2011

2011

Articles

  • 1 – 2011 ; Bornot, A. ; Etchebest, C. ; de Brevern, A. G.
    Predicting protein flexibility through the prediction of local structures
    PROTEINS ; 79 ; (3) 839-52 ; [google scholar] 
  • 2 – 2011 ; Esque, J. ; Oguey, C. ; de Brevern, A. G.
    Comparative analysis of threshold and tessellation methods for determining protein contacts
    J CHEM INF MODEL ; 51 ; (2) 493-507 ; [google scholar] 
  • 3 – 2011 ; de Brevern, A.G.; Joseph, A.P.
    Species Specific Amino Acid Sequence – Protein Local Structure Relationships: an analysis in the light of a structural alphabet.
    J. THEO. BIOL. ; 276 ; (1) 209-17 ; [google scholar] 
  • 4 – 2011 ; Jallu, V.; Poulain, P.; Kaplan, C.; de Brevern, A.G.
    3D protein structure modeling: A tool to provide insight into the platelet alloimmune response
    TRANSFUSION TODAY ; in press ; [google scholar] 
  • 5 – 2011 ; Morin, N. ; Cescut, J. ; Beopoulos, A. ; Lelandais, G. ; Le Berre, V. ; Uribelarrea, J. L. ; Molina-Jouve, C. ; Nicaud, J. M.
    Transcriptomic analyses during the transition from biomass production to lipid accumulation in the oleaginous yeast Yarrowia lipolytica
    PLOS ONE ; 6 ; (11) e27966 ; [google scholar] 
  • 6 – 2011 ; Gelly, J. C. ; de Brevern, A. G.
    Protein Peeling 3D: new tools for analyzing protein structures
    BIOINFORMATICS ; 27 ; 132–133 ; [pmid:21075745] [doi:10.1093/bioinformatics/btq610] [google scholar] 
  • 7 – 2011 ; Gelly, J. C. ; Orgeur, M. ; Jacq, C. ; Lelandais, G.
    MitoGenesisDB: an expression data mining tool to explore spatio-temporal dynamics of mitochondrial biogenesis
    NUCLEIC ACIDS RES. ; 39 ; D1079–1084 ; [pmid:20833631] [doi:10.1093/nar/gkq781] [google scholar] 
  • 8 – 2011 ; Agarwal, G. ; Mahajan, S. ; Srinivasan, N. ; de Brevern, A. G.
    Identification of local conformational similarity in structurally variable regions of homologous proteins using protein blocks
    PLOS ONE ; 6 ; e17826 ; [google scholar] 
  • 9 – 2011 ; Mansiaux, Y. ; Joseph, A.P. ; Gelly, J.C.. ; de Brevern, A. G.
    Assignment of PolyProline II conformation and analysis of sequence – structure relationship
    PLOS ONE ; 6 ; e18401 ; [google scholar] 
  • 10 – 2011 ; Goudot, C. ; Etchebest, C. ; Devaux, F. ; Lelandais, G.
    The Reconstruction of Condition-Specific Transcriptional Modules Provides New Insights in the Evolution of Yeast AP-1 Proteins
    PLOS ONE ; 6 ; e20924 ; [google scholar] 
  • 11 – 2011 ; Gelly, J. C. ; Joseph, A. P. ; Srinivasan, N. ; de Brevern, A. G.
    iPBA: a tool for protein structure comparison using sequence alignment strategies
    NUCLEIC ACIDS RES. ; 39 ; 18–23 ; [google scholar] 
  • 12 – 2011 ; Joseph, A. P. ; Srinivasan, N. ; de Brevern, A. G.
    Improvement of protein structure comparison using a structural alphabet
    BIOCHIMIE ; 93 ; 1434–1445 ; [google scholar] 
  • 13 – 2011 ; Chilamakuri, C. S. ; Joshi, A. ; Rani, S. S. ; Offmann, B. ; Sowdhamini, R.
    Cross-Genome Comparisons of Newly Identified Domains in Mycoplasma gallisepticum and Domain Architectures with Other Mycoplasma species
    COMP. FUNCT. GENOMICS ; 2011 ; 878973 ; [google scholar] 
  • 14 – 2011 ; Gonzalez-Rubio, P. ; Gautier, R. ; Etchebest, C. ; Fuchs, P. F.
    Amphipathic-Lipid-Packing-Sensor interactions with lipids assessed by atomistic molecular dynamics
    BIOCHIM. BIOPHYS. ACTA ; 1808 ; 2119–2127 ; [google scholar] 
  • 15 – 2011 ; Pham, V. L. ; Gouzy-Darmon, C. ; Pernier, J. ; Hanquez, C. ; Hook, V. ; Beinfeld, M. C. ; Nicolas, P. ; Etchebest, C. ; Foulon, T. ; Cadel, S.
    Mutation in the substrate-binding site of aminopeptidase B confers new enzymatic properties
    BIOCHIMIE ; 93 ; 730–741 ; [google scholar] 
  • 16 – 2011 ; Dall’Olio, G. M. ; Marino, J. ; Schubert, M. ; Keys, K. L. ; Stefan, M. I. ; Gillespie, C. S. ; Poulain, P. ; Shameer, K. ; Sugar, R. ; Invergo, B. M. ; Jensen, L. J. ; Bertranpetit, J. ; Laayouni, H.
    Ten simple rules for getting help from online scientific communities
    PLOS COMPUT. BIOL. ; 7 ; (9) e1002202 ; [pmid:21980280] [doi:10.1371/journal.pcbi.1002202] [google scholar] 
  • 17 – 2011 ; Horta, B. A. C.; Fuchs, P. F. J.; van Gunsteren, W. F.; H├╝nenberger, P. H.
    New Interaction Parameters for Oxygen Compounds in the GROMOS Force Field: Improved Pure-Liquid and Solvation Properties for Alcohols, Ethers, Aldehydes, Ketones, Carboxylic Acids, and Esters
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION ; 7 ; (4) 1016-1031 ; [doi:10.1021/ct1006407] [google scholar] 
  • 18 – 2011 ; Olivieri, Lilian; Gardebien, Fabrice
    Molecular Dynamics Simulations of a Binding Intermediate between FKBP12 and a High-Affinity Ligand
    JOURNAL OF CHEMICAL THEORY AND COMPUTATION ; 7 ; (3) 725-741 ; [doi:10.1021/ct100394d] [google scholar] 
  • 19 – 2011 ; Rossi, Giulia; Monticelli, Luca; Puisto, Sakari R.; Vattulainen, Ilpo; Ala-Nissila, Tapio
    Coarse-graining polymers with the MARTINI force-field: polystyrene as a benchmark case
    SOFT MATTER ; 7 ; (2) 698-708 ; [doi:10.1039/c0sm00481b] [google scholar] 
  • 20 – 2011 ; Amiard, A.; Baczynski, C. ; Blanchet C.; de Brevern, A.G.; Dorlanne-Messiaen, E. ; Grognard, E.; Kisselova, G.; Malpertuy, A.; Menez-Jamet, J. ; Racle I.; Rouger, C.
    Electronic laboratory notebook (eLN)
    STP PHARMA PRATIQUES ; 21 ; (6) 475-503 ; [google scholar] 




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