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- last update : September, 2nd 2010

Patents

  • 6 patents, one of them lead to the creation of a start-up in Sweden in 2008 called Wnt-Cancer Research AB

Publications  
| 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 |

Year 2010

  • Letouzé E., Allory Y., Bollet M.A. , Radvanyi F. and Guyon F.
    Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis.
    Genome Biology; In press
  • Deschavanne P, DuBow M.S., Regeard C.
    The use of genomic signature distance between bacteriophages and their hosts displays evolutionary relationships and phage growth cycle determination
    Virology Journal; In press
  • Brouillet S, Valere T, Ollivier E, Marsan L, and Vanet A.
    Co-lethality studied as an asset against viral drug escape: the HIV protease case.
    Biology Direct. 2010; 5:40
  • Schmidtke P, Le-Guilloux V, Maupetit J, Tufféry P.
    Fpocket: online tools for protein ensemble pocket detection and tracking.
    Nucleic Acids Res; In press
  • Pérot S, Sperandio O, Miteva MA, Camproux AC, Villoutreix BO.
    Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery
    Drug Discov Today; In press
  • Siegfried G, Khatib A-M, Lahlil R, Scamuffa N, Akimenko M-A, Ernest S, Lomri A, Lalou C, Seidah N, Villoutreix BO, Calvo F.
    Regulation of VEGF-C-induced functions and fin regeneration in zebrafish by the proprotein convertases.
    PLoS ONE; In press
  • Becq J., Churlaud C., and Deschavanne P.
    A benchmark of parametric methods for horizontal transfers detection.
    PLoS ONE. 2010; 5(4):e9989.
  • Mallet L., Becq J., Deschavanne P.
    Whole genome evaluation of horizontal transfers in the pathogenic fungus Aspergillus fumigatus.
    BMC Genomics. 2010; 11:171
  • Guyon F., Tufféry P.
    Assessing 3D scores for protein structure fragment mining.
    Open Access Bioinformatics; In press
  • Regad L., Martin J., Nuel G. and Camproux A.C.
    Mining protein loops using a structural alphabet and statistical exceptionality
    BMC Bioinformatics. 2010; 11:75.
  • Sperandio O, Mouawad L, Pinto E, Villoutreix BO, Perahia D, Miteva MA.
    How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis.
    European Biophysics Journal; In press
  • Antoniou X, Sclip A, Ploia C, Colombo A, Moroy G, Borsello T.
    JNK Contributes To Hif-1alpha Regulation In Hypoxic Neurons
    Molecules. 2010; 15:114-127
  • Petitjean M.
    Chirality in Metric Spaces.
    Symmetry Cult. Sci. 2010; 21(1-3):27-36
  • Maupetit J., Derreumaux Ph, Tufféry P.
    A fast method for large-scale De Novo peptide structure prediction.
    Journal of Computational Chemistry. 2010; 31:726-38.
  • Nilsson S.C, Nita I, Mansson L, Groeneveld T.W.L, Trouw L.A, Villoutreix BO, and Blom A.M.
    Analysis of binding sites on complement factor I that are required for its activity.
    J. Biol. Chem. 2010; 285:6235-45
  • Guénoche A., Guyon F.
    Alignment free string distances for phylogeny. Classification as a Tool for Research.
    Proceedings of the 11th IFCS Biennial Conference,
    Studies in Classification, Data Analysis, and Knowledge Organization.     2010.
  • Guénoche A., Guyon F.
    An evolutionary distance based on maximal unique matches
    Communications in Statistics-Theory and Medthods. 2010; 39(03):385-397.
  • Bienaime F, Dragon-Durey M-A, Regnier C.H, Nilsson S.C, Kwan W.H, Blouin J, Jablonski M, Renault N, Rameix-Welti M-A, Loirat C, Sautes-Fridman C, Villoutreix BO, Blom A.M & Fremeaux-Bacchi V.
    Mutations in components of complement influence the outcome of Factor I-associated atypical hemolytic uremic syndrome.
    Kidney International. 2010; 77:339-49
  • Pencheva T., Samna Soumana O., Pajeva I., Miteva MA
    Post-docking virtual screening of diverse binding pockets: comparative study using DOCK, AMMOS, X-Score and FRED scoring functions.
    Eur J Med Chem. 2010; 45:2622-8
  • Basse N, Montes M, Maréchal X, Qin L, Bouvier-Durand M, Genin E, Vidal J, Villoutreix BO, Reboud-Ravaux M.
    Novel organic proteasome inhibitors identified by virtual and in vitro screening.
    J Med Chem. 2010; 53(1):509-13.
  • Nuel G.,Regad L., Martin J.,Camproux A-C.
    Exact distribution of a pattern in a set of random sequences generated by a Markov source: applications to biological data
    Algorithms for Molecular Biology. 2010; 5:15
  • Nilsson SC, Kalchishkova N, Trouw LA, Fremeaux-Bacchi V, Villoutreix BO, Blom AM.
    Mutations in complement factor I as found in atypical hemolytic uremic syndrome lead either to altered secretion or altered function of factor I.
    Eur J Immunol. 2010; 40:172-85

Reviews

  • Villoutreix BO, Sperandio O.
    In silico studies of blood coagulation proteins: from mosaic proteases to non-enzymatic cofactor inhibitors.
    Current Opinion in Structural Biology. 2010; 20:1-12.

Book Chapters

  • Benkaidali L, Mansouri K, Tufféry P, André F, and Petitjean M
    How well is conformational space covered?
    NOVA Science Publishers, New York (USA) - Chemistry Information and Computation in 21st. Mihai Putz, Editor.
  • Guyon F., Tufféry P.
    Chapter 3: 3D similarity search for lead compound identification
    Bentham Science Publishers, eBook «In silico lead discovery»; in press
  • Lagorce D, Sperandio O, Miteva MA, Villoutreix BO.
    Chapter 1: Chemical Libraries for Virtual Screening.
    Bentham Science Publishers, eBook «In silico lead discovery»; in press
  • Sperandio O, Villoutreix BO, Miteva MA.
    Chapter 2: Structure-Based Virtual Screening.
    Bentham Science Publishers, eBook «In silico lead discovery»; in press
  • Miteva MA, Robert C.H, Maréchal J.D., Perahia D.
    Chapter 6: Receptor Flexibility in Ligand Docking and Virtual Screening.
    Bentham Science Publishers, eBook «In silico lead discovery»; in press
  • Sperandio O, Miteva MA, Villoutreix BO.
    Target-based virtual screening to address protein-protein interfaces.
    Wiley-VCH, «Virtual Screening - Principles, Challenges, and Practical Guidelines»
  • Lagorce D, Reynes C, Camproux A-C, Miteva MA, Sperandio O, Villoutreix BO.
    In silico ADME/Tox predictions.
    J Wiley & Sons. In press

Submitted

  • Petitjean M.
    About the Algebraic Solutions of Smallest Enclosing Cylinders Problems
    Discrete & Computational Geometry
  • Letouzé E., Allory Y., Bollet M.A. , Radvanyi F. and Guyon F.
    Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis. (submitted)
    • Hafizi S, Gustafsson A, Oslakovic C, Idevall-Hagren O, Tengholm A, Sperandio O, Villoutreix BO, Dahlback B.
      Tensin2, but not Tensin3, reduces intracellular phosphatidylinositol 3,4,5-trisphosphate levels at the plasma membrane.
      FEBS Letters.


    Year 2009  

    • Deschavanne P. and Tufféry P.
      Enhanced protein fold recognition using a structural alphabet.
      Proteins. 2009; 76:129-37
    • Meslamani J.E., Andre F., Petitjean M.
      Assessing the Geometric Diversity of Cytochrome P450 Ligand Conformers by Hierarchical Clustering with a Stop Criterion.
      J. Chem. Inf. Model. 2009; 49[2]:330-337.
    • Lescat M, Hoede C, Clermont O, Garry L, Darlu P, Tufféry P, Denamur E and Picard B.
      aes, the gene encoding the esterase B in Escherichia coli, is a powerful phylogenetic marker of the species.
      BMC Microbiology. 2009; 9:273 doi:10.1186/1471-2180-9-273.
    • Pencheva T., Lagorce D., Pajeva I., Villoutreix B.O., Miteva M.A.
      AMMOS: A Software Platform to Assist in silico Screening.
      Bioautomation. 2009; 13:143-150.
    • Lagorce D, Pencheva T, Villoutreix BO and Miteva MA.
      DG-AMMOS: A New tool to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening.
      BMC Chem Biol. 2009; 9:6.
    • Noll C, Planque C, Ripoll C, Guedj F, Diez A, Ducros V, Belin N, Duchon A, Paul JL, Badel A, de Freminville B, Grattau Y, Bléhaut H, Herault Y, Janel N, Delabar JM.
      DYRK1A, a novel determinant of the methionine-homocysteine cycle in different mouse models overexpressing this Down-syndrome-associated kinase.
      PLoS One. 2009; 4(10):e7540.
    • Néron B, Ménager H, Maufrais C, Joly N, Maupetit J, Letort S, Carrere S, Tuffery P, Letondal C.
      Mobyle: a new full web bioinformatics framework.
      Bioinformatics. 2009; 25(22):3005-3011
    • Quintus F, Sperandio O, Grynberg J, Petitjean M, Tuffery P.
      Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity.
      BMC Bioinformatics. 2009; 10:245.
    • Guyon F,Brochier-Armanet C,Guénoche A.
      Comparison of alignment free string distances for complete genome phylogeny
      In Advances in Data Analysis and Classification. 2009; 3:95-108
    • Le Guilloux V, Schmidtke P, and Tufféry P.
      Fpocket : An open source platform for ligand pocket detection.
      BMC bioinformatics. 2009; 10:168
    • Kolb S, Mondésert O, Goddard ML, Jullien D, Villoutreix BO, Ducommun B, Garbay C, Braud E.
      Development of Novel Thiazolopyrimidines as CDC25B Phosphatase Inhibitors.
      ChemMedChem. 2009; 4:633-648.
    • Nilsson SC, Trouw LA, Renault N, Miteva MA, Genel F, Zelazko M, Marquart H, Muller K, Sjöholm AG, Truedsson L, Villoutreix BO, Blom AM.
      Genetic, molecular and functional analyses of complement factor I deficiency.
      Eur J Immunol. 2009; 39:310-23.
    • Sperandio O, Souaille M, Delfaud F, Miteva MA, Villoutreix BO.
      MED-3DMC: a new tool to generate 3D conformation ensembles of small molecules with a Monte Carlo sampling of the conformational space.
      Eur J Med Chem. 2009; 44:1405-9
    • Okroj M, Mark L, Stokowska A, Wong SW, Rose N, Blackbourn DJ, Villoutreix BO, Spiller OB, Blom AM.
      Characterization of the complement inhibitory function of rhesus rhadinovirus complement control protein (RCP).
      J Biol Chem. 2009; 284:505-14.

    Reviews

    • Tufféry P.
      La molécule sur l’écran
      DocSciences. 2009; 8:34-39.
    • Villoutreix BO, Eudes R, Miteva MA.
      Structure-based virtual ligand screening: recent success stories.
      Combinatorial Chemistry and High Throughput Screening. 2009; 2:1000-1016,


    Year 2008  

    • Sauton N, Lagorce D, Villoutreix BO, Miteva MA.
      MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for  multi-step virtual ligand screening.
      BMC Bioinformatics. 2008; 9:184
    • Lagorce D, Sperandio O, Galons H, Miteva MA, Villoutreix BO.
      FAF-Drugs2: free ADME/tox filtering tool to assist drug discovery and chemical biology projects.
      BMC Bioinformatics. 2008; 9:396.
    • Montes M, Braud E, Miteva MA, Goddard ML, Mondesert O, Kolb S, Brun MP, Ducommun B, Garbay C, Villoutreix BO.
      Receptor-based virtual ligand screening for the identification of novel CDC25 phosphatase inhibitors.
      J Chem Inf Model. 2008; 48:157-65
    • Pencheva T, Lagorce D, Pajeva I, Villoutreix BO and Miteva MA.
      AMMOS: Automated Molecular Mechanics Optimization tool for in silico Screening.
      BMC Bioinformatics. 2008; 9:438
    • Blom AM, Bergstrom F, Edey M, Diaz-Torres M, Kavanagh D, Lampe A, Goodship JA, Strain L, Moghal N, McHugh M, Inward C, Tomson C, Fremeaux-Bacchi V, Villoutreix BO, Goodship THJ.
      A novel non-synonymous polymorphism (p.Arg240His) in C4b-binding protein is associated with atypical hemolytic uremic syndrome and leads to impaired alternative pathway cofactor activity.
      The Journal of Immunology. 2008; 180:6385-91.
    • Mazuc E, Villoutreix BO, Malbec O, Leonetti J-P, Dombrowicz D, Daeron M, Martineau P, Dariavach P.
      A novel Syk binding small molecule prevents anaphylactic shocks when administrered orally.
      Journal of Allergy and Clinical Immunology. 2008; 122:188-94.
    • Steen M, Tran S, Autin L, Villoutreix BO, Tholander A-L, Dahlback B.
      Mapping of the FXa-binding site on factor Va by site-directed mutagenesis.
      J. Biol. Chem; 2008; 283:20805-12.
    • Stoilova-McPhie S, Parmenter CDJ, Segers K, Villoutreix BO, Nicolaes GAF.
      Defining the structure of membrane-bound human blood coagulation Factor Va.
      J. Thrombosis and Haemostatis. 2008; 6:76-82.
    • Regad L., Guyon F., Maupetit J., Tuffery P., Camproux AC.
      A Hidden Markov Model applied to proteins 3D structures analysis.
      Computational Statistics and Data Analysis. 2008; 52:3198-3207.
    • Martin J., Regad L., Lecornet H., Camproux A.C.
      Structural deformation upon protein-protein interaction : a structural alphabet approach.
      BMC Structural Biology. 2008; 8:12.
    • Martin J., Regad L., Echebest C., Camproux A.C.
      Inter-residue contact analysing using local structure descriptors.
      Proteins. 2008; 19;73(3):672-689.
    • Martin J, de Brevern AG, Camproux AC.
      In silico local structure approach: a case study on outer membrane proteins.
      Proteins. 2008; 71(1):92-109.
    • Deschavanne P. and Tuffery P
      Exploring an alignment free approach for protein classification and structural class prediction.
      Biochimie 2008;(4):615-25.
    • Jang J., Becq j., Gicquel B., Deschavanne P. and Neyrolles O.
      Horizontally acquired genomic islands in the tubercle bacilli.
      Trends in Microbiology. 2008; 16:303-308.
    • Guyon F. Guénoche A.
      Comparing bacterial genomes from linear orders of patterns.
      Discrete Applied Mathematics. 2008; 156:1251-1262.

    Reviews

    • Miteva MA.
      Hierarchical structure-based virtual screening for drug design.
      Biotechnol & Biotechnol Equip. 2008; 1:634-638
    • Mitra R, Shyam R., Mitra I, Miteva MA and Emil Alexov.
      Calculating the Protonation States of Proteins and Small Molecules: Implications to Ligand-Receptor Interactions.
      Current Computer-Aided Drug Design. 2008; 4:169-179
    • Sperandio O, Miteva MA, Villoutreix BO.
      Combining structure-based and ligand-based virtual ligand screening: recent success stories.
      Current Computer-Aided Drug Design. 2008; 4:250-258.
    • Villoutreix BO, Bastard K, Sperandio O, Fahraeus R, Poyet JL, Calvo F, Deprez B, Miteva MA.
      In silico-in vitro screening of protein-protein interactions: towards the next generation of therapeutics.
      Curr Pharm Biotechnol. 2008; 9:103-22
    • Sperandio O, Miteva M, Segers K, Nicolaes G, Villoutreix BO.
      Screening outside the catalytic site: Inhibition of macromolecular interactions through structure-based virtual ligand screening experiments.
      The Open Biochemistry Journal. 2008; 2:29-37

    Year 2007  

    • Sperandio O, Andrieu O, Miteva MA, Vo M-Q, Souaille M, Delfaud F, Villoutreix, BO.
      MED-SuMoLig: A new ligand-based screening tool for efficient scaffold hopping.
      J Chem Inf Model 2007; 47:1097-110.
    • Shedlock AM, Botka CW, Zhao S, Shetty J, Zhang T, Liu JS, Deschavanne P, Edwards SV.
      Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome.
      Proc. Natl. Acad. Sci. 2007; 104: 2767-72.
    • Becq J, Gutierrez MC,Rosas-Magallanes V, Rauzier J, Gicquel B, Neyrolles O,Deschavanne P.
      Contributions of horizontally acquired genomic Islands to the evolution of the tubercle bacilli.
      Mol Biol Evol.2007; 24(8):1861-71
    • Jarva H, Ngampasutadol J, Ram S, Rice PA, Villoutreix BO, Blom AM.
      Molecular characterization of the interaction between porins of Neisseria gonorrhoeae and C4b-binding protein.
      J. Immunology. 2007; 179(1):540-7. 179:540-7.
    • Maupetit J.,Tuffery P., Derreumaux P. ,
      A coarse-grained protein force field for folding and structure prediction
      Proteins. 2007; 69(2):394-408
    • Autin L., Tuffery P.
      PMG: online generation of high-quality molecular pictures and storyboarded animations
      Nucleic Acids Res. 2007;35:W483-48.
    • Bohme T, Gomes D, Chomillier J, Miteva MA, Villoutreix BO, Tuffery P.
      Frog: a FRee Online druG 3D conformation generator.
      Nucleic Acids Res. 2007; 35:W568-72.
    • Montes M, Miteva MA, Villoutreix BO.
      Structure-based virtual ligand screening with Ligand Fit: pose prediction and enrichment of compound collections.
      Proteins. 2007; 68:712-25.
    • Segers K, Sperandio O, Sack M, Fischer R, Miteva MA, Rosing J, Nicolaes GAF, Villoutreix BO.
      Design of protein-membrane interaction inhibitors by virtual ligand screening, proof of concept with the C2 domain of factor V.
      Proc. Natl. Acad. Sci. 2007; 104:12697-702.

    Reviews

    • Mark L, Spiller BO, Villoutreix BO, Blom AM.
      Kaposis sarcoma associated herpes virus complement inhibitor: KCP-- complement inhibitor and more.
      Molecular Immunology. 2007; 44(1-3):11-22.
    • Villoutreix BO, Renault N, Lagorce D, Sperandio O, Montes M and Miteva MA.
      Free Resources In Structure-Based Virtual Ligand Screening For The Protein Scientist.
      Current Protein and Peptide Science. 2007; 8:381-411.


    Year 2006  

    • Maupetit J. Gautier R. Tuffery P.
      SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace.
      Nucleic Acids Res. 2006; 34(Web Server issue) W147-51
    • Miteva M.A., Violas S. Montes M, Gomez D, Tuffery P, Villoutreix B.O.
      FAF-Drugs: free ADME/tox filtering of compound collections.
      Nucleic Acids Res. 2006; 34(Web Server issue) W738-44
    • Rosas-Magallanes V, Deschavanne P, Quintana-Murci L, Brosch R, Gicquel B. Neyrolles O.
      Horizontal Transfer of a Virulence Operon to the Ancestor of Mycobacterium tuberculosis.
      Mol Biol Evol. 2006; 23:1129-1135.
    • Regad L, Martin J, Camproux A.C.
      Identification of non random motifs in loops using a structural alphabet.
      IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology proceeding. 2006; 92-98
    • Stanchev H, Philips M, Villoutreix BO, Aksglæde L, Lethagen S, and Thorsen S.
      Prothrombin deficiency caused by compound heterozygosity for two novel mutations in the prothrombin gene associated with a bleeding tendency.
      Thrombosis and Haemostasis. 2006; 95:195-198
    • Autin L, Steen M, Dahlbäck B, Villoutreix BO.
      Proposed structural models of the prothrombinase (FXa-FVa) complex.
      Proteins. 2006; 63:440-450.
    • Safholm A, Leandersson K, Dejmek J, Kamp Nielsen, Villoutreix BO, Andersson T.
      A formylated hexapeptide ligand mimics the ability of Wnt-5a to impair breast cancer cell migration.
      J Biol Chem. 2006; 281:2740-2749.
    • Mark L, Lee WH, Spiller OB, Villoutreix BO and Blom AM.
      The Kaposi's sarcoma-associated human herpesvirus complement control protein (KCP) binds to heparin and cell surfaces via positively charged amino acids in CCP 1-2.
      Mol. Immunology. 2006; 43:1665-1675.
    • B.Knobe KE, Persson KE, Sjorin E, Villoutreix BO, Ljung RC.
      Functional Analysis of the Factor IX Epidermal Growth Factor-Like Domain Mutation Ile66Thr Associated with Mild Hemophilia
      Pathophysiol Haemost Thromb. 2006; 35(5):370-5.

    Reviews

    • Sperandio O, Miteva MA, Delfaud F, Villoutreix BO.
      Receptor-Based Computational Screening of Compound Databases: the main docking/scoring engines.
      Current Protein and Peptide Science (special issue on Drug Design, Guest editor). 2006; 7:369-393 (cover page).
    • Villoutreix BO.Bioinformatique structurale, criblage in silico en 3D.
      Bioinformatique structurale, criblage in silico en 3D.
      Sci Tech Anim Lab. Colloque OPAL. Recherche experimentale et protection de l'animal de laboratoire.2006; 22-26


    Year 2005  

    • Camproux A.C., Tuffery P.
      Hidden Markov model-derived structural alphabet for proteins: the learning of protein local shapes captures sequence specificity.
      Biochim Biophys Acta. 2005; 1724:394-403
    • Alland C., Moreews F. Boens D., Carpentier M. Chiusa S., Lonquety M. Renault N., Wong Y. Cantalloube H., Chomilier J. Hochez J. Pothier J., Villoutreix B.O. Zagury J.F. Tuffery P.
      RPBS: a web resource for structural bioinformatics.
      Nucleic Acids Res. 2005; 33(Web Server issue) W44-9 .
    • Binisti C., Salim A.A., Tuffery P.
      PPG: online generation of protein pictures and animations.
      Nucleic Acids Res. 2005; 33(Web Server issue) W320-3.
    • Chapus C., Dufraigne C., Edwards S., Giron A., Fertil B., Deschavanne P.
      Exploration of phylogenetic data using a global sequence analysis method.
      BMC Evolutionary Biology. 2005; 5:63.
    • Dufraigne C., Fertil B., Lespinats S., Giron A., Deschavanne P.
      Detection and characterization of horizontal transfers in prokaryotes using genomic signature.
      Nucleic Acids Res. 2005; 33(1)
    • Miteva M.A., Tuffery P., Villoutreix B.O.
      PCE: web tools to compute protein continuum electrostatics.
      Nucleic Acids Res. 2005; 33(Web Server issue) W372-5 .
    • Regeard C. Maillard J. Dufraigne C. Deschavanne P. Holliger C.
      Indications for the acquisition of reductive dehalogenase genes through horizontal gene transfer by Dehalococcoides ethenogenes strain 195.
      Applied and Environmental Microbiology. 2005; 71:2955-2961.
    • Tuffery P., Guyon F., Derreumaux P.
      Improved greedy algorithm for protein structure reconstruction.
      J Comput Chem. 2005; 26(5):506-13.
    • Lee WH, Raas-Rotschild A, Miteva MA, Bolasco G, Rein AJ, Gillis D, Vidaud D, Vidaud M, Villoutreix BO, Parfait B.
      Noonan Syndrome type I with PTPN11 3 bp deletion - structure-function implications.
      Proteins. 2005; 58:7-13.
    • Saller F, Villoutreix BO, Amelot A, Kaabache T, Le Bonniec BF, Aiach M, Gandrille S, Borgel D.
      The gamma-carboxyglutamic acid (Gla) domain of anticoagulant protein S is involved in activated protein C cofactor activity independently of phospholipid binding.
      Blood. 2005; 105:122-130.
    • Akhavan S, Miteva M, Villoutreix BO, Venisse L, Peyvandi F, Mannucci PM, Guillin M-C, Bezeaud A.
      A critical role for Gly25 in the B chain of human thrombin.
      J Thrombosis Haemost. 2005; 3:139-145.
    • Autin L, Miteva M, Lee WH, Mertens K, Radtke KP and Villoutreix BO.
      Molecular Models of the Procoagulant Intrinsic Tenase Complex.
      J. Thrombosis and Haemostatis. 2005; 3:2044-56.
    • Miteva MA, Lee WH, Montes MO, Villoutreix BO
      .Fast structure-based virtual ligand screening by combining FRED, DOCK and Surflex.
      J Med Chem. 2005; 48:6012-22.
    • Benali-Furet NL, Chami M, Houel L, De Giorgi F, Vernejoul F, Lagorce D, Buscail L, Bartenschlager R, Ichas F, Rizzuto R, Paterlini-Brechot P.
      Hepatitis C virus core triggers apoptosis in liver cells by inducing ER stress and ER calcium depletion.
      Oncogene. 2005; 24(31):4921-33.
    • Tuffery P., Derreumaux P.
      Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm.
      Proteins. 2005; 61(4):732-40.

    Reviews

    • Dahlback B and Villoutreix BO.
      Regulation of blood coagulation by the protein C anticoagulant pathway, novel insights into structure-function relationships and molecular recognition.
      Arteriosclerosis, Thrombosis and Vascular Biology (ATVB).2005; 25:1311-1320.
    • Dahlback B and Villoutreix BO.
      The anticoagulant protein C pathway.
      FEBS Letters.2005; 579:3310-3316.


    Year 2004  

    • Camproux A.C, Gautier R. Tuffery P.
      A Hidden Markov Model Derived Structural Alphabet for Proteins
      Journal of Molecular Biology. 2004; 339(3) 591-605.
    • Gautier R., Camproux A-C., Tuffery P.
      SCit: web tools for protein side chain conformation analysis.
      Nucleic Acid Res. 2004; 32(Web Server Issue) W508-W511.
    • Luersen, M.A., Le Riche, R. and Guyon, F.
      A constrained globalized and bounded Nelder-Mead method for engineering optimization
      Structural and Multidisciplinary Optimization. 2004; 27(1-2):43-54
    • Guyon F., Camproux A.C., Hochez J., Tuffery P.
      SA-Search: a Web tool for protein structures mining based on a structural alphabet.
      Nucleic Acids Res. 2004; 32(Web Server Issue) W545-W548.
    • Lespinats S, Giron A, Deschavanne P, Fertil B.
      Comparaison des coronavirus par signature genomique : application a l'analyse du SARS.
      Virologie. 2004; 33.
    • Miteva M, Brugge JM, Rosing J, Nicolaes GAF, Villoutreix BO.
      Theoretical and experimental study of the Asp2194Gly mutation in the C2 domain of coagulation factor V.
      Biophysical Journal. 2004; 86:488-498
    • Kask L, Villoutreix BO, Steen M, Dahlback B, Blom AM.
      Structural stability and heat-induced conformational change of two complement inhibitors: C4b-binding protein and factor H.
      Protein Science. 2004; 13:1356-64.
    • Nicolaes GAF, Sørensen KW, Friedrich U, Tans G, Rosing J, Autin L, Dahlbäck B, Villoutreix BO.
      Altered inactivation pathway of factor Va by activated protein C in the presence of heparin.
      Eur J Biochem. 2004; 271:2724-2736.
    • Sorensen K, Nicolaes GAF, Villoutreix BO, Yamazaki T, Tans G, Rosing J, Dahlback B.
      Functional properties of recombinant factor V mutated in a potential calcium-binding site.
      Biochemistry. 2004; 43:5803-5810.
    • Mark L, Lee WH, Spiller B, Proctor D, Blackbourn D, Villoutreix BO, Blom AM.
      KSHV complement control protein mimics human molecular mechanisms for inhibition of the complement system.
      J Biol Chem. 2004; 279:45093-101.

    Reviews

    • Blom AM, Villoutreix BO, Dahlback B.
      Complement inhibitor C4b-binding protein-friend or foe of the immune system.
      Molecular Immunology. 2004; 40:1333-1346.



    Présentation orales  

    • Moroy G., Bourguet E., Lorimier S., Emonard H., Bellon G. Janos S., Alix A.J-P. and Hornebeck W.
      Mechanisms of Elastolysis and control by fatty acids and derivatives.
      Sixth European Symposium Elastin, 28 June - 2 July, 2010, Maratea (Italy).
    • Sperandio O.
      Design Focused Librairies for Protein-Protein Interaction Inhibitors
      Round Table: Academic Screening Platforms Worldwide and valorization experiences
      Atelier de formation INSERM - 23-25 Mars 2010, Saint Raphaël, France.
    • Miteva M.A.
      Structure-based virtual screening: an overview and hierarchical protocols.
      International workshop Inserm « In silico discovery of molecular probes and drug-like compounds: Success & Challenges »
      23-25 Mars 2010, Saint Raphaël, France.
    • Guyon F, Brochier C, Guénoche A.
      Comparison of alignment free string distances for complete genome phylogeny
      International Federation of Classification Societies 2009 Conference - 15 March 2009, Dresde.
    • Miteva MA.
      Structure-based virtual ligand screening: overview and receptor flexibility
      International Workshop New Tendencies in Computanional Biophysics west University of Timisoara, Romania, 4-6 june 2009.
    • Reynès C., Regad L., Sabatier R. and Camproux, AC.
      Prédiction de la structure 3D des boucles protéiques
      41èmes Journées de Statistique, SFdS/2009, Bordeaux, France.
    • Sperandio O.
      High-throughput machine learning technologies to design protein-protein interaction inhibitor focused libraries
      Journées de la Société Francaise de Chémoinformatique (SFCi). (24-25 Juin 2009) Montpellier, France.
    • Sperandio O.
      Rationalizing the chemical space of protein-protein interaction inhibitors
      Académie des sciences - Nov 2009, Timisoara/Roumanie
    • Tufféry P.
      PEP-FOLD: A Fast and Accurate Method for Large-Scale de novo Peptide Structure Prediction Peptides Europe,
      17-18 September, 2009, Berlin, Germany.
    • Villoutreix BO.
      Computer-assisted drug discovery.
      Karolinska Institutet. Department of Biosciences and Nutrition. Novum,March 2-3,2009, Stockholm, Sweden.
    • Villoutreix BO.
      In silico screening, hit2lead et ADMET
      Fac Pharmacie Paris 5, Mardi 28 Avril 2009, France.
    • Villoutreix BO.
      Recherche in silico de sondes pharmacologiques.
      Symposium Drug Discovery, Fac Pharmacie - Pasteur, 13 Mai 2009, Lille, France.
    • Villoutreix BO.
      Plenary lecture: Structure-based in silico screening: free tools and applications.
      45th edition of the International Symposium on Medicinal Chemistry (RICT), July 1-3, 2009 Orleans, France.
    • Villoutreix BO.
      Plenary lecture: Computational methods to assist drug discovery: free structure-based screening resources.
      Member of the International Scientific Advisory Board and invited speaker at the Fifth International Symposium on Computational Methods in Pharmacology and Toxicology Integrating Internet Resources, July 4-8, 2009, Istanbul, Turkey.
    • Villoutreix BO.
      In silico screening of compound collections: methods and applications for drug discovery and chemical biology.
      XXII Congress International Society on Thrombosis and Haemostasis (ISTH), July 11-16, 2009, Boston USA.
    • Villoutreix BO.
      Plenary lecture. Drug design and structure-based virtual screening of compound collections: methods and applications.
      «FEBS Sofia School of Protein Science: From basic research to drug design», September 21-26, 2009, Bulgaria.


    Posters  


    • Moroy G., Martiny V., Badel A., Lagorce D., Miteva M.A.
      Toward's prediction of drugs'modification by sulfotransferases.
      «Interfacing Chemical Biology and Drug Discovery», 46th International Conference on Medicinal Chemistry , June 30 - July 2, 2010, Reims, France.
    • Lorimier S., Moroy G., Bourguet E., Decarme M., Alix A.J-P., Sapi J. and Hornebeck W.
      Mechanisms of Elastolysis and control by fatty acids and derivatives.
      Sixth European Symposium Elastin, 28 June - 2 July, 2010, Maratea (Italy).
    • Pérot S. , Reynes C. , Sperandio O. , Miteva M.A. , Villoutreix B.O. , Camproux A-C.
      Anatomy of druggable pockets and associated ligands.
      2nde Ecole d’été de Strasbourg en Chémoinformatique, 20-24 Juin 2010, Obernai, France.
    • Martiny V.Y, Moroy G, Badel A et Miteva M.A.
      Analyse des interactions entre les Sulfotransférases et leurs inhibiteurs : Perspectives de prédiction de la toxicité induite par les Sulfotransférases.
      Congrès «Toxicologie prédictive : les voies du futur» organisé par la Société de Pharmaco-Toxicologie Cellulaire, 18-19 Mai 2010, Paris.
    • Badel A, Isvoran A, Samna Soumana O, Craescu C, Miteva M.A
      Docking Studies of NMR structures of Ca binding proteins: Perspectives for inhibition of protein-protein interactions and drug design.
      International Workshop New Tendencies in Computanional Biophysics west University of Timisoara, Romania, 4-6 june 2009.
    • Lagorce D, Sperandio O, Miteva M.A, Villoutreix B.O
      FAF-Drugs2: Free ADME/Tox filtering tool of compound collections
      Screening, MedChem and ADMET Europe 23-25 Feb 2009, Berlin, Germany.
    • Lagorce D, Sperandio O, Galons H, Miteva MA, Villoutreix BO.
      AF-Drugs2: free ADME/tox filtering tool to assist drug discovery and chemical biology projects.
      MedChemEurope-FAF-Drugs2: free ADME/tox filtering tool to assist drug discovery and chemical biology projects. - Feb25-28-2009, Berlin, Germany.
    • Le Guilloux V, Schmidtke P, Tufféry P.
      Fpocket: An open source platform for ligand pocket detection, XVIème Colloque du Groupe de Graphisme et de Modélisation Moléculaire.
      GGMM’2009, 2009 - Mittelwihr, Alsace, France.
    • Letouzé E, Allory Y, Radvanyi F, Guyon F.
      TUMULT : An Algorithm to analyze multiple tumors from a same patient.
      Pacific Symposium of Bio-computing 2009, January 4-8, 2009, Hawai.
    • Letouzé E, Allory Y, Radvanyi F, Guyon F.
      Comparative analysis of primary bladder and breast tumors and their recurrences with the TUMULT algoritm.
      ISMB, Intelligent Systems for Molecular Biology, June 27 - July 2, 2009, Stockholm,Sweden.
    • Mallet L, Becq J, Deschavanne P.
      Whole genome evaluation of horizontal transferts for the pathogenic fungus aspergillus fumigatus.
      JOBIM, Journées Ouvertes en Biologie, Informatique et Mathématiques, 9-11 june 2009, Nantes, France.
    • Pencheva T., Lagorce D., Pajeva I., Villoutreix B.O., Miteva M.A.
      AMMOS: A Software Platform to Assist in silico Screening.
      First National Conference with International Participation on Biomedical and Bioprocess Engineering BM& BP’2009, QSAR and Molecular Modelling, 3-4 December 2009, Sofia, Bulgaria.
    • Pencheva T., Lagorce D., Pajeva I., Villoutreix B.O., Miteva M.A.
      Postdocking Optimization of Protein-ligand Complexes using AMMOS Software Tool
      Second Humboldt Conference on Noncovalent Interactions, 22-25 October, 2009, Vrsac, Serbia,
    • Pérot S, Sperandio O, Miteva M.A, Villoutreix B.O, Camproux A.C.
      Statistical modelisation of protein-ligand interactions
      JOBIM, Journées Ouvertes en Biologie, Informatique et Mathématiques, 9-11 june 2009, Pays de la Loire, France.
    • Reynès C, Regad L, Sabatier R and Camproux AC.
      A new method to predict protein loops 3D structure ,
      17th Annual Intelligent Systems for Molecular Biology (ISMB) & 8th European Conference on Computational Biology (ECCB) /, Stockholm, Sweden.
    • Samna Soumana O, Isvoran A, Badel A, Craescu C, Miteva M.A
      Efficient molecular docking of NMR structures: application to human centrin 2 and calmodulin.
      GGMM, 5-7 may 2009, Mittelwihr, Alsace, France


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