• 2023
  Temmam S, Montagutelli X, Herate C, Donati F, Regnault B, Attia M, Baquero Salazar E, Chretien D, Conquet L, Jouvion G, Pipoli Da Fonseca J, Cokelaer T, Amara F, Relouzat F, Naninck T, Lemaitre J, Derreudre-Bosquet N, Pascal Q, Bonomi M, Bigot T, Munier S, Rey FA, Le Grand R, van der Werf S, Eloit M, , SARS-CoV-2-related bat virus behavior in human-relevant models sheds light on the origin of COVID-19., EMBO Rep 2023 Mar; (): e56055.
• 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
  Davi M, Sadi M, Pitard I, Chenal A, Ladant D, , A Robust and Sensitive Spectrophotometric Assay for the Enzymatic Activity of Bacterial Adenylate Cyclase Toxins., Toxins (Basel) 2022 Oct; 14(10): .
• 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): .
• 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
  Belyy A, Lindemann F, Roderer D, Funk J, Bardiaux B, Protze J, Bieling P, Oschkinat H, Raunser S, , Mechanism of threonine ADP-ribosylation of F-actin by a Tc toxin., Nat Commun 2022 Jul; 13(1): 4202.
• 2022
  Chen KY, Krischuns T, Varga LO, Harigua-Souiai E, Paisant S, Zettor A, Chiaravalli J, Delpal A, Courtney D, O'Brien A, Baker SC, Decroly E, Isel C, Agou F, Jacob Y, Blondel A, Naffakh N, , A highly sensitive cell-based luciferase assay for high-throughput automated screening of SARS-CoV-2 nsp5/3CLpro inhibitors., Antiviral Res 2022 May; 201(): 105272.
• 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
  Valérie Biou, Ricardo Jorge Diogo Adaixo, Mohamed Chami , Pierre-Damien Coureux, Benoist Laurent, Véronique Yvette Ntsogo Enguéné, Gisele Cardoso de Amorim, Nadia Izadi-Pruneyre, Christian Malosse, Julia Chamot-Rooke, Henning Stahlberg, Philippe Delepelaire, Structural and molecular determinants for the interaction of ExbB from Serratia marcescens and HasB, a TonB paralog, Commun Biol . 2022 Apr 13;5(1):355. .
• 2022
  S. Temmam, K. Vongphayloth, E. Baquero Salazar, S. Munier⋆, M. Bonomi, et al., Discovery of bat coronaviruses close to SARS-CoV-2 and infectious for human cells., Nautre 604 (2022) 330.
• 2022
  Decool H, Bardiaux B, Checa Ruano L, Sperandio O, Fix J, Gutsche I, Richard CA, Bajorek M, Eléouët JF, Galloux M, , Characterization of the Interaction Domains between the Phosphoprotein and the Nucleoprotein of Human Metapneumovirus., J Virol 2022 01; 96(2): e0090921.
• 2022
  Colcombet-Cazenave B, Cordier F, Zhu Y, Bouvier G, Litsardaki E, Laserre L, Prevost MS, Raynal B, Caillet-Saguy C, Wolff N, , Deciphering the Molecular Interaction Between the Adhesion G Protein-Coupled Receptor ADGRV1 and its PDZ-Containing Regulator PDZD7., Front Mol Biosci 2022 ; 9(): 923740.
• 2021
  Mallet V, Checa Ruano L, Moine Franel A, Nilges M, Druart K, Bouvier G, Sperandio O, , InDeep: 3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions., Bioinformatics 2021 Dec; (): .
• 2021
  Decool H, Bardiaux B, Checa Ruano L, Sperandio O, Fix J, Gutsche I, Richard CA, Bajorek M, Eléouët JF, Galloux M, , Characterization of the interaction domains between the phosphoprotein and the nucleoprotein of human Metapneumovirus., J Virol 2021 Nov; (): JVI0090921.
• 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
  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 Sep; (): .
• 2021
  Rachel-Ann A. Garibsingh, Elias Ndaru, Alisa A. Garaeva, Yueyue Shi, Laura Zielewicz, Paul Zakrepine, Massimiliano Bonomi, Dirk J. Slotboom, Cristina Paulino, Christof Grewer, and Avner Schlessinger, Rational design of ASCT2 inhibitors using an integrated experimental-computational approach, Proc. Natl. Acad. Sci. USA 118 (2021) e21040931188.
• 2021
  Mariagrazia Fortino, Concetta Cozza, Massimiliano Bonomi, Adriana Pietropaolo, Multi-replica biased sampling for photoisomerization processes in conjugated polymers, J. Chem. Phys. 154, 174108 (2021).
• 2021
  Cardone C, Caseau CM, Bardiaux B, Thureaux A, Galloux M, Bajorek M, Eléouët JF, Litaudon M, Bontems F, Sizun C, , A Structural and Dynamic Analysis of the Partially Disordered Polymerase-Binding Domain in RSV Phosphoprotein., Biomolecules 2021 Aug; 11(8): .
• 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
  Colcombet-Cazenave B, Druart K, Bonnet C, Petit C, Spérandio O, Guglielmini J, Wolff N, , Phylogenetic analysis of Harmonin homology domains., BMC Bioinformatics 2021 Apr; 22(1): 190.
• 2021
  Rey M, Dhenin J, Kong Y, Nouchikian L, Filella I, Duchateau M, Dupré M, Pellarin R, Duménil G, Chamot-Rooke J, , Advanced In Vivo Cross-Linking Mass Spectrometry Platform to Characterize Proteome-Wide Protein Interactions., Anal Chem 2021 Feb; (): .
• 2021
  Guedes IA, Barreto AMS, Marinho D, Krempser E, Kuenemann MA, Sperandio O, Dardenne LE, Miteva MA, , New machine learning and physics-based scoring functions for drug discovery., Sci Rep 2021 Feb; 11(1): 3198.
• 2021
  Torchet R, Druart K, Ruano LC, Moine-Franel A, Borges H, Doppelt-Azeroual O, Brancotte B, Mareuil F, Nilges M, Ménager H, Sperandio O, , The iPPI-DB initiative: A Community-centered database of Protein-Protein Interaction modulators., Bioinformatics 2021 Jan; (): .
• 2021
  Khakzad H, Happonen L, Karami Y, Chowdhury S, Bergdahl GE, Nilges M, Tran Van Nhieu G, Malmström J, Malmström L, , Structural determination of Streptococcus pyogenes M1 protein interactions with human immunoglobulin G using integrative structural biology., PLoS Comput Biol 2021 Jan; 17(1): e1008169.
• 2021
  Daskalov A, Martinez D, Coustou V, El Mammeri N, Berbon M, Andreas LB, Bardiaux B, Stanek J, Noubhani A, Kauffmann B, Wall JS, Pintacuda G, Saupe SJ, Habenstein B, Loquet A, , Structural and molecular basis of cross-seeding barriers in amyloids., Proc Natl Acad Sci U S A 2021 Jan; 118(1): .
• 2021
  Spill YG, Karami Y, Maisonneuve P, Wolff N, Nilges M, , Automatic Bayesian Weighting for SAXS Data., Front Mol Biosci 2021 ; 8(): 671011.
• 2021
  Daskalov A, El Mammeri N, Lends A, Shenoy J, Lamon G, Fichou Y, Saad A, Martinez D, Morvan E, Berbon M, Grélard A, Kauffmann B, Ferber M, Bardiaux B, Habenstein B, Saupe SJ, Loquet A, , Structures of Pathological and Functional Amyloids and Prions, a Solid-State NMR Perspective., Front Mol Neurosci 2021 ; 14(): 670513.
• 2020
  Karami Y, Saighi P, Vanderhaegen R, Gerlier D, Longhi S, Laine E, Carbone A, , Predicting substitutions to modulate disorder and stability in coiled-coils., BMC Bioinformatics 2020 Dec; 21(Suppl 19): 573.
• 2020
  Zhu Y, Delhommel F, Cordier F, Lüchow S, Mechaly A, Colcombet-Cazenave B, Girault V, Pepermans E, Bahloul A, Gautier C, Brûlé S, Raynal B, Hoos S, Haouz A, Caillet-Saguy C, Ivarsson Y, Wolff N, , Deciphering the Unexpected Binding Capacity of the Third PDZ Domain of Whirlin to Various Cochlear Hair Cell Partners., J Mol Biol 2020 11; 432(22): 5920-5937.
• 2020
  Gautier C, Troilo F, Cordier F, Malagrinò F, Toto A, Visconti L, Zhu Y, Brunori M, Wolff N, Gianni S, , Hidden kinetic traps in multidomain folding highlight the presence of a misfolded but functionally competent intermediate., Proc Natl Acad Sci U S A 2020 08; 117(33): 19963-19969.
• 2020
  Ciudad S, Puig E, Botzanowski T, Meigooni M, Arango AS, Do J, Mayzel M, Bayoumi M, Chaignepain S, Maglia G, Cianferani S, Orekhov V, Tajkhorshid E, Bardiaux B, Carulla N, , Aβ(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism for membrane damage., Nat Commun 2020 Jun; 11(1): 3014.
• 2020
  Allain F, Mareuil F, Ménager H, Nilges M, Bardiaux B, , ARIAweb: a server for automated NMR structure calculation., Nucleic Acids Res. 2020 May; (): .
• 2020
  Bosc N, Muller C, Hoffer L, Lagorce D, Bourg S, Derviaux C, Gourdel ME, Rain JC, Miller TW, Villoutreix BO, Miteva MA, Bonnet P, Morelli X, Sperandio O, Roche P, Fr-PPIChem: An academic compound library dedicated to protein-protein interactions, ACS Chem. Biol. 2020 Apr;.
• 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
  Jacobsen T, Bardiaux B, Francetic O, Izadi-Pruneyre N, Nilges M, Structure and function of minor pilins of type IV pili, Med. Microbiol. Immunol. 2019 Nov;.
• 2019
  Filella-Merce I, Bardiaux B, Nilges M, Bouvier G, Quantitative Structural Interpretation of Protein Crosslinks, Structure 2019 Nov;.
• 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
  Laine E, Karami Y, Carbone A, GEMME: a simple and fast global epistatic model predicting mutational effects, Mol. Biol. Evol. 2019 Aug;.
• 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
  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
  Karami Y, Rey J, Postic G, Murail S, Tufféry P, de Vries SJ, DaReUS-Loop: a web server to model multiple loops in homology models, Nucleic Acids Res. 2019 May;.
• 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
  Singh H, Verma D, Bardiaux B, Single-site phosphorylation within the His-tag sequence attached to a recombinant protein, Anal. Biochem. 2019 Feb;.
• 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
  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.
• 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
  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
  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
  Rangan R, Bonomi M, Heller GT, Cesari A, Bussi G, Vendruscolo M, Determination of Structural Ensembles of Proteins: Restraining vs Reweighting, J. Chem. Theory Comput. 2018, 14, 6632−6641.
• 2018
  Cozza C, Bonomi M, Pietropaolo A, A Versatile Computational Strategy To Characterize the Free-Energy Landscape of Excited States in Oligofluorenes, J Chem Theory Comput 2018 Nov;14(11):5441-5445.
• 2018
  Karami Y, Bitard-Feildel T, Laine E, Carbone A, “Infostery” analysis of short molecular dynamics simulations identifies highly sensitive residues and predicts deleterious mutations, Sci Rep 2018 Oct;8(1):16126.
• 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
  Cherrak Y, Rapisarda C, Pellarin R, Bouvier G, Bardiaux B, Allain F, Malosse C, Rey M, Chamot-Rooke J, Cascales E, Fronzes R, Durand E, Biogenesis and structure of a type VI secretion baseplate, Nat Microbiol 2018 Oct;.
• 2018
  Spronk CAEM, Żerko S, Górka M, Koźmiński W, Bardiaux B, Zambelli B, Musiani F, Piccioli M, Basak P, Blum FC, Johnson RC, Hu H, Merrell DS, Maroney M, Ciurli S, Structure and dynamics of Helicobacter pylori nickel-chaperone HypA: an integrated approach using NMR spectroscopy, functional assays and computational tools, J. Biol. Inorg. Chem. 2018 Sep;.
• 2018
  Karami Y, Guyon F, De Vries S, Tufféry P, DaReUS-Loop: accurate loop modeling using fragments from remote or unrelated proteins, Sci Rep 2018 Sep;8(1):13673.
• 2018
  Prakash A, Fu CD, Bonomi M, Pfaendtner J, Biasing Smarter, Not Harder, by Partitioning Collective Variables into Families in Parallel Bias Metadynamics, J Chem Theory Comput 2018 Oct;14(10):4985-4990.
• 2018
  Delhommel F, Cordier F, Saul F, Chataigner L, Haouz A, Wolff N, Structural plasticity of the HHD2 domain of whirlin, FEBS J. 2018 10;285(20):3738-3752.
• 2018
  Pham CLL, Rodríguez de Francisco B, Valsecchi I, Dazzoni R, Pillé A, Lo V, Ball SR, Cappai R, Wien F, Kwan AH, Guijarro JI, Sunde M, , Probing Structural Changes during Self-assembly of Surface-Active Hydrophobin Proteins that Form Functional Amyloids in Fungi., J Mol Biol 2018 10; 430(20): 3784-3801.
• 2018
  Vahidi S, Ripstein ZA, Bonomi M, Yuwen T, Mabanglo MF, Juravsky JB, Rizzolo K, Velyvis A, Houry WA, Vendruscolo M, Rubinstein JL, Kay LE, Reversible inhibition of the ClpP protease via an N-terminal conformational switch, Proc. Natl. Acad. Sci. U.S.A. 2018 07;115(28):E6447-E6456.
• 2018
  Kyrmizi I, Ferreira H, Carvalho A, Figueroa JAL, Zarmpas P, Cunha C, Akoumianaki T, Stylianou K, Deepe GS, Samonis G, Lacerda JF, Campos A, Kontoyiannis DP, Mihalopoulos N, Kwon-Chung KJ, El-Benna J, Valsecchi I, Beauvais A, Brakhage AA, Neves NM, Latge JP, Chamilos G, Calcium sequestration by fungal melanin inhibits calcium-calmodulin signalling to prevent LC3-associated phagocytosis, Nat Microbiol 2018 May;.
• 2018
  de Freitas MS, Rezaei Araghi R, Brandenburg E, Leiterer J, Emmerling F, Folmert K, Gerling-Driessen UIM, Bardiaux B, Böttcher C, Pagel K, Diehl A, Berlepsch HV, Oschkinat H, Koksch B, The protofilament architecture of a de novo designed coiled coil-based amyloidogenic peptide, J. Struct. Biol. 2018 May;.
• 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
  Bonomi M, Pellarin R, Vendruscolo M, Simultaneous Determination of Protein Structure and Dynamics Using Cryo-Electron Microscopy, Biophys. J. 2018 Apr;114(7):1604-1613.
• 2018
  Loquet A, El Mammeri N, Stanek J, Berbon M, Bardiaux B, Pintacuda G, Habenstein B, 3D Structure Determination of Amyloid Fibrils using Solid-State NMR Spectroscopy, Methods 2018 Apr;.
• 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
  Heller GT, Bonomi M, Vendruscolo M, Structural Ensemble Modulation upon Small-Molecule Binding to Disordered Proteins, J. Mol. Biol. 430 (2018) 2288.
• 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
  Kim SJ, Fernandez-Martinez J, Nudelman I, Shi Y, Zhang W, Raveh B, Herricks T, Slaughter BD, Hogan JA, Upla P, Chemmama IE, Pellarin R, Echeverria I, Shivaraju M, Chaudhury AS, Wang J, Williams R, Unruh JR, Greenberg CH, Jacobs EY, Yu Z, de la Cruz MJ, Mironska R, Stokes DL, Aitchison JD, Jarrold MF, Gerton JL, Ludtke SJ, Akey CW, Chait BT, Sali A, Rout MP, Integrative structure and functional anatomy of a nuclear pore complex, Nature 2018 03;555(7697):475-482.
• 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.
• 2018
  Stappers MHT, Clark AE, Aimanianda V, Bidula S, Reid DM, Asamaphan P, Hardison SE, Dambuza IM, Valsecchi I, Kerscher B, Plato A, Wallace CA, Yuecel R, Hebecker B, da Glória Teixeira Sousa M, Cunha C, Liu Y, Feizi T, Brakhage AA, Kwon-Chung KJ, Gow NAR, Zanda M, Piras M, Zanato C, Jaeger M, Netea MG, van de Veerdonk FL, Lacerda JF, Campos A, Carvalho A, Willment JA, Latgé JP, Brown GD, Recognition of DHN-melanin by a C-type lectin receptor is required for immunity to Aspergillus, Nature 2018 Mar;555(7696):382-386.
• 2018
  Morellet N, Li X, Wieninger SA, Taylor JL, Bischerour J, Moriau S, Lescop E, Bardiaux B, Mathy N, Assrir N, Bétermier M, Nilges M, Hickman AB, Dyda F, Craig NL, Guittet E, Sequence-specific DNA binding activity of the cross-brace zinc finger motif of the piggyBac transposase, Nucleic Acids Res. 2018 Jan;.
• 2018
  Webb B, Viswanath S, Bonomi M, Pellarin R, Greenberg CH, Saltzberg D, Sali A, Integrative structure modeling with the Integrative Modeling Platform, Protein Sci. 2018 01;27(1):245-258.
• 2017
  Valsecchi I, Dupres V, Stephen-Victor E, Guijarro JI, Gibbons J, Beau R, Bayry J, Coppee JY, Lafont F, Latgé JP, Beauvais A, Role of Hydrophobins in Aspergillus fumigatus, J Fungi (Basel) 2017 Dec;4(1).
• 2017
  Bonomi M, Camilloni C, Integrative structural and dynamical biology with PLUMED-ISDB, Bioinformatics 2017 Dec;33(24):3999-4000.
• 2017
  Retel JS, Nieuwkoop AJ, Hiller M, Higman VA, Barbet-Massin E, Stanek J, Andreas LB, Franks WT, van Rossum BJ, Vinothkumar KR, Handel L, de Palma GG, Bardiaux B, Pintacuda G, Emsley L, Kühlbrandt W, Oschkinat H, Structure of outer membrane protein G in lipid bilayers, Nat Commun 2017 Dec;8(1):2073.
• 2017
  López-Castilla A, Thomassin JL, Bardiaux B, Zheng W, Nivaskumar M, Yu X, Nilges M, Egelman EH, Izadi-Pruneyre N, Francetic O, Structure of the calcium-dependent type 2 secretion pseudopilus, Nat Microbiol 2017 Dec;2(12):1686-1695.
• 2017
  Delhommel F, Cordier F, Bardiaux B, Bouvier G, Colcombet-Cazenave B, Brier S, Raynal B, Nouaille S, Bahloul A, Chamot-Rooke J, Nilges M, Petit C, Wolff N, Structural Characterization of Whirlin Reveals an Unexpected and Dynamic Supramodule Conformation of Its PDZ Tandem, Structure 2017 11;25(11):1645-1656.e5.
• 2017
  Bosc N, Kuenemann MA, Bécot J, Vavrusa M, Cerdan AH, Sperandio O, Privileged Substructures to Modulate Protein-Protein Interactions, J Chem Inf Model 2017 Oct;57(10):2448-2462.
• 2017
  Viswanath S, Bonomi M, Kim SJ, Klenchin VA, Taylor KC, Yabut KC, Umbreit NT, Van Epps HA, Meehl J, Jones MH, Russel D, Velazquez-Muriel JA, Winey M, Rayment I, Davis TN, Sali A, Muller EG, The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling, Mol. Biol. Cell 2017 Nov;28(23):3298-3314.
• 2017
  Amel Bahloul, Elise Pepermans, Bertrand Raynal, Nicolas Wolff, Florence Cordier, Patrick England, Sylvie Nouaille, Bruno Baron, Aziz El-Amraoui, Jean-Pierre Hardelin, Dominique Durand, Christine Petit, Conformational switch of harmonin, a submembrane scaffold protein of the hair cell mechanoelectrical transduction machinery, FEBS Letters, 2017, 591 (15), pp.2299 - 2310. ⟨10.1002/1873-3468.12729⟩.
• 2017
  Heller GT, Aprile FA, Bonomi M, Camilloni C, De Simone A, Vendruscolo M, Sequence Specificity in the Entropy-Driven Binding of a Small Molecule and a Disordered Peptide, J. Mol. Biol. 2017 Sep;429(18):2772-2779.
• 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).
• 2017
  Sormanni P, Piovesan D, Heller GT, Bonomi M, Kukic P, Camilloni C, Fuxreiter M, Dosztanyi Z, Pappu RV, Babu MM, Longhi S, Tompa P, Dunker AK, Uversky VN, Tosatto SC, Vendruscolo M, Simultaneous quantification of protein order and disorder, Nat. Chem. Biol. 2017 03;13(4):339-342.
• 2017
  Obayashi E, Luna RE, Nagata T, Martin-Marcos P, Hiraishi H, Singh CR, Erzberger JP, Zhang F, Arthanari H, Morris J, Pellarin R, Moore C, Harmon I, Papadopoulos E, Yoshida H, Nasr ML, Unzai S, Thompson B, Aube E, Hustak S, Stengel F, Dagraca E, Ananbandam A, Gao P, Urano T, Hinnebusch AG, Wagner G, Asano K, Molecular Landscape of the Ribosome Pre-initiation Complex during mRNA Scanning: Structural Role for eIF3c and Its Control by eIF5, Cell Rep 2017 03;18(11):2651-2663.
• 2017
  Bonomi M, Heller GT, Camilloni C, Vendruscolo M, Principles of protein structural ensemble determination, Curr. Opin. Struct. Biol. 2017 02;42:106-116.
• 2016
  Saltzberg DJ, Broughton HB, Pellarin R, Chalmers MJ, Espada A, Dodge JA, Pascal BD, Griffin PR, Humblet C, Sali A, A Residue-Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen-Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein-Ligand Interactions, J Phys Chem B 2017 04;121(15):3493-3501.
• 2016
  Fernandez-Martinez J, Kim SJ, Shi Y, Upla P, Pellarin R, Gagnon M, Chemmama IE, Wang J, Nudelman I, Zhang W, Williams R, Rice WJ, Stokes DL, Zenklusen D, Chait BT, Sali A, Rout MP, Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform, Cell 2016 11;167(5):1215-1228.e25.
• 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.
• 2016
  Pérez-Regidor L, Zarioh M, Ortega L, Martín-Santamaría S, Virtual Screening Approaches towards the Discovery of Toll-Like Receptor Modulators, Int J Mol Sci 2016;17(9).
• 2016
  Bonomi M, Camilloni C, Vendruscolo M, Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics, Sci Rep 2016 08;6:31232.
• 2016
  Delhommel F, Wolff N, Cordier F, (1)H, (13)C and (15)N backbone resonance assignments and dynamic properties of the PDZ tandem of Whirlin, Biomol NMR Assign 2016 10;10(2):361-5.
• 2016
  Chen ZA, Pellarin R, Fischer L, Sali A, Nilges M, Barlow PN, Rappsilber J, Structure of Complement C3(H2O) Revealed By Quantitative Cross-Linking/Mass Spectrometry And Modeling, Mol. Cell Proteomics 2016 08;15(8):2730-43.
• 2016
  Maisonneuve P, Caillet-Saguy C, Vaney MC, Bibi-Zainab E, Sawyer K, Raynal B, Haouz A, Delepierre M, Lafon M, Cordier F, Wolff N, , Molecular Basis of the Interaction of the Human Protein Tyrosine Phosphatase Non-receptor Type 4 (PTPN4) with the Mitogen-activated Protein Kinase p38γ., J Biol Chem 2016 08; 291(32): 16699-708.
• 2016
  Ferber M, Kosinski J, Ori A, Rashid UJ, Moreno-Morcillo M, Simon B, Bouvier G, Batista PR, Müller CW, Beck M, Nilges M, Automated structure modeling of large protein assemblies using crosslinks as distance restraints, Nat. Methods 2016 Jun;13(6):515-20.
• 2016
  Yang J, Bonomi M, Calero C, Martí J, Free energy landscapes of sodium ions bound to DMPC-cholesterol membrane surfaces at infinite dilution, Phys Chem Chem Phys 2016 Apr;18(13):9036-41.
• 2016
  Bonomi M, Camilloni C, Cavalli A, Vendruscolo M, Metainference: A Bayesian inference method for heterogeneous systems, Sci Adv 2016 Jan;2(1):e1501177.
• 2016
  Karami Y, Laine E, Carbone A, Dissecting protein architecture with communication blocks and communicating segment pairs, BMC Bioinformatics 2016 Jan;17 Suppl 2:13.
• 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
  Zelter A, Bonomi M, Kim Jo, Umbreit NT, Hoopmann MR, Johnson R, Riffle M, Jaschob D, MacCoss MJ, Moritz RL, Davis TN, The molecular architecture of the Dam1 kinetochore complex is defined by cross-linking based structural modelling, Nat Commun 2015 Nov;6:8673.
• 2015
  Mainz A, Peschek J, Stavropoulou M, Back KC, Bardiaux B, Asami S, Prade E, Peters C, Weinkauf S, Buchner J, Reif B, The chaperone αB-crystallin uses different interfaces to capture an amorphous and an amyloid client, Nat. Struct. Mol. Biol. 2015 Oct;.
• 2015
  Pfaendtner J, Bonomi M, Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics, J Chem Theory Comput 2015 Nov;11(11):5062-7.
• 2015
  Colas C, Grewer C, Otte NJ, Gameiro A, Albers T, Singh K, Shere H, Bonomi M, Holst J, Schlessinger A, Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening, PLoS Comput. Biol. 2015 Oct;11(10):e1004477.
• 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
  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
  Luo J, Cimermancic P, Viswanath S, Ebmeier CC, Kim B, Dehecq M, Raman V, Greenberg CH, Pellarin R, Sali A, Taatjes DJ, Hahn S, Ranish J, Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH, Mol. Cell 2015 Sep;59(5):794-806.
• 2015
  Shahid SA, Nagaraj M, Chauhan N, Franks TW, Bardiaux B, Habeck M, Orwick-Rydmark M, Linke D, van Rossum BJ, Solid-state NMR Study of the YadA Membrane-Anchor Domain in the Bacterial Outer Membrane, Angew. Chem. Int. Ed. Engl. 2015 Aug;.
• 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
  Yang J, Calero C, Bonomi M, Martí J, Specific Ion Binding at Phospholipid Membrane Surfaces, J Chem Theory Comput 2015 Sep;11(9):4495-9.
• 2015
  Roy Choudhury A, Sikorska E, van den Boom J, Bayer P, Popenda Ł, Szutkowski K, Jurga S, Bonomi M, Sali A, Zhukov I, Passamonti S, Novič M, Structural Model of the Bilitranslocase Transmembrane Domain Supported by NMR and FRET Data, PLoS ONE 2015;10(8):e0135455.
• 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
  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
  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
  Agejas J, Ortega L, Synthesis of Spirocyclic Pyrazolones by Oxidative C-N Bond Formation, J. Org. Chem. 2015 Jun;80(12):6509-14.
• 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
  Gutmanas A, Adams PD, Bardiaux B, Berman HM, Case DA, Fogh RH, Güntert P, Hendrickx PM, Herrmann T, Kleywegt GJ, Kobayashi N, Lange OF, Markley JL, Montelione GT, Nilges M, Ragan TJ, Schwieters CD, Tejero R, Ulrich EL, Velankar S, Vranken WF, Wedell JR, Westbrook J, Wishart DS, Vuister GW, NMR Exchange Format: a unified and open standard for representation of NMR restraint data, Nat. Struct. Mol. Biol. 2015 Jun;22(6):433-4.
• 2015
  Varela Chavez C, Hoos S, Haustant GM, Chenal A, England P, Blondel A, Pauillac S, Lacy DB, Popoff MR, The catalytic domains of Clostridium sordellii lethal toxin and related large clostridial glucosylating toxins specifically recognize the negatively charged phospholipids phosphatidylserine and phosphatidic acid, Cell. Microbiol. 2015 Oct;17(10):1477-93.
• 2015
  Wieninger SA, Ullmann GM, CoMoDo: Identifying Dynamic Protein Domains Based on Covariances of Motion, J Chem Theory Comput 2015 Jun;11(6):2841-54.
• 2015
  Delhommel F, Chaffotte A, Terrien E, Raynal B, Buc H, Delepierre M, Cordier F, Wolff N, Deciphering the unconventional peptide binding to the PDZ domain of MAST2, Biochem. J. 2015 Jul;469(1):159-68.
• 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
  Caillet-Saguy C, Maisonneuve P, Delhommel F, Terrien E, Babault N, Lafon M, Cordier F, Wolff N, , Strategies to interfere with PDZ-mediated interactions in neurons: What we can learn from the rabies virus., Prog Biophys Mol Biol 2015 Oct; 119(1): 53-9.
• 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.
• 2015
  Palazzesi F, Prakash MK, Bonomi M, Barducci A, Accuracy of current all-atom force-fields in modeling protein disordered states, J. Chem. Theory Comput. 11 (2015) 2.
• 2015
  Barducci A, Pfaendtner J, Bonomi M, Tackling sampling challenges in biomolecular simulations, Methods Mol. Biol. 2015;1215:151-71.
• 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
  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
  Desdouits N, Nilges M, Blondel A, Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins, J. Mol. Graph. Model. 2015 Feb;55:13-24.
• 2014
  Cordier F, Chaffotte A, Wolff N, Quantitative and dynamic analysis of PTEN phosphorylation by NMR, Methods 2015 May;77-78:82-91.
• 2014
  Maisonneuve P, Caillet-Saguy C, Raynal B, Gilquin B, Chaffotte A, Pérez J, Zinn-Justin S, Delepierre M, Buc H, Cordier F, Wolff N, , Regulation of the catalytic activity of the human phosphatase PTPN4 by its PDZ domain., FEBS J 2014 Nov; 281(21): 4852-65.
• 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.
• 2014
  Schneidman-Duhovny D, Pellarin R, Sali A, Uncertainty in integrative structural modeling, Curr. Opin. Struct. Biol. 2014 Oct;28:96-104.
• 2014
  Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CH, Cimermančič P, Boehringer D, Sali A, Aebersold R, Ban N, Molecular architecture of the 40S⋅eIF1⋅eIF3 translation initiation complex, Cell 2014 Aug;158(5):1123-35.
• 2014
  Shi Y, Fernandez-Martinez J, Tjioe E, Pellarin R, Kim SJ, Williams R, Schneidman-Duhovny D, Sali A, Rout MP, Chait BT, Structural characterization by cross-linking reveals the detailed architecture of a coatomer-related heptameric module from the nuclear pore complex, Mol. Cell Proteomics 2014 Nov;13(11):2927-43.
• 2014
  Zeng-Elmore X, Gao XZ, Pellarin R, Schneidman-Duhovny D, Zhang XJ, Kozacka KA, Tang Y, Sali A, Chalkley RJ, Cote RH, Chu F, Molecular architecture of photoreceptor phosphodiesterase elucidated by chemical cross-linking and integrative modeling, J. Mol. Biol. 2014 Nov;426(22):3713-28.
• 2014
  Bonomi M, Pellarin R, Kim SJ, Russel D, Sundin BA, Riffle M, Jaschob D, Ramsden R, Davis TN, Muller EG, Sali A, Determining protein complex structures based on a Bayesian model of in vivo Förster resonance energy transfer (FRET) data, Mol. Cell Proteomics 2014 Nov;13(11):2812-23.
• 2014
  Molnar KS, Bonomi M, Pellarin R, Clinthorne GD, Gonzalez G, Goldberg SD, Goulian M, Sali A, DeGrado WF, Cys-scanning disulfide crosslinking and bayesian modeling probe the transmembrane signaling mechanism of the histidine kinase, PhoQ, Structure 2014 Sep;22(9):1239-1251.
• 2014
  Algret R, Fernandez-Martinez J, Shi Y, Kim SJ, Pellarin R, Cimermancic P, Cochet E, Sali A, Chait BT, Rout MP, Dokudovskaya S, Molecular architecture and function of the SEA complex, a modulator of the TORC1 pathway, Mol. Cell Proteomics 2014 Nov;13(11):2855-70.
• 2014
  Linser R, Bardiaux B, Andreas LB, Hyberts SG, Morris VK, Pintacuda G, Sunde M, Kwan AH, Wagner G, Solid-state NMR structure determination from diagonal-compensated, sparsely nonuniform-sampled 4D proton-proton restraints, J. Am. Chem. Soc. 2014 Aug;136(31):11002-10.
• 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
  Street TO, Zeng X, Pellarin R, Bonomi M, Sali A, Kelly MJ, Chu F, Agard DA, Elucidating the mechanism of substrate recognition by the bacterial Hsp90 molecular chaperone, J. Mol. Biol. 2014 Jun;426(12):2393-404.
• 2014
  Nivaskumar M, Bouvier G, Campos M, Nadeau N, Yu X, Egelman EH, Nilges M, Francetic O, Distinct docking and stabilization steps of the Pseudopilus conformational transition path suggest rotational assembly of type IV pilus-like fibers, Structure 2014 May;22(5):685-96.
• 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
  Peng LX, Hsu MT, Bonomi M, Agard DA, Jacobson MP, The free energy profile of tubulin straight-bent conformational changes, with implications for microtubule assembly and drug discovery, PLoS Comput. Biol. 2014 Feb;10(2):e1003464.
• 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
  Webb B, Lasker K, Velázquez-Muriel J, Schneidman-Duhovny D, Pellarin R, Bonomi M, Greenberg C, Raveh B, Tjioe E, Russel D, Sali A, Modeling of proteins and their assemblies with the Integrative Modeling Platform, Methods Mol. Biol. 2014;1091:277-95.
• 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
  Barducci A, Bonomi M, Prakash MK, Parrinello M, Free-energy landscape of protein oligomerization from atomistic simulations, Proc. Natl. Acad. Sci. U.S.A. 2013 Dec;110(49):E4708-13.
• 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.
• 2013
  Waight AB, Pedersen BP, Schlessinger A, Bonomi M, Chau BH, Roe-Zurz Z, Risenmay AJ, Sali A, Stroud RM, Structural basis for alternating access of a eukaryotic calcium/proton exchanger, Nature 2013 Jul;499(7456):107-10.
• 2013
  Berneman A, Montout L, Goyard S, Chamond N, Cosson A, d'Archivio S, Gouault N, Uriac P, Blondel A, Minoprio P, Combined approaches for drug design points the way to novel proline racemase inhibitor candidates to fight Chagas’ disease, PLoS ONE 2013;8(4):e60955.
• 2013
  Limongelli V, Bonomi M, Parrinello M, Funnel metadynamics as accurate binding free-energy method, Proc. Natl. Acad. Sci. U.S.A. 2013 Apr;110(16):6358-63.
• 2013
  Pedersen BP, Kumar H, Waight AB, Risenmay AJ, Roe-Zurz Z, Chau BH, Schlessinger A, Bonomi M, Harries W, Sali A, Johri AK, Stroud RM, Crystal structure of a eukaryotic phosphate transporter, Nature 2013 Apr;496(7446):533-6.
• 2013
  Scherzer-Attali R, Convertino M, Pellarin R, Gazit E, Segal D, Caflisch A, Methylations of tryptophan-modified naphthoquinone affect its inhibitory potential toward Aβ aggregation, J Phys Chem B 2013 Feb;117(6):1780-9.
• 2012
  Cordier F, Chaffotte A, Terrien E, Préhaud C, Theillet FX, Delepierre M, Lafon M, Buc H, Wolff N, Ordered phosphorylation events in two independent cascades of the PTEN C-tail revealed by NMR, J. Am. Chem. Soc. 2012 Dec;134(50):20533-43.
• 2012
  Spill YG, Bouvier G, Nilges M, A convective replica-exchange method for sampling new energy basins, J Comput Chem 2013 Jan;34(2):132-40.
• 2012
  Mantsyzov AB, Bouvier G, Evrard-Todeschi N, Bertho G, Contact-based ligand-clustering approach for the identification of active compounds in virtual screening, Adv Appl Bioinform Chem 2012;5:61-79.
• 2012
  Alfarano P, Varadamsetty G, Ewald C, Parmeggiani F, Pellarin R, Zerbe O, Plückthun A, Caflisch A, Optimization of designed armadillo repeat proteins by molecular dynamics simulations and NMR spectroscopy, Protein Sci. 2012 Sep;21(9):1298-314.
• 2012
  Kalev I, Mechelke M, Kopec KO, Holder T, Carstens S, Habeck M, CSB: a Python framework for structural bioinformatics, Bioinformatics 2012 Nov;28(22):2996-7.
• 2012
  Schlessinger A, Wittwer MB, Dahlin A, Khuri N, Bonomi M, Fan H, Giacomini KM, Sali A, High selectivity of the γ-aminobutyric acid transporter 2 (GAT-2, SLC6A13) revealed by structure-based approach, J. Biol. Chem. 2012 Nov;287(45):37745-56.
• 2012
  Terrien E, Chaffotte A, Lafage M, Khan Z, Préhaud C, Cordier F, Simenel C, Delepierre M, Buc H, Lafon M, Wolff N, Interference with the PTEN-MAST2 interaction by a viral protein leads to cellular relocalization of PTEN, Sci Signal 2012 Aug;5(237):ra58.
• 2012
  Rücker P, Wieninger SA, Ullmann GM, Sticht H, pH-dependent molecular dynamics of vesicular stomatitis virus glycoprotein G, Proteins 2012 Nov;80(11):2601-13.
• 2012
  Waldauer SA, Hassan S, Paoli B, Donaldson PM, Pfister R, Hamm P, Caflisch A, Pellarin R, Photocontrol of reversible amyloid formation with a minimal-design peptide, J Phys Chem B 2012 Aug;116(30):8961-73.
• 2012
  Deighan M, Bonomi M, Pfaendtner J, Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble, J Chem Theory Comput 2012 Jul;8(7):2189-92.
• 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
  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
  Babault N, Cordier F, Lafage M, Cockburn J, Haouz A, Prehaud C, Rey FA, Delepierre M, Buc H, Lafon M, Wolff N, Peptides targeting the PDZ domain of PTPN4 are efficient inducers of glioblastoma cell death, Structure 2011 Oct;19(10):1518-24.
• 2011
  Frydman-Marom A, Convertino M, Pellarin R, Lampel A, Shaltiel-Karyo R, Segal D, Caflisch A, Shalev DE, Gazit E, Structural basis for inhibiting β-amyloid oligomerization by a non-coded β-breaker-substituted endomorphin analogue, ACS Chem. Biol. 2011 Nov;6(11):1265-76.
• 2011
  Mourier G, Hajj M, Cordier F, Zorba A, Gao X, Coskun T, Herbet A, Marcon E, Beau F, Delepierre M, Ducancel F, Servent D, Pharmacological and structural characterization of long-sarafotoxins, a new family of endothelin-like peptides: Role of the C-terminus extension, Biochimie 2012 Feb;94(2):461-70.
• 2011
  Pietropaolo A, Branduardi D, Bonomi M, Parrinello M, A chirality-based metrics for free-energy calculations in biomolecular systems, J Comput Chem 2011 Sep;32(12):2627-37.
• 2011
  Barducci A, Bonomi M, Derreumaux P, Assessing the Quality of the OPEP Coarse-Grained Force Field, J Chem Theory Comput 2011 Jun;7(6):1928-34.
• 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
  Wieninger SA, Serpersu EH, Ullmann GM, ATP binding enables broad antibiotic selectivity of aminoglycoside phosphotransferase(3′)-IIIa: an elastic network analysis, J. Mol. Biol. 2011 Jun;409(3):450-65.
• 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
  Pellarin R, Schuetz P, Guarnera E, Caflisch A, Amyloid fibril polymorphism is under kinetic control, J. Am. Chem. Soc. 2010 Oct;132(42):14960-70.
• 2010
  Bonomi M, Barducci A, Gervasio FL, Parrinello M, Multiple routes and milestones in the folding of HIV-1 protease monomer, PLoS ONE 2010 Oct;5(10):e13208.
• 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
  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
  Scherzer-Attali R, Pellarin R, Convertino M, Frydman-Marom A, Egoz-Matia N, Peled S, Levy-Sakin M, Shalev DE, Caflisch A, Gazit E, Segal D, Complete phenotypic recovery of an Alzheimer’s disease model by a quinone-tryptophan hybrid aggregation inhibitor, PLoS ONE 2010;5(6):e11101.
• 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.
• 2010
  Barducci A, Bonomi M, Parrinello M, Linking well-tempered metadynamics simulations with experiments, Biophys. J. 2010 May;98(9):L44-6.
• 2010
  Limongelli V, Bonomi M, Marinelli L, Gervasio FL, Cavalli A, Novellino E, Parrinello M, Molecular basis of cyclooxygenase enzymes (COXs) selective inhibition, Proc. Natl. Acad. Sci. U.S.A. 2010 Mar;107(12):5411-6.
• 2010
  Préhaud C, Wolff N, Terrien E, Lafage M, Mégret F, Babault N, Cordier F, Tan GS, Maitrepierre E, Ménager P, Chopy D, Hoos S, England P, Delepierre M, Schnell MJ, Buc H, Lafon M, Attenuation of rabies virulence: takeover by the cytoplasmic domain of its envelope protein, Sci Signal 2010 Jan;3(105):ra5.
• 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
  Bouvier G, Evrard-Todeschi N, Girault JP, Bertho G, Automatic clustering of docking poses in virtual screening process using self-organizing map, Bioinformatics 2010 Jan;26(1):53-60.
• 2009
  Grubisha O, Kaminska M, Duquerroy S, Fontan E, Cordier F, Haouz A, Raynal B, Chiaravalli J, Delepierre M, Israël A, Véron M, Agou F, DARPin-assisted crystallography of the CC2-LZ domain of NEMO reveals a coupling between dimerization and ubiquitin binding, J. Mol. Biol. 2010 Jan;395(1):89-104.
• 2009
  Guarnera E, Pellarin R, Caflisch A, How does a simplified-sequence protein fold?, Biophys. J. 2009 Sep;97(6):1737-46.
• 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
  Convertino M, Pellarin R, Catto M, Carotti A, Caflisch A, 9,10-Anthraquinone hinders beta-aggregation: how does a small molecule interfere with Abeta-peptide amyloid fibrillation?, Protein Sci. 2009 Apr;18(4):792-800.
• 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
  Friedman R, Pellarin R, Caflisch A, Amyloid aggregation on lipid bilayers and its impact on membrane permeability, J. Mol. Biol. 2009 Mar;387(2):407-15.
• 2008
  Cordier F, Grubisha O, Traincard F, Véron M, Delepierre M, Agou F, The zinc finger of NEMO is a functional ubiquitin-binding domain, J. Biol. Chem. 2009 Jan;284(5):2902-7.
• 2008
  Markwick PR, Malliavin T, Nilges M, Structural biology by NMR: structure, dynamics, and interactions, PLoS Comput. Biol. 2008;4(9):e1000168.
• 2008
  Bonomi M, Branduardi D, Gervasio FL, Parrinello M, The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin, J. Am. Chem. Soc. 2008 Oct;130(42):13938-44.
• 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
  Bertho G, Bouvier G, Hoa GH, Girault JP, The key-role of tyrosine 155 in the mechanism of prion transconformation as highlighted by a study of sheep mutant peptides, Peptides 2008 Jul;29(7):1073-84.
• 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.
• 2008
  Bjelić S, Wieninger S, Jelesarov I, Karshikoff A, Electrostatic contribution to the thermodynamic and kinetic stability of the homotrimeric coiled coil Lpp-56: A computational study, Proteins 2008 Feb;70(3):810-22.
• 2008
  Cordier F, Vinolo E, Véron M, Delepierre M, Agou F, Solution structure of NEMO zinc finger and impact of an anhidrotic ectodermal dysplasia with immunodeficiency-related point mutation, J. Mol. Biol. 2008 Apr;377(5):1419-32.
• 2008
  Cordier F, Nisius L, Dingley AJ, Grzesiek S, Direct detection of N-H[…]O=C hydrogen bonds in biomolecules by NMR spectroscopy, Nat Protoc 2008;3(2):235-41.
• 2008
  Dingley AJ, Nisius L, Cordier F, Grzesiek S, Direct detection of N-H[…]N hydrogen bonds in biomolecules by NMR spectroscopy, Nat Protoc 2008;3(2):242-8.
• 2007
  Parmeggiani F, Pellarin R, Larsen AP, Varadamsetty G, Stumpp MT, Zerbe O, Caflisch A, Plückthun A, Designed armadillo repeat proteins as general peptide-binding scaffolds: consensus design and computational optimization of the hydrophobic core, J. Mol. Biol. 2008 Mar;376(5):1282-304.
• 2007
  Pellarin R, Guarnera E, Caflisch A, Pathways and intermediates of amyloid fibril formation, J. Mol. Biol. 2007 Dec;374(4):917-24.
• 2007
  Bonomi M, Gervasio FL, Tiana G, Provasi D, Broglia RA, Parrinello M, Insight into the folding inhibition of the HIV-1 protease by a small peptide, Biophys. J. 2007 Oct;93(8):2813-21.
• 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
  Cordier F, Hartmann B, Rogowski M, Affolter M, Grzesiek S, DNA recognition by the brinker repressor–an extreme case of coupling between binding and folding, J. Mol. Biol. 2006 Aug;361(4):659-72.
• 2006
  Pellarin R, Caflisch A, Interpreting the aggregation kinetics of amyloid peptides, J. Mol. Biol. 2006 Jul;360(4):882-92.
• 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
  Tartaglia GG, Cavalli A, Pellarin R, Caflisch A, Prediction of aggregation rate and aggregation-prone segments in polypeptide sequences, Protein Sci. 2005 Oct;14(10):2723-34.
• 2005
  Tartaglia GG, Pellarin R, Cavalli A, Caflisch A, Organism complexity anti-correlates with proteomic beta-aggregation propensity, Protein Sci. 2005 Oct;14(10):2735-40.
• 2004
  Gorfe AA, Pellarin R, Caflisch A, Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simulations, J. Am. Chem. Soc. 2004 Nov;126(46):15277-86.
• 2004
  Tartaglia GG, Cavalli A, Pellarin R, Caflisch A, The role of aromaticity, exposed surface, and dipole moment in determining protein aggregation rates, Protein Sci. 2004 Jul;13(7):1939-41.
• 2004
  Blondel A, Ensemble variance in free energy calculations by thermodynamic integration: theory, optimal “Alchemical” path, and practical solutions, J Comput Chem 2004 May;25(7):985-93.
• 2004
  Dam J, Blondel A, Effect of multiple symmetries on the association of R67 DHFR subunits bearing interfacial complementing mutations, Protein Sci. 2004 Jan;13(1):1-14.