• 2025
  Mareuil F, Torchet R, Ruano LC, Mallet V, Nilges M, Bouvier G, Sperandio O, InDeepNet: a web platform for predicting functional binding sites in proteins using InDeep., Nucleic Acids Res 2025 May; (): .
• 2024
  Kamolrat Somboon, Oliver Melling, Maylis Lejeune, Glaucia M S Pinheiro, Annick Paquelin, Benjamin Bardiaux, Michael Nilges, Phillippe Delepelaire, Syma Khalid, Nadia Izadi-Pruneyre, Dynamic interplay between a TonB-dependent heme transporter and a TonB protein in a membrane environment, mBio, In press, pp.e0178124. ⟨10.1128/mbio.01781-24⟩.
• 2024
  Izadi-Pruneyre, N., Karami, Y., Nilges, M., Structure and Dynamics of Type 4a Pili and Type 2 Secretion System Endopili, In: Macromolecular Protein Complexes V, vol 104. Chapter 21. p549-563.
• 2024
  Alexandra Moine-Franel, Fabien Mareuil, Michael Nilges, Constantin Bogdan Ciambur, Olivier Sperandio, A comprehensive dataset of protein-protein interactions and ligand binding pockets for advancing drug discovery, Scientific Data , 2024, 11 (1), pp.402. ⟨10.1038/s41597-024-03233-z⟩.
• 2023
  Dazzoni R, Li Y, López-Castilla A, Brier S, Mechaly A, Cordier F, Haouz A, Nilges M, Francetic O, Bardiaux B, Izadi-Pruneyre N, Structure and dynamic association of an assembly platform subcomplex of the bacterial type II secretion system., Structure 2023 Feb; 31(2): 152-165.e7.
• 2022
  Bouvier G, Bardiaux B, Pellarin R, Rapisarda C, Nilges M, , Building Protein Atomic Models from Cryo-EM Density Maps and Residue Co-Evolution., Biomolecules 2022 Sep; 12(9): .
• 2022
  Jacobsen T, Dazzoni R, Renault MG, Bardiaux B, Nilges M, Shevchik V, Izadi-Pruneyre N, , Secondary structure and 1H, 15 N & 13C resonance assignments of the periplasmic domain of OutG, major pseudopilin from Dickeya dadantii type II secretion system., Biomol NMR Assign 2022 Apr; (): .
• 2022
  Temmam S, Vongphayloth K, Baquero E, Munier S, Bonomi M, Regnault B, Douangboubpha B, Karami Y, Chrétien D, Sanamxay D, Xayaphet V, Paphaphanh P, Lacoste V, Somlor S, Lakeomany K, Phommavanh N, Pérot P, Dehan O, Amara F, Donati F, Bigot T, Nilges M, Rey FA, van der Werf S, Brey PT, Eloit M, Bat coronaviruses related to SARS-CoV-2 and infectious for human cells., Nature 2022 Apr; 604(7905): 330-336.
• 2022
  Vincent Mallet, Luis Checa Ruano, Alexandra Moine Franel, Michael Nilges, Karen Druart, Guillaume Bouvier, Olivier Sperandio, InDeep: 3D fully convolutional neural networks to assist in silico drug design on protein–protein interactions, Bioinformatics, 2021, 38 (5), pp.1261 - 1268. ⟨10.1093/bioinformatics/btab849⟩.
• 2021
  Dazzoni R, López-Castilla A, Cordier F, Bardiaux B, Nilges M, Francetic O, Izadi-Pruneyre N, , 1 H, 15 N and 13 C resonance assignments of the C-terminal domain of PulL, a component of the Klebsiella oxytoca type II secretion system, Biomol NMR Assign . 2021 Oct;15(2):455-459. .
• 2021
  Sarah Temmam, Khamsing Vongphayloth, Eduard Baquero Salazar, Sandie Munier, Massimiliano Bonomi, Béatrice Régnault, Bounsavane Douangboubpha, Yasaman Karami, Delphine Chretien, Daosavanh Sanamxay, Vilakhan Xayaphet, Phetphoumin Paphaphanh, Vincent Lacoste, Somphavanh Somlor, Khaithong Lakeomany, Nothasin Phommavanh, Philippe Pérot, Flora Donati, Thomas Bigot, Michael Nilges, Félix Rey, Sylvie van Der Werf, Paul Brey, Marc Eloit, Coronaviruses with a SARS-CoV-2-like receptor-binding domain allowing ACE2-mediated entry into human cells isolated from bats of Indochinese peninsula, 2021.
• 2021
  Karami Y, López-Castilla A, Ori A, Thomassin JL, Bardiaux B, Malliavin T, Izadi-Pruneyre N, Francetic O, Nilges M, Computational and biochemical analysis of type IV pilus dynamics and stability., Structure 2021 Dec; 29(12): 1397-1409.e6.
• 2021
  van Belkum A, Almeida C, Bardiaux B, Barrass SV, Butcher SJ, Çaykara T, Chowdhury S, Datar R, Eastwood I, Goldman A, Goyal M, Happonen L, Izadi-Pruneyre N, Jacobsen T, Johnson PH, Kempf VAJ, Kiessling A, Bueno JL, Malik A, Malmström J, Meuskens I, Milner PA, Nilges M, Pamme N, Peyman SA, Rodrigues LR, Rodriguez-Mateos P, Sande MG, Silva CJ, Stasiak AC, Stehle T, Thibau A, Vaca DJ, Linke D, , Host-Pathogen Adhesion as the Basis of Innovative Diagnostics for Emerging Pathogens., Diagnostics (Basel) 2021 Jul; 11(7): .
• 2021
  Rachel Torchet, Karen Druart, Luis Checa Ruano, Alexandra Moine-Franel, Hélène Borges, Olivia Doppelt-Azeroual, Bryan Brancotte, Fabien Mareuil, Michael Nilges, Hervé Ménager, Olivier Sperandio, The iPPI-DB initiative: a community-centered database of protein–protein interaction modulators, Bioinformatics, 2021, 37 (1), pp.89-96. ⟨10.1093/bioinformatics/btaa1091⟩.
• 2019
  Bardiaux B, Cordier F, Brier S, López-Castilla A, Izadi-Pruneyre N, Nilges M, Dynamics of a type 2 secretion system pseudopilus unraveled by complementary approaches, J. Biomol. NMR 2019 Jul;73(6-7):293-303.
• 2019
  Bardiaux B, de Amorim GC, Luna Rico A, Zheng W, Guilvout I, Jollivet C, Nilges M, Egelman EH, Izadi-Pruneyre N, Francetic O. , Structure and Assembly of the Enterohemorrhagic Escherichia coli Type 4 Pilus., Structure. 2019 Apr 9. doi: 10.1016/j.str.2019.03.021..
• 2019
  Bonomi M, Hanot S, Greenberg CH, Sali A, Nilges M, Vendruscolo M, Pellarin R, Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling, Structure 27 (2019) 175-188.
• 2018
  Bouvier G, Simenel C, Jang J, Kalia NP, Choi I, Nilges M, Pethe K, Izadi-Pruneyre N. , Target engagement and binding mode of an anti-tuberculosis drug to its bacterial target deciphered in whole living cells by NMR., Biochemistry. 2019 Feb 12;58(6):526-533. doi: 10.1021/acs.biochem.8b00975. .
• 2018
  Xu C, Bouvier G, Bardiaux B, Nilges M, Malliavin T, Lisser A, Ordering Protein Contact Matrices, Comput Struct Biotechnol J. 2018 Mar;16:140-56.
• 2018
  Worley B, Delhommel F, Cordier F, Malliavin TE, Bardiaux B, Wolff N, Nilges M, Lavor C, Liberti L, Tuning interval Branch-and-Prune for protein structure determination, J Glob Optim. 2018 Sep; 72(1):109–27.
• 2016
  He L, Bardiaux B, Ahmed M, Spehr J, König R, Lünsdorf H, Rand U, Lührs T, Ritter C, Structure determination of helical filaments by solid-state NMR spectroscopy, Proc. Natl. Acad. Sci. U.S.A. 2016 Jan;113(3):E272-81.
• 2015
  Gault J, Ferber M, Machata S, Imhaus AF, Malosse C, Charles-Orszag A, Millien C, Bouvier G, Bardiaux B, Péhau-Arnaudet G, Klinge K, Podglajen I, Ploy MC, Seifert HS, Nilges M, Chamot-Rooke J, Duménil G, Neisseria meningitidis Type IV Pili Composed of Sequence Invariable Pilins Are Masked by Multisite Glycosylation, PLoS Pathog. 2015 Sep;11(9):e1005162.
• 2015
  Durand E, Nguyen VS, Zoued A, Logger L, Péhau-Arnaudet G, Aschtgen MS, Spinelli S, Desmyter A, Bardiaux B, Dujeancourt A, Roussel A, Cambillau C, Cascales E, Fronzes R, Biogenesis and structure of a type VI secretion membrane core complex, Nature 2015 Jul;523(7562):555-60.
• 2015
  Mareuil F, Malliavin TE, Nilges M, Bardiaux B, Improved reliability, accuracy and quality in automated NMR structure calculation with ARIA, J. Biomol. NMR 2015 Aug;62(4):425-38.
• 2014
  Bouvier G, Desdouits N, Ferber M, Blondel A, Nilges M, An automatic tool to analyze and cluster macromolecular conformations based on self-organizing maps, Bioinformatics 2015 May;31(9):1490-2.
• 2014
  Goyal P, Krasteva PV, Van Gerven N, Gubellini F, Van den Broeck I, Troupiotis-Tsaïlaki A, Jonckheere W, Péhau-Arnaudet G, Pinkner JS, Chapman MR, Hultgren SJ, Howorka S, Fronzes R, Remaut H, Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG, Nature 2014 Dec;516(7530):250-3.
• 2012
  Bardiaux B, van Rossum BJ, Nilges M, Oschkinat H, Efficient modeling of symmetric protein aggregates from NMR data, Angew. Chem. Int. Ed. Engl. 2012 Jul;51(28):6916-9.
• 2012
  Bardiaux B, Malliavin T, Nilges M, ARIA for solution and solid-state NMR, Methods Mol. Biol. 2012;831:453-83.
• 2011
  Mareuil F, Blanchet C, Malliavin TE, Nilges M, Grid computing for improving conformational sampling in NMR structure calculation, Bioinformatics 2011 Jun;27(12):1713-4.
• 2011
  Bernard A, Vranken WF, Bardiaux B, Nilges M, Malliavin TE, Bayesian estimation of NMR restraint potential and weight: a validation on a representative set of protein structures, Proteins 2011 May;79(5):1525-37.
• 2010
  Ramboarina S, Garnett JA, Zhou M, Li Y, Peng Z, Taylor JD, Lee WC, Bodey A, Murray JW, Alguel Y, Bergeron J, Bardiaux B, Sawyer E, Isaacson R, Tagliaferri C, Cota E, Nilges M, Simpson P, Ruiz T, Wu H, Matthews S, Structural insights into serine-rich fimbriae from Gram-positive bacteria, J. Biol. Chem. 2010 Oct;285(42):32446-57.
• 2010
  Bardiaux B, Favier A, Etzkorn M, Baldus M, Böckmann A, Nilges M, Malliavin TE, Simultaneous use of solution, solid-state NMR and X-ray crystallography to study the conformational landscape of the Crh protein during oligomerization and crystallization, Adv Appl Bioinform Chem 2010;3:25-38.
• 2009
  Bardiaux B, Bernard A, Rieping W, Habeck M, Malliavin TE, Nilges M, Influence of different assignment conditions on the determination of symmetric homodimeric structures with ARIA, Proteins 2009 May;75(3):569-85.
• 2009
  Duclert-Savatier N, Poggi L, Miclet E, Lopes P, Ouazzani J, Chevalier N, Nilges M, Delarue M, Stoven V, Insights into the enzymatic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei using structural data and molecular dynamics simulation, J. Mol. Biol. 2009 May;388(5):1009-21.
• 2008
  Nilges M, Bernard A, Bardiaux B, Malliavin T, Habeck M, Rieping W, Accurate NMR structures through minimization of an extended hybrid energy, Structure 2008 Sep;16(9):1305-12.
• 2008
  Bardiaux B, Bernard A, Rieping W, Habeck M, Malliavin TE, Nilges M, Graphical analysis of NMR structural quality and interactive contact map of NOE assignments in ARIA, BMC Struct. Biol. 2008;8:30.
• 2008
  Loquet A, Bardiaux B, Gardiennet C, Blanchet C, Baldus M, Nilges M, Malliavin T, Böckmann A, 3D structure determination of the Crh protein from highly ambiguous solid-state NMR restraints, J. Am. Chem. Soc. 2008 Mar;130(11):3579-89.
• 2006
  Delarue M, Duclert-Savatier N, Miclet E, Haouz A, Giganti D, Ouazzani J, Lopez P, Nilges M, Stoven V, Three dimensional structure and implications for the catalytic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei, J. Mol. Biol. 2007 Feb;366(3):868-81.
• 2006
  Rieping W, Habeck M, Bardiaux B, Bernard A, Malliavin TE, Nilges M, ARIA2: automated NOE assignment and data integration in NMR structure calculation, Bioinformatics 2007 Feb;23(3):381-2.
• 2006
  Loth K, Abergel D, Pelupessy P, Delarue M, Lopes P, Ouazzani J, Duclert-Savatier N, Nilges M, Bodenhausen G, Stoven V, Determination of dihedral Psi angles in large proteins by combining NH(N)/C(alpha)H(alpha) dipole/dipole cross-correlation and chemical shifts, Proteins 2006 Sep;64(4):931-9.
• 2006
  Bardiaux B, Malliavin TE, Nilges M, Mazur AK, Comparison of different torsion angle approaches for NMR structure determination, J. Biomol. NMR 2006 Mar;34(3):153-66.
• 2005
  Taly A, Delarue M, Grutter T, Nilges M, Le Novère N, Corringer PJ, Changeux JP, Normal mode analysis suggests a quaternary twist model for the nicotinic receptor gating mechanism, Biophys. J. 2005 Jun;88(6):3954-65.