• 2022
  Cottone G, Chiodo L, Maragliano L, Popoff MR, Rasetti-Escargueil C, Lemichez E, Malliavin TE, , In Silico Conformational Features of Botulinum Toxins A1 and E1 According to Intraluminal Acidification., Toxins (Basel) 2022 Sep; 14(9): .
• 2021
  Paillares E, Marechal M, Swistak L, Tsoumtsa Meda L, Lemichez E, Malliavin TE, , Conformational Insights into the Control of CNF1 Toxin Activity by Peptidyl-Prolyl Isomerization: A Molecular Dynamics Perspective., Int J Mol Sci 2021 Sep; 22(18): .
• 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.
• 2020
  Pitard I, Monet D, Goossens PL, Blondel A, Malliavin TE, , Analyzing In Silico the Relationship Between the Activation of the Edema Factor and Its Interaction With Calmodulin., Front Mol Biosci 2020 ; 7(): 586544.
• 2019
  Malliavin TE, Mucherino A, Lavor C, Liberti L, Systematic Exploration of Protein Conformational Space Using a Distance Geometry Approach, J Chem Inf Model 2019 Sep;.
• 2019
  Pitard I, Malliavin TE, Structural Biology and Molecular Modeling to Analyze the Entry of Bacterial Toxins and Virulence Factors into Host Cells, Toxins (Basel) 2019 Jun;11(6).
• 2019
  Weill FX, Domman D, Njamkepo E, Almesbahi AA, Naji M, Nasher SS, Rakesh A, Assiri AM, Sharma NC, Kariuki S, Pourshafie MR, Rauzier J, Abubakar A, Carter JY, Wamala JF, Seguin C, Bouchier C, Malliavin T, Bakhshi B, Abulmaali HHN, Kumar D, Njoroge SM, Malik MR, Kiiru J, Luquero FJ, Azman AS, Ramamurthy T, Thomson NR, Quilici ML, , Publisher Correction: Genomic insights into the 2016-2017 cholera epidemic in Yemen., Nature 2019 02; 566(7745): E14.
• 2019
  Weill FX, Domman D, Njamkepo E, Almesbahi AA, Naji M, Nasher SS, Rakesh A, Assiri AM, Sharma NC, Kariuki S, Pourshafie MR, Rauzier J, Abubakar A, Carter JY, Wamala JF, Seguin C, Bouchier C, Malliavin T, Bakhshi B, Abulmaali HHN, Kumar D, Njoroge SM, Malik MR, Kiiru J, Luquero FJ, Azman AS, Ramamurthy T, Thomson NR, Quilici ML, , Genomic insights into the 2016-2017 cholera epidemic in Yemen., Nature 2019 01; 565(7738): 230-233.
• 2018
  Duclert-Savatier N, Bouvier G, Nilges M, Malliavin TE, Conformational sampling of CpxA: Connecting HAMP motions to the histidine kinase function, PLoS ONE 2018;13(11):e0207899.
• 2018
  Chiodo L, Malliavin TE, Giuffrida S, Maragliano L, Cottone G, Closed-locked and Apo-resting State Structures of the Human α7 Nicotinic Receptor: a Computational Study, J Chem Inf Model 2018 Oct;.
• 2018
  Lavor C, Liberti L, Donald B, Worley B, Bardiaux B, Malliavin TE, Nilges M, Minimal NMR distance information for rigidity of protein graphs, Discrete Appl Math 2019 Mar;256:91-104.
• 2018
  Lamothe G, Malliavin TE, re-TAMD: exploring interactions between H3 peptide and YEATS domain using enhanced sampling, BMC Struct. Biol. 2018 04;18(1):4.
• 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.
• 2017
  Chiodo L, Malliavin TE, Maragliano L, Cottone G, A possible desensitized state conformation of the human α7 nicotinic receptor: A molecular dynamics study, Biophys. Chem. 2017 10;229:99-109.
• 2017
  Malliavin TE, Molecular Modeling of the Catalytic Domain of CyaA Deepened the Knowledge of Its Functional Dynamics, Toxins (Basel) 2017 06;9(7).
• 2016
  Martinez M, Duclert-Savatier N, Betton JM, Alzari PM, Nilges M, Malliavin TE, Modification in hydrophobic packing of HAMP domain induces a destabilization of the auto-phosphorylation site in the histidine kinase CpxA, Biopolymers 2016 Oct;105(10):670-82.
• 2016
  Duclert-Savatier N, Bouvier G, Nilges M, Malliavin TE, Building Graphs To Describe Dynamics, Kinetics, and Energetics in the d-ALa:d-Lac Ligase VanA, J Chem Inf Model 2016 09;56(9):1762-75.
• 2015
  Cortés-Ciriano I, van Westen GJ, Bouvier G, Nilges M, Overington JP, Bender A, Malliavin TE, , Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel., Bioinformatics 2016 Jan; 32(1): 85-95.
• 2015
  Murrell DS, Cortes-Ciriano I, van Westen GJP, Stott IP, Bender A, Malliavin TE, Glen RC, , Chemically Aware Model Builder (camb): an R package for property and bioactivity modelling of small molecules., J Cheminform 2015 ; 7(): 45.
• 2015
  Chiodo L, Malliavin TE, Maragliano L, Cottone G, Ciccotti G, A Structural Model of the Human α7 Nicotinic Receptor in an Open Conformation, PLoS ONE 2015;10(7):e0133011.
• 2015
  Cortes-Ciriano I, Bender A, Malliavin TE, Comparing the Influence of Simulated Experimental Errors on 12 Machine Learning Algorithms in Bioactivity Modeling Using 12 Diverse Data Sets, J Chem Inf Model 2015 Jul;55(7):1413-25.
• 2015
  Cortes-Ciriano I, Bouvier G, Nilges M, Maragliano L, Malliavin TE, Temperature Accelerated Molecular Dynamics with Soft-Ratcheting Criterion Orients Enhanced Sampling by Low-Resolution Information, J Chem Theory Comput 2015 Jul;11(7):3446-54.
• 2015
  Paricharak S, Cortés-Ciriano I, IJzerman AP, Malliavin TE, Bender A, , Proteochemometric modelling coupled to in silico target prediction: an integrated approach for the simultaneous prediction of polypharmacology and binding affinity/potency of small molecules., J Cheminform 2015 ; 7(): 15.
• 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.
• 2015
  Harigua-Souiai E, Cortes-Ciriano I, Desdouits N, Malliavin TE, Guizani I, Nilges M, Blondel A, Bouvier G, Identification of binding sites and favorable ligand binding moieties by virtual screening and self-organizing map analysis, BMC Bioinformatics 2015 Mar;16:93.
• 2015
  Cortés-Ciriano I, Bender A, Malliavin T, Prediction of PARP Inhibition with Proteochemometric Modelling and Conformal Prediction, Mol Inform 2015 Jun;34(6-7):357-66.
• 2015
  Cassioli A, Bardiaux B, Bouvier G, Mucherino A, Alves R, Liberti L, Nilges M, Lavor C, Malliavin TE, , An algorithm to enumerate all possible protein conformations verifying a set of distance constraints., BMC Bioinformatics 2015 Jan; 16(): 23.
• 2015
  Cortes-Ciriano I, Murrell DS, van Westen GJ, Bender A, Malliavin TE, Prediction of the potency of mammalian cyclooxygenase inhibitors with ensemble proteochemometric modeling, J Cheminform 2015;7:1.
• 2014
  Ain QU, Méndez-Lucio O, Ciriano IC, Malliavin T, van Westen GJ, Bender A, Modelling ligand selectivity of serine proteases using integrative proteochemometric approaches improves model performance and allows the multi-target dependent interpretation of features, Integr Biol (Camb) 2014 Nov;6(11):1023-33.
• 2014
  Cortes-Ciriano I, van Westen GJ, Lenselink EB, Murrell DS, Bender A, Malliavin T, Proteochemometric modeling in a Bayesian framework, J Cheminform 2014;6:35.
• 2014
  Selwa E, Huynh T, Ciccotti G, Maragliano L, Malliavin TE, Temperature-accelerated molecular dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain, Proteins 2014 Oct;82(10):2483-96.
• 2014
  Mohammad Hosseini Naveh Z, Malliavin TE, Maragliano L, Cottone G, Ciccotti G, Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics, PLoS ONE 2014;9(2):e88555.
• 2014
  Bouvier G, Duclert-Savatier N, Desdouits N, Meziane-Cherif D, Blondel A, Courvalin P, Nilges M, Malliavin TE, Functional motions modulating VanA ligand binding unraveled by self-organizing maps, J Chem Inf Model 2014 Jan;54(1):289-301.
• 2014
  Liggi S, Drakakis G, Koutsoukas A, Cortes-Ciriano I, Martínez-Alonso P, Malliavin TE, Velazquez-Campoy A, Brewerton SC, Bodkin MJ, Evans DA, Glen RC, Carrodeguas JA, Bender A, Extending in silico mechanism-of-action analysis by annotating targets with pathways: application to cellular cytotoxicity readouts, Future Med Chem 2014;6(18):2029-56.
• 2013
  Miri L, Bouvier G, Kettani A, Mikou A, Wakrim L, Nilges M, Malliavin TE, Stabilization of the integrase-DNA complex by Mg2+ ions and prediction of key residues for binding HIV-1 integrase inhibitors, Proteins 2014 Mar;82(3):466-78.
• 2013
  Prevost MS, Delarue-Cochin S, Marteaux J, Colas C, Van Renterghem C, Blondel A, Malliavin T, Corringer PJ, Joseph D, Identification of cinnamic acid derivatives as novel antagonists of the prokaryotic proton-gated ion channel GLIC, J. Med. Chem. 2013 Jun;56(11):4619-30.
• 2012
  Selwa E, Laine E, Malliavin TE, Differential role of calmodulin and calcium ions in the stabilization of the catalytic domain of adenyl cyclase CyaA from Bordetella pertussis, Proteins 2012 Apr;80(4):1028-40.
• 2012
  Bardiaux B, Malliavin T, Nilges M, ARIA for solution and solid-state NMR, Methods Mol. Biol. 2012;831:453-83.
• 2011
  Duclert-Savatier N, Martínez L, Nilges M, Malliavin TE, The redundancy of NMR restraints can be used to accelerate the unfolding behavior of an SH3 domain during molecular dynamics simulations, BMC Struct. Biol. 2011;11:46.
• 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
  Martínez L, Malliavin TE, Blondel A, Mechanism of reactant and product dissociation from the anthrax edema factor: a locally enhanced sampling and steered molecular dynamics study, Proteins 2011 May;79(5):1649-61.
• 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
  Laine E, Martínez L, Blondel A, Malliavin TE, Activation of the edema factor of Bacillus anthracis by calmodulin: evidence of an interplay between the EF-calmodulin interaction and calcium binding, Biophys. J. 2010 Oct;99(7):2264-72.
• 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.
• 2010
  Laine E, Goncalves C, Karst JC, Lesnard A, Rault S, Tang WJ, Malliavin TE, Ladant D, Blondel A, Use of allostery to identify inhibitors of calmodulin-induced activation of Bacillus anthracis edema factor, Proc. Natl. Acad. Sci. U.S.A. 2010 Jun;107(25):11277-82.
• 2009
  Martínez L, Laine E, Malliavin TE, Nilges M, Blondel A, ATP conformations and ion binding modes in the active site of anthrax edema factor: a computational analysis, Proteins 2009 Dec;77(4):971-83.
• 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
  Laine E, Blondel A, Malliavin TE, Dynamics and energetics: a consensus analysis of the impact of calcium on EF-CaM protein complex, Biophys. J. 2009 Feb;96(4):1249-63.
• 2008
  Markwick PR, Malliavin T, Nilges M, Structural biology by NMR: structure, dynamics, and interactions, PLoS Comput. Biol. 2008;4(9):e1000168.
• 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
  Laine E, Yoneda JD, Blondel A, Malliavin TE, The conformational plasticity of calmodulin upon calcium complexation gives a model of its interaction with the oedema factor of Bacillus anthracis, Proteins 2008 Jun;71(4):1813-29.
• 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
  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
  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.