Bioinformatics

  Analysis and prediction of protein quaternary structure A. Poupon & Joël Janin Methods in Molecular Biology, in press.

  Mesures Hiérarchiques pondérées pour l’évaluation d’ un système semi-automatique d’annotation de génomes utilisant des arbres de décision Lucie Gentils, Jérôme Azé, Claire Toffano-Nioche, Valentin Loux, Anne Poupon, Jean-François Gibrat, Christine Froidevaux Proceedings de EGC 2008

  The VIZIER project: Preparedness against pathogenic RNA viruses. Coutard B, Gorbalenya AE, Snijder EJ, Leontovich AM, Poupon A, De Lamballerie X, Charrel R, Gould EA, Gunther S, Norder H, Klempa B, Bourhy H, Rohayem J, L’hermite E, Nordlund P, Stuart DI, Owens RJ, Grimes JM, Tucker PA, Bolognesi M, Mattevi A, Coll M, Jones TA, Aqvist J, Unge T, Hilgenfeld R, Bricogne G, Neyts J, La Colla P, Puerstinger G, Gonzalez JP, Leroy E, Cambillau C, Romette JL, Canard B. Antiviral Res. 2008 Apr;78(1):37-46

  DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions. Bernauer J, Bahadur RP, Rodier F, Janin J, Poupon A. Bioinformatics. 2008 Mar 1;24(5):652-8

  Towards a semi-automatic functional annotation tool based on decision tree techniques. J. Azé, L. Gentils, C. Toffano-Nioche, V. Loux, J-F. Gibrat, P. Bessières, C. Rouveirol, A. Poupon, and C. Froidevaux. In Proceedings of the International Conference on Machine Learning in Systems Biology (MLSB 2007), in press

  Production and crystallization of protein domains: how useful are disorder predictions ? S. Quevillon-Cheruel, N. Leulliot, L. Gentils, H. van Tilbeurgh and A. Poupon Curr Protein Pept Sci. 2007 Apr;8(2):151-60. Review.

  Data Management in Structural Genomics: an Overview S. Haquin, E. Oeuillet, A. Pajon, M. Harris, A.T. Jones, H. van Tilbeurgh, J.L. Markley, Z. Zolnai, and A. Poupon Methods in Molecular Biology, in press.

  A new protein-protein docking scoring function based on interface residue properties Bernauer J, Aze J, Janin J, Poupon A. Bioinformatics. 2007 Mar 1;23(5):555-62

  Une nouvelle fonction de score pour l’amarrage protéine-protéine fondée sur les diagrammes de Voronoï Julie Bernauer, Jérôme Azé, Joël Janin, Anne Poupon Proceedings de JOBIM 2005

  HalX: an open-source LIMS (Laboratory Information Management System) for small to large scale labs Jaime Prilusky, Eric Oeuillet, Nathalie Ulryck, Anne Pajon, Julie Bernauer, Isabelle Krimm, Sophie Quevillon-Cheruel, Nicolas Leulliot, Marc Graille, Dominique Liger, Lionel Trésaugues, Joel L. Sussman, Joël Janin, Herman van Tilbeurgh, and Anne Poupon Acta Crystallogr D Biol Crystallogr. 2005 Jun;61(Pt 6):671-8.

  A docking analysis of the statistical physics of protein protein recognition Julie Bernauer, Anne, Poupon, Jerome Aze, Joel Janin Physical Biology, 2005, 2, S17-S23

  Prediction of unfolded segments in a protein sequence based on amino acid composition Karen Coeytaux and Anne Poupon Bioinformatics 2005 21: 1891 - 1900.

  Design of a data model for developing laboratory information management and analysis systems for protein production Pajon A, Ionides J, Diprose J, Fillon J, Fogh R, Ashton AW, Berman H, Boucher W, Cygler M, Deleury E, Esnouf R, Janin J, Kim R, Krimm I, Lawson CL, Oeuillet E, Poupon A, Raymond S, Stevens T, van Tilbeurgh H, Westbrook J, Wood P, Ulrich E, Vranken W, Xueli L, Laue E, Stuart DI, Henrick K Proteins. 2005 Feb 1;58(2):278-84.

  Voronoi and Voronoi-related tessellations in studies of protein structure and interaction Poupon A Curr Opin Struct Biol. 2004 Apr;14(2):233-41. Review.

  Origin and evolution of transmembrane Chl-binding proteins: hydrophobic cluster analysis suggests a common one-helix ancestor for prokaryotic (Pcb) and eukaryotic (LHC) antenna protein superfamilies Garczarek L, Poupon A, Partensky F FEMS Microbiol Lett. 2003 May 16;222(1):59-68.

  Exp-DB: Fast Development of Information Naem NA, Raymond S, Poupon A, Cygler M, Kemme B CAiSE Short Paper Proceedings 2003

  Links between topological and physicochemical properties of amino acids in globular proteins constrain ab-initio fold prediction. A. Poupon & J.P. Mornon (2001) Theoretical Chemistry Accounts, 106, 113-120.

  Beta-sheet modeling by helical surfaces. Znamenskiy D, Le Tuan K, Poupon A, Chomilier J, Mornon JP. Protein Eng. 2000 Jun;13(6):407-12.

  "Topohydrophobic positions" as key markers of globular protein folds, 4. A. Poupon & J-P Mornon (1999) Theoretical Chemistry Accounts, 101, 2-8.

  The immunoglobulin fold family: sequence analysis and 3D structure comparisons. Halaby DM, Poupon A, Mornon J. Protein Eng. 1999 Jul;12(7):563-71.

  Predicting the protein folding nucleus from sequences. Poupon A, Mornon JP. FEBS Lett. 1999 Jun 11;452(3):283-9. Erratum in: FEBS Lett 1999 Sep 3:457(3):525.

  Populations of hydrophobic amino acids within protein globular domains: identification of conserved "topohydrophobic" positions. Poupon A, Mornon JP. Proteins. 1998 Nov 15;33(3):329-42.

  Deciphering protein sequence information through hydrophobic cluster analysis (HCA): current status and perspectives. Callebaut I, Labesse G, Durand P, Poupon A, Canard L, Chomilier J, Henrissat B, Mornon JP. Cell Mol Life Sci. 1997 Aug;53(8):621-45. Review.

Structural genomics

  Cloning, production and purification of proteins for a small scale structural genomics project Bruno Collinet, Lionel Trésaugues, Philippe Minard, Gilles Henkes, Robert Aufrère, Karine Blondeau, Nabila Bettache, Cong-Zhao Zhou, Dominique Liger, Joël Janin, Anne Poupon, Herman van Tilbeurgh and Sophie Quevillon-Cheruel Methods Mol Biol. 2007;363:21-37.

  Crystal structure and confirmation of the alanine:glyoxylate aminotransferase activity of the YFL030w yeast protein. Meyer P, Liger D, Leulliot N, Quevillon-Cheruel S, Zhou CZ, Borel F, Ferrer JL, Poupon A, Janin J, van Tilbeurgh H. Biochimie. 2005 Dec;87(12):1041-7.

  High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics Project: one size fits all? Leulliot N, Tresaugues L, Bremang M, Sorel I, Ulryck N, Graille M, Aboulfath I, Poupon A, Liger D, Quevillon-Cheruel S, Janin J, van Tilbeurgh H. Acta Crystallogr D Biol Crystallogr. 2005 61(Pt 6):664-70.

  Crystal structure of the YML079w protein from Saccharomyces cerevisiae reveals a new sequence family of the jelly-roll fold. Zhou CZ, Meyer P, Quevillon-Cheruel S, De La Sierra-Gallay IL, Collinet B, Graille M, Blondeau K, Francois JM, Leulliot N, Sorel I, Poupon A, Janin J, Van Tilbeurgh H Protein Sci. 2005 Jan;14(1):209-15.

  The Paris-Sud yeast structural genomics pilot-project: from structure to function Quevillon-Cheruel S, Liger D, Leulliot N, Graille M, Poupon A, de La Sierra-Gallay IL, Zhou CZ, Collinet B, Janin J, Van Tilbeurgh H Biochimie. 2004 Sep-Oct;86(9-10):617-23.

  Crystal structure of the YDR533c S. cerevisiae protein, a class II member of the Hsp31 family. Graille M, Quevillon-Cheruel S, Leulliot N, Zhou CZ, de la Sierra Gallay IL, Jacquamet L, Ferrer JL, Liger D, Poupon A, Janin J, van Tilbeurgh H Structure (Camb). 2004 May;12(5):839-47.

  Crystal structure of the YGR205w protein from Saccharomyces cerevisiae: close structural resemblance to E. coli pantothenate kinase de La Sierra-Gallay IL, Collinet B, Graille M, Quevillon-Cheruel S, Liger D, Minard P, Blondeau K, Henckes G, Aufrere R, Leulliot N, Zhou CZ, Sorel I, Ferrer JL, Poupon A, Janin J, van Tilbeurgh H Proteins. 2004 Mar 1;54(4):776-83.

  Structure of protein phosphatase methyltransferase 1 (PPM1), a leucine carboxyl methyltransferase involved in the regulation of protein phosphatase 2A activity Leulliot N, Quevillon-Cheruel S, Sorel I, de La Sierra-Gallay IL, Collinet B, Graille M, Blondeau K, Bettache N, Poupon A, Janin J, van Tilbeurgh H J Biol Chem. 2004 Feb 27;279(9):8351-8.

  Crystal structure of the bifunctional chorismate synthase from Saccharomyces cerevisiae Quevillon-Cheruel S, Leulliot N, Meyer P, Graille M, Bremang M, Blondeau K, Sorel I, Poupon A, Janin J, van Tilbeurgh H J Biol Chem. 2004 Jan 2;279(1):619-25.

  Crystal structure of the yeast Phox homology (PX) domain protein Grd19p complexed to phosphatidylinositol-3-phosphate. Zhou CZ, de La Sierra-Gallay IL, Quevillon-Cheruel S, Collinet B, Minard P, Blondeau K, Henckes G, Aufrere R, Leulliot N, Graille M, Sorel I, Savarin P, de la Torre F, Poupon A, Janin J, van Tilbeurgh H J Biol Chem. 2003 Dec 12;278(50):50371-6.

  A structural genomics initiative on yeast proteins Quevillon-Cheruel S, Collinet B, Zhou CZ, Minard P, Blondeau K, Henkes G, Aufrere R, Coutant J, Guittet E, Lewit-Bentley A, Leulliot N, Ascone I, Sorel I, Savarin P, de La Sierra Gallay IL, de la Torre F, Poupon A, Fourme R, Janin J, van Tilbeurgh H. J Synchrotron Radiat. 2003 Jan 1;10(Pt 1):4-8. Epub 2002 Dec 24.

Other projects

  The uteroglobin fold. Callebaut I, Poupon A, Bally R, Demaret JP, Housset D, Delettre J, Hossenlopp P, Mornon JP. Ann N Y Acad Sci. 2000;923:90-112. Review.

  Functional specificity conferred by the unique plasticity of fully alpha-helical Ras and Rho GAPs. Souchet M, Poupon A, Callebaut I, Leger I, Mornon J, Bril A, Calmels TP. FEBS Lett. 2000 Jul 14;477(1-2):99-105.

  Sequence and structural features of the T-fold, an original tunnelling building unit. Colloc’h N, Poupon A, Mornon JP. Proteins. 2000 May 1;39(2):142-54.

  Structure modelling and site-directed mutagenesis of the rat aromatic L-amino acid pyridoxal 5’-phosphate-dependent decarboxylase: a functional study. Poupon A, Jebai F, Labesse G, Gros F, Thibault J, Mornon JP, Krieger M. Proteins. 1999 Nov 1;37(2):191-203.

  Hexokinase mitochondriale, enzyme clé de la bioénergétique cellulaire : une cible potentielle pour une thérapeutique anticancéreuse. 1. S. Oudard, E. Boitier, A. Poupon, L. Miccoli & M-F. Poupon. (1995) Médecine/science, 11, 1121-1129.