. ,
The SuMo server: 3D search for protein functional sites, Bioinformatics, vol.21, issue.20, pp.3929-3959, 2005. ,
DOI : 10.1093/bioinformatics/bti645
URL : https://hal.archives-ouvertes.fr/hal-00313736
Molecular shape comparisons in searches for active sites and functional similarity, Protein Engineering Design and Selection, vol.11, issue.4, pp.263-77, 1998. ,
DOI : 10.1093/protein/11.4.263
A New Method to Detect Related Function Among Proteins Independent of Sequence and Fold Homology, Journal of Molecular Biology, vol.323, issue.2, pp.387-406, 2002. ,
DOI : 10.1016/S0022-2836(02)00811-2
Functional annotation strategy for protein structures, Bioinformation, vol.1, issue.9, pp.357-366, 2007. ,
DOI : 10.6026/97320630001357
URL : https://hal.archives-ouvertes.fr/inserm-00143366
MED-SuMo Applications, Infectious Disorders-Drug Targets, 2009. ,
Analysis of HSP90 related folds with MED-SuMo classification approach. Drug Design Development and Therapy, 2009. ,
URL : https://hal.archives-ouvertes.fr/inserm-00348737
Computational Fragment-Based Approach at PDB Scale by Protein Local Similarity, Journal of Chemical Information and Modeling, vol.49, issue.2, pp.280-294, 2009. ,
DOI : 10.1021/ci8003094
Finishing the euchromatic sequence of the human genome, Nature, vol.8, issue.7011, pp.931-976, 2004. ,
DOI : 10.1073/pnas.0307971100
Protein structure prediction in the postgenomic era, Current Opinion in Structural Biology, vol.10, issue.3, 2000. ,
DOI : 10.1016/S0959-440X(00)00099-3
Iterated profile searches with PSI-BLAST???a tool for discovery in protein databases, Trends in Biochemical Sciences, vol.23, issue.11, pp.444-451, 1998. ,
DOI : 10.1016/S0968-0004(98)01298-5
Hidden Markov models, Current Opinion in Structural Biology, vol.6, issue.3, pp.361-366, 1996. ,
DOI : 10.1016/S0959-440X(96)80056-X
Finding families for genomic ORFans, Bioinformatics, vol.15, issue.9, pp.759-62, 1999. ,
DOI : 10.1093/bioinformatics/15.9.759
Keynote review: Structural biology and drug discovery, Drug Discovery Today, vol.10, issue.13, pp.895-907, 2005. ,
DOI : 10.1016/S1359-6446(05)03484-7
La RMN pour comprendre les protéines, 2007. ,
ARIA2: Automated NOE assignment and data integration in NMR structure calculation, Bioinformatics, vol.23, issue.3, pp.381-383, 2007. ,
DOI : 10.1093/bioinformatics/btl589
Structure of the Histone Chaperone Asf1 Bound to the Histone H3 C-Terminal Helix and Functional Insights, Structure, vol.15, issue.2, pp.191-200, 2007. ,
DOI : 10.1016/j.str.2007.01.002
URL : https://hal.archives-ouvertes.fr/hal-00259215
The structural basis of actin filament branching by the Arp2/3 complex, The Journal of Cell Biology, vol.180, issue.5, pp.887-95, 2008. ,
DOI : 10.1016/S0960-9822(99)80218-8
The Impact of Structural Genomics: Expectations and Outcomes, Science, vol.311, issue.5759, pp.347-51, 2006. ,
DOI : 10.1126/science.1121018
Structural genomics and drug discovery: all in the family, Current Opinion in Chemical Biology, vol.12, issue.1, pp.32-41, 2008. ,
DOI : 10.1016/j.cbpa.2008.01.045
The protein data bank: A computer-based archival file for macromolecular structures, Journal of Molecular Biology, vol.112, issue.3, pp.535-577, 1977. ,
DOI : 10.1016/S0022-2836(77)80200-3
Errors in protein structures, Nature, vol.381, issue.6580, p.272, 1996. ,
DOI : 10.1038/381272a0
Structural Bioinformatics, 2003. ,
DOI : 10.1002/0471721204
Conformation of Polypeptides and Proteins, Adv Protein Chem, vol.23, pp.283-438, 1968. ,
DOI : 10.1016/S0065-3233(08)60402-7
[11] Model building and refinement practice, Methods Enzymol, vol.277, pp.208-238, 1997. ,
DOI : 10.1016/S0076-6879(97)77013-7
Free R value: a novel statistical quantity for assessing the accuracy of crystal structures, Nature, vol.355, issue.6359, pp.472-477, 1992. ,
DOI : 10.1038/355472a0
Prediction of protein B-factor profiles, Proteins: Structure, Function, and Bioinformatics, vol.50, issue.4, pp.905-917, 2005. ,
DOI : 10.1002/prot.20375
Analysis of Catalytic Residues in Enzyme Active Sites, Journal of Molecular Biology, vol.324, issue.1, pp.105-126, 2002. ,
DOI : 10.1016/S0022-2836(02)01036-7
How flexible protein structures are? New questions on the protein structure plasticity, BIOFORUM Europe, vol.11, pp.24-25, 2007. ,
URL : https://hal.archives-ouvertes.fr/inserm-00189079
Statistical and conformational analysis of the electron density of protein side chains, Proteins: Structure, Function, and Bioinformatics, vol.12, issue.Part 12, pp.279-303, 2007. ,
DOI : 10.1002/prot.21150
The PyMoL Molecular Graphics System DeLano Scientific, 2002. ,
SCOP: A structural classification of proteins database for the investigation of sequences and structures, Journal of Molecular Biology, vol.247, issue.4, pp.536-576, 1995. ,
DOI : 10.1016/S0022-2836(05)80134-2
CATH ??? a hierarchic classification of protein domain structures, Structure, vol.5, issue.8, pp.1093-108, 1997. ,
DOI : 10.1016/S0969-2126(97)00260-8
Mapping the Protein Universe, Science, vol.273, issue.5275, pp.595-603, 1996. ,
DOI : 10.1126/science.273.5275.595
The protein threading problem with sequence amino acid interaction preferences is NP-complete, "Protein Engineering, Design and Selection", vol.7, issue.9, pp.1059-68, 1994. ,
DOI : 10.1093/protein/7.9.1059
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
Protein Structure Comparison by Alignment of Distance Matrices, Journal of Molecular Biology, vol.233, issue.1, pp.123-161, 1993. ,
DOI : 10.1006/jmbi.1993.1489
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path, Protein Engineering Design and Selection, vol.11, issue.9, pp.739-786, 1998. ,
DOI : 10.1093/protein/11.9.739
The FSSP database: fold classification based on structure-structure alignment of proteins, Nucleic Acids Research, vol.24, issue.1, pp.206-215, 1996. ,
DOI : 10.1093/nar/24.1.206
A general method applicable to the search for similarities in the amino acid sequence of two proteins, Journal of Molecular Biology, vol.48, issue.3, pp.443-53, 1970. ,
DOI : 10.1016/0022-2836(70)90057-4
Protein structure alignment, Journal of Molecular Biology, vol.208, issue.1, pp.1-22, 1989. ,
DOI : 10.1016/0022-2836(89)90084-3
A method for the systematic comparison of the three-dimensional structures of proteins and some results, Acta Crystallographica Section A Foundations of Crystallography, vol.40, issue.5, pp.600-610, 1984. ,
DOI : 10.1107/S0108767384001239
Protein structural homology: a metric approach, International Journal of Peptide and Protein Research, vol.5, issue.Suppl. 2, 1986. ,
DOI : 10.1111/j.1399-3011.1986.tb03267.x
YAKUSA: A fast structural database scanning method, Proteins: Structure, Function, and Bioinformatics, vol.49, issue.Suppl 6, pp.137-51, 2005. ,
DOI : 10.1002/prot.20517
Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers, vol.33, issue.12, pp.2577-637, 1983. ,
DOI : 10.1002/bip.360221211
Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions, Acta Crystallographica Section D Biological Crystallography, vol.60, issue.12, pp.2256-68, 2004. ,
DOI : 10.1107/S0907444904026460
PROMOTIF-A program to identify and analyze structural motifs in proteins, Protein Science, vol.3, issue.2, pp.212-232, 1996. ,
DOI : 10.1002/pro.5560050204
Surprising similarities in structure comparison, Current Opinion in Structural Biology, vol.6, issue.3, pp.377-85, 1996. ,
DOI : 10.1016/S0959-440X(96)80058-3
Quantifying the Similarities within Fold Space, Journal of Molecular Biology, vol.323, issue.5, pp.909-935, 2002. ,
DOI : 10.1016/S0022-2836(02)00992-0
Hierarchical protein structure superposition using both secondary structure and atomic representations, Proc Int Conf Intell Syst Mol Biol, vol.5, pp.284-93, 1997. ,
FoldMiner and LOCK 2: protein structure comparison and motif discovery on the web, Nucleic Acids Research, vol.32, issue.Web Server, pp.536-577, 2004. ,
DOI : 10.1093/nar/gkh389
FoldMiner: Structural motif discovery using an improved superposition algorithm, Protein Science, vol.13, issue.1, pp.278-94, 2004. ,
DOI : 10.1110/ps.03239404
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2286532
: a new method for protein structure comparisons and similarity searches, Journal of Applied Crystallography, vol.33, issue.1, pp.176-183, 2000. ,
DOI : 10.1107/S0021889899012339
WHAT IF: A molecular modeling and drug design program, Journal of Molecular Graphics, vol.8, issue.1, pp.52-58, 1990. ,
DOI : 10.1016/0263-7855(90)80070-V
Flexible protein alignment and hinge detection, Proteins: Structure, Function, and Genetics, vol.335, issue.2, pp.242-56, 2002. ,
DOI : 10.1002/prot.10100
FlexProt: Alignment of Flexible Protein Structures Without a Predefinition of Hinge Regions, Journal of Computational Biology, vol.11, issue.1, pp.83-106, 2004. ,
DOI : 10.1089/106652704773416902
Improved tools for biological sequence comparison., Proceedings of the National Academy of Sciences, vol.85, issue.8, pp.2444-2452, 1988. ,
DOI : 10.1073/pnas.85.8.2444
Flexible structure alignment by chaining aligned fragment pairs allowing twists, Bioinformatics, vol.19, issue.Suppl 2, pp.246-55, 2003. ,
DOI : 10.1093/bioinformatics/btg1086
Local Protein Structures, Current Bioinformatics, vol.2, issue.3, pp.165-202, 2007. ,
DOI : 10.2174/157489307781662105
URL : https://hal.archives-ouvertes.fr/inserm-00175058
Protein structure mining using a structural alphabet, Proteins: Structure, Function, and Bioinformatics, vol.5, issue.2, pp.920-957, 2008. ,
DOI : 10.1002/prot.21776
URL : https://hal.archives-ouvertes.fr/inserm-00176443
Protein structure database search and evolutionary classification, Nucleic Acids Research, vol.34, issue.13, pp.3646-59, 2006. ,
DOI : 10.1093/nar/gkl395
URL : http://doi.org/10.1093/nar/gkl395
New assessment of a structural alphabet, In Silico Biol, vol.5, pp.283-292, 2005. ,
URL : https://hal.archives-ouvertes.fr/inserm-00132875
Bayesian probabilistic approach for predicting backbone structures in terms of protein blocks, Proteins: Structure, Function, and Genetics, vol.7, issue.3, pp.271-87, 2000. ,
DOI : 10.1002/1097-0134(20001115)41:3<271::AID-PROT10>3.0.CO;2-Z
URL : https://hal.archives-ouvertes.fr/inserm-00132821
A structural alphabet for local protein structures: Improved prediction methods, Proteins: Structure, Function, and Bioinformatics, vol.20, issue.4, pp.810-837, 2005. ,
DOI : 10.1002/prot.20458
URL : https://hal.archives-ouvertes.fr/inserm-00143564
Structural patterns in globular proteins, Nature, vol.70, issue.5561, pp.552-560, 1976. ,
DOI : 10.1038/261552a0
GHKL, an emergent ATPase/kinase superfamily, Trends in Biochemical Sciences, vol.25, issue.1, pp.24-32, 2000. ,
DOI : 10.1016/S0968-0004(99)01503-0
The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies, Nucleic Acids Research, vol.37, issue.Database, 2008. ,
DOI : 10.1093/nar/gkn877
Analysis of Domain Structural Class Using an Automated Class Assignment Protocol, Journal of Molecular Biology, vol.262, issue.2, pp.168-85, 1996. ,
DOI : 10.1006/jmbi.1996.0506
The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution, Nucleic Acids Research, vol.35, issue.Database, pp.291-298, 2007. ,
DOI : 10.1093/nar/gkl959
Prediction of protein function from protein sequence and structure, Quarterly Reviews of Biophysics, vol.36, issue.3, pp.307-347, 2003. ,
DOI : 10.1017/S0033583503003901
Exploring the structure and function paradigm, Current Opinion in Structural Biology, vol.18, issue.3, pp.394-402, 2008. ,
DOI : 10.1016/j.sbi.2008.05.007
The TIM-barrel fold: a versatile framework for efficient enzymes, FEBS Letters, vol.1, issue.3, pp.193-201, 2001. ,
DOI : 10.1016/S0014-5793(01)02236-0
The relationship between protein structure and function: a comprehensive survey with application to the yeast genome, Journal of Molecular Biology, vol.288, issue.1, pp.147-64, 1999. ,
DOI : 10.1006/jmbi.1999.2661
Hydrophobic bonding and accessible surface area in proteins, Nature, vol.76, issue.5446, pp.338-347, 1974. ,
DOI : 10.1038/248338a0
Principles of protein???protein recognition, Nature, vol.71, issue.5520, pp.705-713, 1975. ,
DOI : 10.1038/256705a0
The atomic structure of protein-protein recognition sites11Edited by A. R. Fersht, Journal of Molecular Biology, vol.285, issue.5, pp.2177-98, 1999. ,
DOI : 10.1006/jmbi.1998.2439
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
ProMate: A Structure Based Prediction Program to Identify the Location of Protein???Protein Binding Sites, Journal of Molecular Biology, vol.338, issue.1, pp.181-99, 2004. ,
DOI : 10.1016/j.jmb.2004.02.040
The structure of protein-protein recognition sites, J Biol Chem, vol.265, pp.16027-16057, 1990. ,
Hydrogen bonds and salt bridges across protein-protein interfaces, Protein Engineering Design and Selection, vol.10, issue.9, pp.999-1012, 1997. ,
DOI : 10.1093/protein/10.9.999
Bound water molecules and conformational stabilization help mediate an antigen-antibody association., Proceedings of the National Academy of Sciences, vol.91, issue.3, pp.1089-93, 1994. ,
DOI : 10.1073/pnas.91.3.1089
Hydration of protein-protein interfaces, Proteins: Structure, Function, and Bioinformatics, vol.280, issue.1, pp.36-45, 2005. ,
DOI : 10.1002/prot.20478
Dissecting protein-protein recognition sites, Proteins: Structure, Function, and Genetics, vol.11, issue.3, pp.334-377, 2002. ,
DOI : 10.1002/prot.10085
Anatomy of hot spots in protein interfaces, Journal of Molecular Biology, vol.280, issue.1, pp.1-9, 1998. ,
DOI : 10.1006/jmbi.1998.1843
Protein???protein interaction and quaternary structure, Quarterly Reviews of Biophysics, vol.31, issue.02, pp.133-80, 2008. ,
DOI : 10.1073/pnas.93.19.10167
Wet and dry interfaces: the role of solvent in protein???protein and protein???DNA recognition, Structure, vol.7, issue.12, pp.277-286, 1999. ,
DOI : 10.1016/S0969-2126(00)88333-1
The role of water in protein???DNA interactions, Current Opinion in Structural Biology, vol.7, issue.1, pp.126-160, 1997. ,
DOI : 10.1016/S0959-440X(97)80016-4
Base and base pair morphologies, helical parameters, and definitions, 1997. ,
Protein-DNA interactions: a structural analysis, Journal of Molecular Biology, vol.287, issue.5, pp.877-96, 1999. ,
DOI : 10.1006/jmbi.1999.2659
Crystal structure of a human TATA box-binding protein/TATA element complex., Proceedings of the National Academy of Sciences, vol.93, issue.10, pp.4862-4869, 1996. ,
DOI : 10.1073/pnas.93.10.4862
Annotating Nucleic Acid-Binding Function Based on Protein Structure, Journal of Molecular Biology, vol.326, issue.4, pp.1065-79, 2003. ,
DOI : 10.1016/S0022-2836(03)00031-7
Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information, Bioinformatics, vol.20, issue.4, pp.477-86, 2004. ,
DOI : 10.1093/bioinformatics/btg432
Identifying DNA-binding proteins using structural motifs and the electrostatic potential, Nucleic Acids Research, vol.32, issue.16, pp.4732-4773, 2004. ,
DOI : 10.1093/nar/gkh803
repressor and its operator DNA, Protein Science, vol.327, issue.8, pp.1276-85, 1994. ,
DOI : 10.1002/pro.5560030814
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules, Journal of Medicinal Chemistry, vol.28, issue.7, pp.849-57, 1985. ,
DOI : 10.1021/jm00145a002
An Evolutionary Trace Method Defines Binding Surfaces Common to Protein Families, Journal of Molecular Biology, vol.257, issue.2, pp.342-58, 1996. ,
DOI : 10.1006/jmbi.1996.0167
Protein interaction networks from yeast to human, Current Opinion in Structural Biology, vol.14, issue.3, pp.292-301, 2004. ,
DOI : 10.1016/j.sbi.2004.05.003
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Research, vol.25, issue.17, pp.3389-402, 1997. ,
DOI : 10.1093/nar/25.17.3389
[5] Rapid and sensitive sequence comparison with FASTP and FASTA, Methods Enzymol, vol.183, pp.63-98, 1990. ,
DOI : 10.1016/0076-6879(90)83007-V
Improving the sensitivity of the sequence profile method, Protein Science, vol.2, issue.3, pp.139-185, 1994. ,
DOI : 10.1002/pro.5560030118
Prosite: a dictionary of sites and patterns in proteins, Nucleic Acids Research, vol.19, issue.suppl, pp.2241-2246, 1991. ,
DOI : 10.1093/nar/19.suppl.2241
The Pfam Protein Families Database, Nucleic Acids Research, vol.28, issue.1, pp.263-269, 2000. ,
DOI : 10.1093/nar/28.1.263
URL : https://hal.archives-ouvertes.fr/hal-01294685
The Catalytic Site Atlas: a resource of catalytic sites and residues identified in enzymes using structural data, Nucleic Acids Research, vol.32, issue.90001, pp.129-162, 2004. ,
DOI : 10.1093/nar/gkh028
[9] Profile analysis, Methods Enzymol, vol.183, pp.146-59, 1990. ,
DOI : 10.1016/0076-6879(90)83011-W
ProRule: a new database containing functional and structural information on PROSITE profiles, Bioinformatics, vol.21, issue.21, pp.4060-4066, 2005. ,
DOI : 10.1093/bioinformatics/bti614
ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins, Nucleic Acids Research, vol.34, issue.Web Server, pp.362-367, 2006. ,
DOI : 10.1093/nar/gkl124
The ENZYME database in 2000, Nucleic Acids Research, vol.28, issue.1, pp.304-309, 2000. ,
DOI : 10.1093/nar/28.1.304
Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design, Il Farmaco, vol.57, issue.3, pp.243-51, 2002. ,
DOI : 10.1016/S0014-827X(02)01211-9
LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins, Journal of Molecular Graphics and Modelling, vol.15, issue.6, pp.359-63, 1997. ,
DOI : 10.1016/S1093-3263(98)00002-3
Fast prediction and visualization of protein binding pockets with PASS, Journal of Computer-Aided Molecular Design, vol.14, issue.4, pp.383-401, 2000. ,
DOI : 10.1023/A:1008124202956
Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes, Molecular & Cellular Proteomics, vol.4, issue.6, pp.752-61, 2005. ,
DOI : 10.1074/mcp.M400159-MCP200
LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation, BMC Struct Biol, vol.6, 2006. ,
Energy parameters in polypeptides. VII. Geometric parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids, The Journal of Physical Chemistry, vol.79, issue.22, pp.2361-2381, 1975. ,
DOI : 10.1021/j100589a006
Solvent-accessible surfaces of proteins and nucleic acids, Science, vol.221, issue.4612, pp.709-722, 1983. ,
DOI : 10.1126/science.6879170
Structural Bases of Stability???function Tradeoffs in Enzymes, Journal of Molecular Biology, vol.321, issue.2, pp.285-96, 2002. ,
DOI : 10.1016/S0022-2836(02)00599-5
Prediction of Functional Sites Based on the Fuzzy Oil Drop Model, PLoS Computational Biology, vol.3, issue.5, p.94, 2007. ,
DOI : 10.1371/journal.pcbi.0030094.sg010
ProFunc: a server for predicting protein function from 3D structure, Nucleic Acids Research, vol.33, issue.Web Server, pp.89-93, 2005. ,
DOI : 10.1093/nar/gki414
A Common Reference Framework for Analyzing/Comparing Proteins and Ligands. Fingerprints for Ligands And Proteins (FLAP):?? Theory and Application, Journal of Chemical Information and Modeling, vol.47, issue.2, pp.279-94, 2007. ,
DOI : 10.1021/ci600253e
Identification of protein biochemical functions by similarity search using the molecular surface database eF-site, Protein Science, vol.297, issue.8, pp.1589-95, 2003. ,
DOI : 10.1110/ps.0368703
Recognition of Functional Sites in Protein Structures, Journal of Molecular Biology, vol.339, issue.3, pp.607-640, 2004. ,
DOI : 10.1016/j.jmb.2004.04.012
Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions, Proteins: Structure, Function, and Bioinformatics, vol.312, issue.Suppl 1, pp.6-20, 2005. ,
DOI : 10.1002/prot.20580
SiteEngines: recognition and comparison of binding sites and protein-protein interfaces, Nucleic Acids Research, vol.33, issue.Web Server, pp.337-378, 2005. ,
DOI : 10.1093/nar/gki482
Relibase: Design and Development of a Database for Comprehensive Analysis of Protein???Ligand Interactions, Journal of Molecular Biology, vol.326, issue.2, pp.607-627, 2003. ,
DOI : 10.1016/S0022-2836(02)01408-0
Comparison of protein active site structures for functional annotation of proteins and drug design, Proteins: Structure, Function, and Bioinformatics, vol.2, issue.6, pp.124-159, 2006. ,
DOI : 10.1002/prot.21092
Crystallographic analysis at 3.0-A resolution of the binding to human thrombin of four active site-directed inhibitors, J Biol Chem, vol.266, pp.20085-93, 1991. ,
Development of New Carboxylic Acid-Based MMP Inhibitors Derived from Functionalized Propargylglycines, Journal of Medicinal Chemistry, vol.44, issue.7, pp.1060-71, 2001. ,
DOI : 10.1021/jm000477l
Protein function annotation by homology-based inference, Genome Biology, vol.10, issue.2, p.207, 2009. ,
DOI : 10.1186/gb-2009-10-2-207
URL : http://doi.org/10.1186/gb-2009-10-2-207
From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase, Journal of Molecular Biology, vol.359, issue.4, pp.1023-1067, 2006. ,
DOI : 10.1016/j.jmb.2006.04.024
Functional Classification of Protein Kinase Binding Sites Using Cavbase, ChemMedChem, vol.10, issue.10, pp.1432-1479, 2007. ,
DOI : 10.1002/cmdc.200700075
Graph Clustering by Flow Simulation, 2000. ,
BioLayout--an automatic graph layout algorithm for similarity visualization, Bioinformatics, vol.17, issue.9, pp.853-857, 2001. ,
DOI : 10.1093/bioinformatics/17.9.853
A Mathematical Theory of Communication, Bell System Technical Journal, vol.27, issue.3, pp.379-423, 1948. ,
DOI : 10.1002/j.1538-7305.1948.tb01338.x
Entropy-derived measures for assessing the accuracy of N-state prediction algorithms, Recent Advances in Structural Bioinformatics. (de Brevern, pp.395-417, 2007. ,
Heat-shock protein 90, a chaperone for folding and regulation, Cellular and Molecular Life Sciences, vol.59, issue.10, pp.1640-1648, 2002. ,
DOI : 10.1007/PL00012491
HSP90 and the chaperoning of cancer, Nature Reviews Cancer, vol.344, issue.10, pp.761-72, 2005. ,
DOI : 10.1038/nrc1716
The Hsp90 chaperone complex as a novel target for cancer therapy, Annals of Oncology, vol.14, issue.8, pp.1169-76, 2003. ,
DOI : 10.1093/annonc/mdg316
A novel Hsp90 inhibitor to disrupt Hsp90/Cdc37 complex against pancreatic cancer cells, Molecular Cancer Therapeutics, vol.7, issue.1, pp.162-70, 2008. ,
DOI : 10.1158/1535-7163.MCT-07-0484
Structural Basis for Inhibition of the Hsp90 Molecular Chaperone by the Antitumor Antibiotics Radicicol and Geldanamycin, Journal of Medicinal Chemistry, vol.42, issue.2, pp.260-266, 1999. ,
DOI : 10.1021/jm980403y
Identification and Structural Characterization of the ATP/ADP-Binding Site in the Hsp90 Molecular Chaperone, Cell, vol.90, issue.1, pp.65-75, 1997. ,
DOI : 10.1016/S0092-8674(00)80314-1
The Hsp90 Inhibitor Radicicol Interacts with the ATP-Binding Pocket of Bacterial Sensor Kinase PhoQ, Journal of Molecular Biology, vol.379, issue.1, pp.82-93, 2008. ,
DOI : 10.1016/j.jmb.2008.03.036
Structural basis for topoisomerase VI inhibition by the anti-Hsp90 drug radicicol, Nucleic Acids Research, vol.34, issue.15, pp.4269-77, 2006. ,
DOI : 10.1093/nar/gkl567
Crystal Structures of Escherichia coli Topoisomerase IV ParE Subunit (24 and 43 Kilodaltons): a Single Residue Dictates Differences in Novobiocin Potency against Topoisomerase IV and DNA Gyrase, Antimicrobial Agents and Chemotherapy, vol.48, issue.5, pp.1856-64, 2004. ,
DOI : 10.1128/AAC.48.5.1856-1864.2004
The Purinome, a Complex Mix of Drug and Toxicity Targets, Current Topics in Medicinal Chemistry, vol.6, issue.11, pp.1117-1144, 2006. ,
DOI : 10.2174/156802606777812059
Atomic structure of the actin: DNase I complex, Nature, vol.347, issue.6288, pp.37-44, 1990. ,
DOI : 10.1038/347037a0
Structural Basis of Transcription, Cell, vol.119, issue.4, pp.481-490, 2004. ,
DOI : 10.1016/j.cell.2004.10.016
Structure and Mechanism of ArnA: Conformational Change Implies Ordered Dehydrogenase Mechanism in Key Enzyme for Polymyxin Resistance, Structure, vol.13, issue.6, pp.929-942, 2005. ,
DOI : 10.1016/j.str.2005.03.018
Toward a Structural Understanding of the Dehydratase Mechanism, Structure, vol.10, issue.1, pp.81-92, 2002. ,
DOI : 10.1016/S0969-2126(01)00694-3
A Tweezers-like Motion of the ATP-Binding Cassette Dimer in an ABC Transport Cycle, Molecular Cell, vol.12, issue.3, pp.651-661, 2003. ,
DOI : 10.1016/j.molcel.2003.08.004
Structure of nucleotide-binding domain 1 of the cystic fibrosis transmembrane conductance regulator, The EMBO Journal, vol.23, issue.2, pp.282-293, 2004. ,
DOI : 10.1038/sj.emboj.7600040
Structure of the Human Multidrug Resistance Protein 1 Nucleotide Binding Domain 1 bound to Mg2+/ATP Reveals a Non-productive Catalytic Site, Journal of Molecular Biology, vol.359, issue.4, pp.940-949, 2006. ,
DOI : 10.1016/j.jmb.2006.04.005
URL : https://hal.archives-ouvertes.fr/hal-00079738
A structural analysis of asymmetry required for catalytic activity of an ABC-ATPase domain dimer, The EMBO Journal, vol.44, issue.14, pp.3432-3443, 2006. ,
DOI : 10.1038/sj.emboj.7601208
Structure of the ABC ATPase domain of human TAP1, the transporter associated with antigen processing, The EMBO Journal, vol.20, issue.17, pp.4964-4972, 2001. ,
DOI : 10.1093/emboj/20.17.4964
Structure, Catalysis and Supramolecular Assembly of Adenylate Kinase from Maize, European Journal of Biochemistry, vol.22, issue.2, pp.326-357, 1997. ,
DOI : 10.1107/S0021889892009944
X-ray Structures of the Signal Recognition Particle Receptor Reveal Targeting Cycle Intermediates, PLoS ONE, vol.54, issue.3, p.607, 2007. ,
DOI : 10.1371/journal.pone.0000607.t001
Nucleotide-Induced Conformational Changes in an Isolated Escherichia coli DNA Polymerase III Clamp Loader Subunit, Structure, vol.11, issue.3, pp.253-63, 2003. ,
DOI : 10.1016/S0969-2126(03)00027-3
Strategies and tactics for optimizing the Hit-to-Lead process and beyond???A computational chemistry perspective, Drug Discovery Today, vol.13, issue.3-4, pp.99-109, 2008. ,
DOI : 10.1016/j.drudis.2007.10.019
Kinomics???structural biology and chemogenomics of kinase inhibitors and targets, Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, vol.1697, issue.1-2, pp.243-57, 2004. ,
DOI : 10.1016/j.bbapap.2003.11.028
The Protein Kinase Complement of the Human Genome, Science, vol.298, issue.5600, pp.1912-1946, 2002. ,
DOI : 10.1126/science.1075762
3-Amino-1,4,5,6-tetrahydropyrrolo[3,4-c]pyrazoles: A new class of CDK2 inhibitors, Bioorganic & Medicinal Chemistry Letters, vol.16, issue.4, pp.1084-90, 2006. ,
DOI : 10.1016/j.bmcl.2005.10.071
Recognizing protein binding sites using statistical descriptions of their 3D environments, Pac Symp Biocomput, pp.497-508, 1998. ,
Automatic generation of 3D motifs for classification of protein binding sites, BMC Bioinformatics, vol.8, issue.1, p.321, 2007. ,
DOI : 10.1186/1471-2105-8-321
Three-dimensional structure analysis of PROSITE patterns, Journal of Molecular Biology, vol.286, issue.5, pp.1673-91, 1999. ,
DOI : 10.1006/jmbi.1999.2581
The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation, Genome Biology, vol.9, issue.1, p.8, 2008. ,
DOI : 10.1186/gb-2008-9-1-r8
The FEATURE framework for protein function annotation: modeling new functions, improving performance, and extending to novel applications, BMC Genomics, vol.9, issue.Suppl 2, p.2, 2008. ,
DOI : 10.1186/1471-2164-9-S2-S2
Functional annotation by identification of local surface similarities: a novel tool for structural genomics, BMC Bioinformatics, vol.6, 0194. ,
BREED: Generating novel inhibitors through hybridization of known ligands, 2004. ,
A novel approach to local similarity of protein binding sites substantially improves computational drug design results, Proteins: Structure, Function, and Bioinformatics, vol.420, issue.2, pp.349-57, 2007. ,
DOI : 10.1002/prot.21487
The Blue Obelisk???Interoperability in Chemical Informatics, Journal of Chemical Information and Modeling, vol.46, issue.3, pp.991-999, 2006. ,
DOI : 10.1021/ci050400b
Discovery of Novel Benzimidazoles as Potent Inhibitors of TIE-2 and VEGFR-2 Tyrosine Kinase Receptors, Journal of Medicinal Chemistry, vol.50, issue.18, pp.4453-70, 2007. ,
DOI : 10.1021/jm0611051
Benchmarking Sets for Molecular Docking, Journal of Medicinal Chemistry, vol.49, issue.23, pp.6789-801, 2006. ,
DOI : 10.1021/jm0608356
Identification of pyrrolo,2,4]triazine-based inhibitors of Met kinase, Bioorg Med Chem Lett, vol.211, issue.18, pp.1945-51, 2008. ,