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- last update : April, 7th 2014







PUBLICATIONS YEAR 2013-2014


  • 29- Fabio Sterpone, Simone Melchionna, Pierre Tufféry, Samuela Pasquali, Normand Mousseau, Tristan Cragnolini, Yassmine Chebaro, Jean-Francois Saint-Pierre, Maria Kalimeri, Alessandro Barducci, Yohan Laurin, Alex Tek, Marc Baaden, Phuong Hoang Nguyen, and Philippe Derreumaux
    The OPEP coarse-grained protein model: from single molecules, amyloid formation, role of macromolecular crowding and hydrodynamics to RNA/DNA complexes
    Chem. Soc. Rev., 2014; in press
  • 28- Borovkov V., Petitjean M.
    Editorial: Chirality and Symmetry in the Chemical and Physical Structure of Matter.
    Symm. Cult. Sci., 2014; 25[2], 53-54 [google scholar]
  • 27- Nicolaes G.A., Kulharia M., Voorberg J., Kaijen P.H., Wroblewska A., Wielders S., Schrijver R., Sperandio O., Villoutreix B.O.
    Rational design of small molecules targeting the C2 domain of coagulation factor VIII.
    Blood 2014; 123(1):113-20. [google scholar]
  • 26- Petitjean M., Vanet A.
    VIRAPOPS: a Forward Simulator Dedicated to Rapidly Evolved Viral Populations
    Bioinformatics 2014; 30[4], 578-580. [google scholar]
  • 25- Benkaidali L., André F., Maouche B., Siregar P., Benyettou M., Maurel F., Petitjean M.
    Computing cavities, channels, pores and pockets in proteins from non spherical ligands models.
    Bioinformatics 2014; 30[6], 792-800. [google scholar]
  • 24- F. Guyon , P. Tufféry
    Fast protein fragment similarity scoring using a Binet-Cauchy Kernel.
    Bioinformatics 2014; 30 (6): 792-800 [google scholar]
  • 23- Moncoq K., Regad L., Mann S., Mejean A., Ploux O.
    Structure of the prolyl-acyl carrier protein oxidase involved in the biosynthesis of the cyanotoxin anatoxin-a.
    Acta Cryst. D. 2013; D69, 2340-2352. [google scholar]
  • 22- Tana X., Bertonati C., Qina L., Furioc L., El Amria C., Hovnanian A., Reboud-Ravaux M., Villoutreix B.O.
    Identification by in silico and in vitro screenings of small organic molecules acting as reversible inhibitors of kallikreins.
    European Journal of Medicinal Chemistry 2013; 70:661-8. [google scholar]
  • 21- Shen Y., Picord G., Guyon F., Tufféry P.
    Detecting protein candidate fragments using a structural alphabet profile comparison approach.
    Plos ONE 2013; 8(11):e80493.
  • 20- Maingot L., Elbakali J., Dumont J., Bosc D., Cousaert N., Urban A., Deglane G., Villoutreix B.O., Nagase H., Sperandio O., Leroux F., Deprez B., Deprez-Poulain R.
    Aggrecanase-2 inhibitors based on the acylthiosemicarbazide zinc-binding group.
    European Journal of Medicinal Chemistry 2013; 69C:244-261. [google scholar]
  • 19- Gautier L., Taboureau O., Audouze K.
    The effect of network biology on drug toxicology.
    Expert Opin Drug Metab Toxicol. 2013; 9(11):1409-18. [google scholar]
  • 18- Martiny V.Y., Carbonell P., Lagorce D., Villoutreix B.O., Moroy G., Miteva M.A.
    In silico mechanistic profiling to probe small molecule binding to sulfotransferases.
    PLos One. 2013; 8(9):e73587 [google scholar]
  • 17- S. Val, C. Liousse, EH. Doumbia, C. Galy-Lacaux, H. Cachier, N. Marchand, A. Badel, E. Gardrat, A. Sylvestre, A. Baeza-Squiban
    Physico-chemical characterization of African urban aerosols (Bamako in Mali and Dakar in Senegal) and their toxic effects in human bronchial epithelial cells: description of a worrying situation.
    Part Fibre Toxicol. 2013; 10(1):10 [google scholar]
  • 16- Martiny V.Y., Miteva M.A.
    Advances in molecular modeling of human cytochrome P450 polymorphism.
    J. Mol. Biol. 2013; 425(21):3978-92. [google scholar]
  • 15- Isvoran A., Craciun D., Martiny V.Y., Sperandio O., Miteva M.A.
    Computational analysis of protein-protein interfaces involving an alpha helix: insights for terphenyl-like molecules binding.
    BMC Pharmacol Toxicol. 2013; 14(1):31. [google scholar]
  • 14- Pérot S. , Regad L. , Reynès C., Sperandio O. , Miteva M.A., Villoutreix B.O., Camproux A-C.
    Insights into an Original Pocket-Ligand Pair Classification: A Promising Tool for Ligand Profile Prediction
    Plos One, 2013; 8(6):e63730 [google scholar]
  • 13- Villoutreix B.O., Largorce D., Labbé C.M., Sperandio O., Miteva M.A.
    One hundred thousand mouse clicks down the road: a compilation of online resources supporting drug discovery collected over a decade.
    Drug Discovery Today, 2013; 18(21-22):1081-9. [google scholar]
  • 12- Tana X., Furio L., Reboud-Ravaux M., Villoutreix B.O., Hovnanian A., El Amri C.
    1,2,4-triazole derivatives as transient inactivators of kallikreins involved in skin diseases
    Bioorganic & Medicinal Chemistry Letters, 2013; 23(16):4547-51. [google scholar]
  • 11- Kouskoumvekaki I;, Petersen R.K;, Fratev F., Taboureau O., Nielsen T.E., Oprea T.I., Sonne S.B., Flindt E.N., Jónsdóttir S.Ó., Kristiansen K.
    Discovery of a Novel Selective PPARγ Ligand with Partial Agonist Binding Properties by Integrated in Silico/in Vitro Work Flow.
    J Chem Inf Model., 2013; 53(4):923-37 [google scholar]
  • 10- Taboureau O., Jacobsen UP., Kalhauge C., Edsgärd D., Rigina O;, Gupta R;, Audouze K.
    HExpoChem: a systems biology resource to explore human exposure to chemicals.
    Bioinformatics, 2013; 29(9):1231-2. [google scholar]
  • 9- Pencheva T., Jereva D., Miteva M.A., Pajeva I.
    Post-docking Optimization and Analysis of Protein-Ligand Interactions of Estrogen Receptor Alpha using AMMOS Software.
    Curr Comput Aided Drug Design, 2013; 9(1):83-94. [google scholar]
  • 8- Labbé C.M., Laconde G., Kuenemann M.A., Villoutreix B.O., Sperandio O.
    iPPI-DB: A manually curated and interactive database of small non-peptide inhibitors of protein–protein interactions.
    Drug Discovery Today. 2013, 18(19-20):958-68. [google scholar]
  • 7- Calzavarini S., Villoutreix B.O., Lunghi B., Livaja R., Bernardi F., Dahlbëack B.
    Molecular basis of coagulation factor V deficiency caused by the R1698W inter-domain mutation.
    Thromb Haemost. 2013, 110(1):31-8. [google scholar]
  • 6- Zhang Z., Witham S., Petukh M., Moroy G., Miteva M.A., Ikeguchi Y., Alexov E.
    A rational free energy-based approach to understanding and targeting disease-causing missense mutations.
    J Am Med Inform Assoc. 2013; 20(4):643-51. [google scholar]
  • 5- Dirami T., Rode B., Jollivet M., Da Silva N., Escalier D., Gaitch N., Norez C., Tufféry P., Wolf J.P., Becq F., Ray P.F., Dulioust E., Gacon G., Bienvenu T., and Touré A.
    Missense mutations in SLC26A8, encoding a sperm-specific activator of the Cystic Fibrosis Transmembrane conductance Regulator.
    The American Journal of Human Genetics, 2013, 92(5):760-6. [google scholar]
  • 4- Marechal X., Genin E., Qin L., Sperandio O., Montes M., Basse N., Richy N., Miteva M.A., Reboud-Ravaux M., Vidal J., Villoutreix B.O.
    1,2,4-Oxadiazoles identified by virtual screening and their non-covalent inhibition of the human 20S proteasome.
    Current Medicinal Chemistry, 2013; 20(18):2351-62. [google scholar]
  • 3- J.J. Chan, D. Flatters, F. Rodrigues-Lima, J. Yan, K. Thalassinos and M. Katan
    Comparative analysis of interactions of RASSF1-10
    Advances in Biological Regulation 2013, 53(2):190-201. [google scholar]
  • 2- Skovstrup S, Le Quement ST, Hansen T, Jakobsen TH, Harmsen M, Tolker-Nielsen T, Nielsen TE, Givskov M, Taboureau O.
    Identification of LasR Ligands through a Virtual Screening Approach.
    ChemMedChem. 2013; 8(1):157-63. [google scholar]
  • 1- Kim Kjærulff S, Wich L, Kringelum J, Jacobsen UP, Kouskoumvekaki I, Audouze K, Lund O, Brunak S, Oprea TI, Taboureau O.
    ChemProt-2.0: visual navigation in a disease chemical biology database.
    Nucleic Acids Res. 2013; 41(D1): D464–D469. [google scholar]



Book Chapters
  • 2- Petitjean M.
    The Chiral Index: Applications to Multivariate Distributions and to 3D molecular graphs.
    Proceedings of 12th International Symposium on Operational Research in Slovenia SOR’13, pp. 11-16,
    L. Zadnik Stirn, J. Zerovnik, J. Povh, S. Drobne, A. Lisec, Eds. Slovenian Society INFORMATIKA (SDI), Section for Operations Research (SOR).
    2013

  • 1- Martiny V., Pajeva I., Wiese M., Davis A., Miteva M.A.
    Chemoinformatic and chemogenomic approach to ADMET.
    «Predictive ADMET: Integrated approaches in Drug Discovery and Development» , John Wiley & Sons, Inc., Eds. J. Wang and L. Urban. 2013, in press










Oral presentations year 2013-2014  


  • 21- Miteva M.A..
    Criblage in silico de molécules à visée thérapeutique: approche et «Success stories».
    SSATT idfinnov, Rencontres «Chimie-Biologie», 18 mars 2014, Paris (Invited plenary lecture)
  • 20- Miteva M.A..
    In Silico Structure-based Approach for ADMET Prediction: Mechanistic Insights from Probing Small Molecule Binding to Metabolizing Enzymes
    SELECTBIO congres "ADME & Predictive Toxicology" , 18-19 February 2014, Barcelona, Spain
  • 19- Leslie REGAD & Claudine Mayer
    Comparative analysis of ATP-binding sites of type II topoisomerase: Preliminary studies for the development of M. tuberculosis DNA gyrase inhibitors
    Journée Scientifique de l’UFR Sciences du Vivant, Université Paris Diderot, 3 décembre 2013, Paris
  • 18- Sperandio O.
    Toward a generation of drug-like inhibitors of protein-protein interactions
    Institut de Recherche Servier, 20 Novembre 2013, Croissy sur Seine.
  • 17- Sperandio O.
    What compounds for what PPI target?
    Sixth Annual meeting Protein-Protein Interactions - Targeting PPI for therapeutic interventions, Avril 17-18 2013, San Diego, Californie, USA.
  • 16- Sperandio O.
    What compounds for what PPI target?
    University of Dusselforf, janvier 2013, Dusselforf, Germany.
  • 15- Kuenemann M., Labbé C.M., Lagorce D., Miteva M.A., Villoutreix B.O., Sperandio O.
    Toward a generation of drug-like inhibitors of protein-protein interactions
    6èmes journées de la Société Française de Chemoinformatique (SFCi), 10 et 11 octobre 2013, Inria Nancy Grand Est - LORIA, Nancy.
  • 14- Benkaidali L., André F., Maurel F., Petitjean M.
    In-silico prediction of P450 cytochromes substrates through virtual screening and geometric modeling of active site access channels. - Best talk award.
    6èmes journées de la Société Française de Chemoinformatique (SFCi), 10 et 11 octobre 2013, Inria Nancy Grand Est - LORIA, Nancy.
  • 13- Petitjean M.
    The Chiral Index: Applications to Multivariate Distributions and to 3D molecular graphs.
    SOR'13, Dolenjske Toplice, Slovenia, September 25-27, 2013 (Invited plenary lecture)
  • 12- Taboureau O.
    Pharmacological profiling of drugs by linking chemoinformatics and bioinformatics data
    ACS national meeting, New Orleans, Louisiana, April 7-11, 2013.
  • 11- Camproux A-C.
    Chair-woman : Biologie Structurale
    JOBIM 2013 (Journées Ouvertes Biologie Informatique Mathématiques), 1-4 juillet 2013, Toulouse, France
  • 10- Miteva M.A.
    Invited spearker : Structure-based approach for ADMET prediction
    Clemson University USA, 16 April 2013
  • 9- Miteva M.A.
    Invited spearker : Predicting ligand interactions with metabolizing enzymes: an in silico structure-based approach.
    Annual meeting of the American Society for Pharmacology and Experimental Therapeutics (ASPET), April 20-24, 2013, Boston, USA
  • 8- Miteva M.A.
    Invited spearker : Introduction to virtual screening and in silico drug design.
    CSB 2013 « 20 Years Structural Biochemistry at Karolinska Institutet NOVUM, the past and the future ». 25-27 May 2013 Stockholm, Sweden
  • 7- Villoutreix B.O.
    Chairman, Upcoming Anticoagulants
    The International Society on Thrombosis and Haemostasis (ISTH), World congress, Monday July 1, 2013, Amsterdam
  • 6- Villoutreix B.O.
    Invited spearker: Rational design of future low molecular weight anticoagulant medications: can we get assistance from novel computational drug discovery methods?
    The International Society on Thrombosis and Haemostasis (ISTH), World congress, Monday July 1, 2013, Amsterdam
  • 5- Gerry A.F. Nicolaes, Oliver Sperandio, Jan Voorberg, Mahesh Kulharia, Aleksandra Wroblewska, Simone Wielders, Roy Schrijver and Bruno O. Villoutreix.
    Targeting of the tenase complex by rational design of factor VIII-membrane interaction inhibitors
    Drug Discovery & Therapy World Congree June 3-6 2013, Boston
  • 4- Villoutreix B.O.
    Chairman, Protein-protein interactions: new perspectives
    1st SCT international Workshop on Biologically Relevant Molecular Diversity, Maison de la Chimie, Avril 2013, Paris
  • 3- Thévenet P., Shen Y., Maupetit J., Guyon F., Derreumaux P., Tufféry P.
    PEP-FOLD, une approche de prédiction de novo de peptides linéaires et cyclisés par des ponts disulfures.
    Groupe de Graphisme et de Modélisation Moléculaire (GGMM 2013), 21-23 mai 2013, Saint-Pierre d’Oléron, France.
  • 2- Regad L., Taboureau O., Camproux A-C.
    Characterization of pocket-ligand interactions in the perspective of prediction of drug side effect
    Groupe de Graphisme et de Modélisation Moléculaire (GGMM 2013), 21-23 mai 2013, Saint-Pierre d’Oléron, France.
  • 1- Martiny V.Y., Moroy G., Villoutreix B.O., Miteva M.A.
    In silico mechanistic approach to probe drug-like molecules binding to sulfotransferases.
    XXème journée des jeunes chercheurs S.C.T, 7-8 février 2013, Romainville, France.





Posters year 2013-2014  


  • 18- Borrel A., Regad L., Camproux A-C., Xhaard H.
    Salt bridges in protein-ligand interactions
    Winter School - National Doctoral Programme in Informational and Structural Biology (ISB) December 9-12, Saariselkä - Finland
  • 17- Martiny V.Y., Chevillard F., Moroy G., Vayer Ph., Villoutreix B.O., Miteva M.A.
    Prédiction d’interactions de molécules « drug-like » avec des enzymes du métabolisme: une approche mécanistique in silico
    6ièmes journée de la SFCI (10-11 Octobre 2013), Nancy
  • 16- Lagorce D., Sperandio O., Miteva M.A., Villoutreix B.O.
    The FAF-Drugs2 server: a multi-step engine to prepare electronic chemical compound collections and to evaluate hit compounds
    6ièmes journée de la SFCI (10-11 Octobre 2013), Nancy
  • 15- Jean-Baptiste Chéron, Alexandre Borrel, Michel Petitjean, Claudine Mayer, Anne-Claude Camproux, Leslie Regad
    Comparison of the inhibitor-binding sites of type II topoisomerase
    6ièmes journée de la SFCI (10-11 Octobre 2013), Nancy
  • 14- Kuenemann M.A., Bourbon L.M.L., Labbé C.M., Sperandio O.
    Understanding the 3D characteristics of the PPI chemical space.
    6ièmes journée de la SFCI (10-11 Octobre 2013), Nancy
  • 13- Kuenemann M.A., Bourbon L.M.L., Labbé C.M., Sperandio O.
    Understanding the 3D characteristics of the PPI chemical space.
    - RICT 2013, Nice, France - July 3-5, 2013.
  • 12- Céline M. Labbé, Guillaume Laconde, Mélaine A. Kuenemann, Bruno O. Villoutreix, Olivier Sperandio
    iPPI-DB : a manually curated and interactive database of small non-peptide inhibitors of protein-protein interactions.
    6ièmes journée de la SFCI (10-11 Octobre 2013), Nancy
  • 11-Karine Moncoq, Leslie Regad, Stéphane Mann, Annick Méjean, Olivier Ploux
    Bases structurales de l’activité oxydase de la flavoprotéine AnaB impliquée dans la biosynthèsede la cyanotoxine anatoxine-a.
    AFC 2013, 02-05 Juillet 2013, Bordeaux France
  • 10- Kringelum, Taboureau O. and Lund O.
    Structural analysis of B cell epitopes and protein binding pockets
    RECOMB 2013, April 7-10, Bejing, China
  • 9- Taboureau O., Jacobsen UP., Kalhauge C., Edsgärd D., Rigina O., Ramneek G., Audouze K.
    HExpoChem: a systems biology resource to explore human exposure to chemicals
    COW workshop 2013, Copenhagen, May 28-31, 2013.
  • 8- Borrel A., Regad L., Xhaard H., Petitjean M., Camproux A.C.
    Druggability pocket prediction from apo and holo proteins.
    JOBIM 2013 (Journées Ouvertes Biologie Informatique Mathématiques), 1-4 juillet 2013, Toulouse, France
  • 7- Regad L., Flatters D., Geneix C., Camproux A.C.
    Modeling the pocket-ligand pairs space in a perspective of a better characterisation of the protein-ligand interactions.
    JOBIM 2013 (Journées Ouvertes Biologie Informatique Mathématiques), 1-4 juillet 2013, Toulouse, France
  • 6- Isvoran A., Craciun D., Martiny V.Y., Ciorsac A., Sperandio O., Miteva M. A.
    Computational analysis of protein-protein interactions involving an alpha helix and their inhibition by small molecular weight mimetics.
    12th National Conference on Biophysics «CNB 2013» - Biophysics for Health, IASI, ROMANIA , JUNE 13-16, 2013.
  • 5- Zhang Z., Martiny V.Y., Lagorce D., Alexov E., Miteva M.A.
    Syndrome: Rescuing the Disease-Causing Effect of G56S mutant by Small Molecule Binding.
    March Meeting of The American Physical Society, March 18-22, 2013, Baltimore, USA.
  • 4- Thévenet P., Shen Y., Maupetit J., Guyon F., Derreumaux P., Tufféry P.
    PEP-FOLD, a de novo approach for the prediction of the structure of linear and disulfide bridge cyclised peptide.
    XVIIIème congrès du Groupe Français des Peptides et des Protéines, 26-31 mai 2013 (Sète),France.
  • 3- Laurent M.A., Theret N., Tufféry P., Moroy G.
    Identification des modes d’interaction entre ADAMTS1 et des peptides dérivant de LAP-TGFb.
    Groupe de Graphisme et de Modélisation Moléculaire (GGMM 2013), 21-23 mai 2013, Saint-Pierre d’Oléron, France.
  • 2- Kuenemann M.A., Labbé C.M., Laconde G., Sperandio O.
    Navigating the chemical space of protein-protein interactions inhibitors. Which chemical compounds for which PPI targets ?
    - Best poster award
    XXème journée des jeunes chercheurs S.C.T, 7-8 février 2013, Romainville, France.
  • 1- Borrel A., Regad L., Xhaard H., Petitjean M., Camproux A.C.
    Statistical models predicting the «druggability» of protein pockets
    XXème journée des jeunes chercheurs S.C.T, 7-8 février 2013, Romainville, France.




- last update : April 2014