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Bibliography

Journal articles

  1. Ferber, M., Kosinski, J., Ori, A., Rashid, U. J., Moreno-Morcillo Marı́a, Simon, B., … others. (2016). Automated structure modeling of large protein assemblies using crosslinks as distance restraints. Nature Methods. https://doi.org/10.1038/nmeth.3838
  2. Bouvier, G., Desdouits, N., Ferber, M., Blondel, A., & Nilges, M. (2015). An automatic tool to analyze and cluster macromolecular conformations based on Self-Organizing Maps. Bioinformatics, 31(9), 1490–1492. https://doi.org/10.1093/bioinformatics/btu849
  3. Cassioli, A., Bardiaux, B., Bouvier, G., Mucherino, A., Alves, R., Liberti, L., … Malliavin, T. E. (2015). An algorithm to enumerate all possible protein conformations verifying a set of distance constraints. BMC Bioinformatics, 16(1), 23. https://doi.org/10.1186/s12859-015-0451-1
  4. Harigua-Souiai, E., Cortes-Ciriano, I., Desdouits, N., Malliavin, T. E., Guizani, I., Nilges, M., … Bouvier, G. (2015). Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis. BMC Bioinformatics, 16(1), 93. https://doi.org/10.1186/s12859-015-0518-z
  5. Cortes-Ciriano, I., Bouvier, G., Nilges, M., Maragliano, L., & Malliavin, T. E. (2015). Temperature Accelerated Molecular Dynamics with Soft-Ratcheting Criterion Orients Enhanced Sampling by Low-Resolution Information. Journal of Chemical Theory and Computation, 11(7), 3446–3454. https://doi.org/10.1021/acs.jctc.5b00153
  6. Cortes-Ciriano, I., van Westen, G. J. P., Bouvier, G., Nilges, M., Overington, J. P., Bender, A., & Malliavin, T. E. (2015). Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel. Bioinformatics. https://doi.org/10.1093/bioinformatics/btv529
  7. Gault, J., Ferber, M., Machata, S., Imhaus, A.-F., Malosse, C., Charles-Orszag, A., … others. (2015). Neisseria meningitidis Type IV Pili Composed of Sequence Invariable Pilins Are Masked by Multisite Glycosylation. PLoS Pathog, 11(9), e1005162. https://doi.org/10.1371/journal.ppat.1005162
  8. Miri, L., Bouvier, G., Kettani, A., Mikou, A., Wakrim, L., Nilges, M., & Malliavin, T. E. (2014). Stabilization of the integrase-DNA complex by Mg2+ ions and prediction of key residues for binding HIV-1 integrase inhibitors: Integrase-DNA Complex and Binding of HIV-1 Integrase Inhibitors. Proteins, 82(3), 466–478. https://doi.org/10.1002/prot.24412
  9. Bouvier, G., Duclert-Savatier, N., Desdouits, N., Meziane-Cherif, D., Blondel, A., Courvalin, P., … Malliavin, T. E. (2014). Functional Motions Modulating VanA Ligand Binding Unraveled by Self-Organizing Maps. J. Chem. Inf. Model., 54(1), 289–301. https://doi.org/10.1021/ci400354b
  10. Nivaskumar, M., Bouvier, G., Campos, M., Nadeau, N., Yu, X., Egelman, E. H., … Francetic, O. (2014). Distinct Docking and Stabilization Steps of the Pseudopilus Conformational Transition Path Suggest Rotational Assembly of Type IV Pilus-like Fibers. Structure, 22(5), 685–696. https://doi.org/10.1016/j.str.2014.03.001
  11. Spill, Y. G., Bouvier, G., & Nilges, M. (2013). A convective replica-exchange method for sampling new energy basins. J. Comput. Chem., 34(2), 132–140. https://doi.org/10.1002/jcc.23113
  12. Mantsyzov, A. B., Bouvier, G., Evrard-Todeschi, N., & Bertho, G. (2012). Contact-based ligand-clustering approach for the identification of active compounds in virtual screening. Adv Appl Bioinform Chem, 5, 61–79. https://doi.org/10.2147/AABC.S30881
  13. Bouvier, G., Evrard-Todeschi, N., Girault, J.-P., & Bertho, G. (2010). Automatic clustering of docking poses in virtual screening process using self-organizing map. Bioinformatics, 26(1), 53–60. https://doi.org/10.1093/bioinformatics/btp623
  14. Bertho, G., Bouvier, G., Hoa, G. H. B., & Girault, J.-P. (2008). The key-role of tyrosine 155 in the mechanism of prion transconformation as highlighted by a study of sheep mutant peptides. Peptides, 29(7), 1073–1084. https://doi.org/10.1016/j.peptides.2008.03.014

International conferences

  1. Simenel, C., Bouvier, G., Nilges, M., & Pruneyre, N. I. (2016). Deciphering the Binding Mode of Promising Antituberculosis Compounds with their Bacterial Membrane Target in Living Cells by NMR. Biophysical Journal, 3(110), 542a.
  2. Ferber, M., Nilges, M., & Bouvier, G. (2016). Automated Cross-Links-Based Conformational Sampling of Protein Assemblies: The Geometrical Challenge of Cross-Links. Biophysical Journal, 110, 539a.
  3. Bouvier, G., Duclert-Savatier, N., Nilges, M., & Malliavin, T. E. (2016). Building Graphs to Describe Dynamics, Kinetics and Energetics in the D-Ala: D-Lac Ligase Vana. Biophysical Journal, 3(110), 378a.
  4. Ciriano, I. C., Bouvier, G., Nilges, M., Maragliano, L., & Malliavin, T. E. (2014). Enhanced Sampling of the Catalytic Domain of the Adenyl Cyclase CyaA from Bordetella Pertussis. Biophysical Journal, 106(2), 610a. https://doi.org/10.1016/j.bpj.2013.11.3374
  5. Nilges, M., Nivaskumar, M., Bouvier, G., Campos, M., Egelman, E. H., Yu, X., & Francetic, O. (2014). Structural Basis of Conformational Transitions Involved in Pseudopilus Assembly and Stability. Biophysical Journal, 106(2, Supplement 1), 26a. https://doi.org/10.1016/j.bpj.2013.11.197
  6. Nilges, M., Bouvier, G., Batista, P. R., & Spill, Y. (2013). Structures of Biomolecular Complexes from Heterogeneous Data and Bayesian Data Analysis. Biophysical Journal, 104(2, Supplement 1), 376a. https://doi.org/10.1016/j.bpj.2012.11.2089
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