Publications

Modélisation Computationnelle des Interactions Protéine-Ligand (ERL U1133 INSERM)

Les publications antérieures à 2019 ont été effectuées au sein de l’UMRS Paris Diderot-Inserm 973 (MTi)

Sélection de publications

1/ Dafniet B, Cerisier N, Audouze K, Taboureau O. Drug-target-ADR Network and Possible Implications of Structural Variants in Adverse Events. Mol Inform. 2020 Dec;39(12):e2000116. doi: 10.1002/minf.202000116. Epub 2020 Aug 28. PMID: 32725965.

2/ Abi Hussein H, Geneix C, Cauvin C, Marc D, Flatters D, Camproux AC. Molecular Dynamics Simulations of Influenza A Virus NS1 Reveal a Remarkably Stable RNA-Binding Domain Harboring Promising Druggable Pockets. Viruses. 2020 May 14;12(5):537. doi: 10.3390/v12050537. PMID: 32422922; PMCID: PMC7290946.

3/ Postic G, Janel N, Tufféry P, Moroy G. An information gain-based approach for evaluating protein structure models. Comput Struct Biotechnol J. 2020;18:2228-2236. doi: 10.1016/j.csbj.2020.08.013. Epub 2020 Aug 18. PMID: 32837711; PMCID: PMC7431362.

4/ Triki D, Kermarrec M, Visseaux B, Descamps D, Flatters D, Camproux AC, Regad L. Exploration of the effects of sequence variations between HIV-1 and HIV-2 proteases on their three-dimensional structures. J Biomol Struct Dyn. 2020 Oct;38(17):5014-5026. doi: 10.1080/07391102.2019.1704877. Epub 2019 Dec 27. PMID: 31830870.

5/ Postic G, Marcoux J, Reys V, Andreani J, Vandenbrouck Y, Bousquet MP, Mouton-Barbosa E, Cianférani S, Burlet-Schiltz O, Guerois R, Labesse G, Tufféry P. Probing Protein Interaction Networks by Combining MS-Based Proteomics and Structural Data Integration. J Proteome Res. 2020 Jul 2;19(7):2807-2820. doi: 10.1021/acs.jproteome.0c00066. Epub 2020 May 7. PMID: 32338910.

Publications dans des journaux à comité de lecture (depuis 2015)

Savier E, Tuffery P, Bruzzoni-Giovanelli H, Rebollo A. Isolation of Primary Hepatocytes for Testing Tumor Penetrating Peptides. Methods Mol Biol. 2022;2383:413-427. doi: 10.1007/978-1-0716-1752-6_26. PMID: 34766304.

Escher SE, Aguayo-Orozco A, Benfenati E, Bitsch A, Braunbeck T, Brotzmann K, Bois F, van der Burg B, Castel J, Exner T, Gadaleta D, Gardner I, Goldmann D, Hatley O, Golbamaki N, Graepel R, Jennings P, Limonciel A, Long A, Maclennan R, Mombelli E, Norinder U, Jain S, Capinha LS, Taboureau OT, Tolosa L, Vrijenhoek NG, van Vugt-Lussenburg BMA, Walker P, van de Water B, Wehr M, White A, Zdrazil B, Fisher C. Integrate mechanistic evidence from new approach methodologies (NAMs) into a read-across assessment to characterise trends in shared mode of action. Toxicol In Vitro. 2022 Mar;79:105269. doi: 10.1016/j.tiv.2021.105269. Epub 2021 Oct 29. PMID: 34757180.

Hardiagon A, Murail S, Huang LB, van der Lee A, Sterpone F, Barboiu M, Baaden M. Molecular dynamics simulations reveal statistics and microscopic mechanisms of water permeation in membrane-embedded artificial water channel nanoconstructs. J Chem Phys. 2021 May 14;154(18):184102. doi: 10.1063/5.0044360. PMID: 34241013.

Postic G, Janel N, Moroy G. Representations of protein structure for exploring the conformational space: A speed-accuracy trade-off. Comput Struct Biotechnol J. 2021 Apr 28;19:2618-2625. doi: 10.1016/j.csbj.2021.04.049. PMID: 34025948; PMCID: PMC8120936.

Savier E, Simon-Gracia L, Charlotte F, Tuffery P, Teesalu T, Scatton O, Rebollo A. Bi-Functional Peptides as a New Therapeutic Tool for Hepatocellular Carcinoma. Pharmaceutics. 2021 Oct 6;13(10):1631. doi: 10.3390/pharmaceutics13101631. PMID: 34683924; PMCID: PMC8541685.

Murail S, de Vries SJ, Rey J, Moroy G, Tufféry P. SeamDock: An Interactive and Collaborative Online Docking Resource to Assist Small Compound Molecular Docking. Front Mol Biosci. 2021 Sep 17;8:716466. doi: 10.3389/fmolb.2021.716466. PMID: 34604303; PMCID: PMC8484321.

Rebollo A, Savier E, Tuffery P. Pepscan Approach for the Identification of Protein-Protein Interfaces: Lessons from Experiment. Biomolecules. 2021 May 21;11(6):772. doi: 10.3390/biom11060772. PMID: 34063976; PMCID: PMC8224071.

Quignot C, Postic G, Bret H, Rey J, Granger P, Murail S, Chacón P, Andreani J, Tufféry P, Guerois R. InterEvDock3: a combined template-based and free docking server with increased performance through explicit modeling of complex homologs and integration of covariation-based contact maps. Nucleic Acids Res. 2021 Jul 2;49(W1):W277-W284. doi: 10.1093/nar/gkab358. PMID: 33978743; PMCID: PMC8265070.

Postic G, Andreani J, Marcoux J, Reys V, Guerois R, Rey J, Mouton-Barbosa E, Vandenbrouck Y, Cianferani S, Burlet-Schiltz O, Labesse G, Tufféry P. Proteo3Dnet: a web server for the integration of structural information with interactomics data. Nucleic Acids Res. 2021 Jul 2;49(W1):W567-W572. doi: 10.1093/nar/gkab332. PMID: 33963857; PMCID: PMC8262742.

Wu Q, Bagdad Y, Taboureau O, Audouze K. Capturing a Comprehensive Picture of Biological Events From Adverse Outcome Pathways in the Drug Exposome. Front Public Health. 2021 Dec 17;9:763962. doi: 10.3389/fpubh.2021.763962. PMID: 34976924; PMCID: PMC8718398.

Dafniet B, Cerisier N, Boezio B, Clary A, Ducrot P, Dorval T, Gohier A, Brown D, Audouze K, Taboureau O. Development of a chemogenomics library for phenotypic screening. J Cheminform. 2021 Nov 24;13(1):91. doi: 10.1186/s13321-021-00569-1. PMID: 34819133; PMCID: PMC8611952.

Rasmussen HB, Jürgens G, Thomsen R, Taboureau O, Zeth K, Hansen PE, Hansen PR. Cellular Uptake and Intracellular Phosphorylation of GS-441524: Implications for Its Effectiveness against COVID-19. Viruses. 2021 Jul 14;13(7):1369. doi: 10.3390/v13071369. PMID: 34372575; PMCID: PMC8310262.

Rugard M, Jaylet T, Taboureau O, Tromelin A, Audouze K. Smell compounds classification using UMAP to increase knowledge of odors and molecular structures linkages. PLoS One. 2021 May 28;16(5):e0252486. doi: 10.1371/journal.pone.0252486. PMID: 34048487; PMCID: PMC8162648.

Bastin M, Busieau P, Kuhn E, Rouault C, Taboureau O, Toulgoat A, Chelabi S, Villemain A, Wright JJ, Spano JP, Andreelli F. Incretin response in immune checkpoint inhibitor-induced diabetes: an observational study. Diabetes Metab. 2021 Sep;47(5):101212. doi: 10.1016/j.diabet.2020.11.004. Epub 2020 Nov 27. PMID: 33253909.

Laville P, Petitjean M, Regad L. Structural Impacts of Drug-Resistance Mutations Appearing in HIV-2 Protease. Molecules. 2021 Jan 25;26(3):611. doi: 10.3390/molecules26030611. PMID: 33503916; PMCID: PMC7865771.

Petitjean M. Chirality in Geometric Algebra. Mathematics , MDPI, 2021, 9 (13), pp.1521. ⟨10.3390/math9131521⟩.

Petitjean M. Global Symmetries, Local Symmetries and Groupoids. Symmetry, MDPI, 2021, 13 (10), pp.1905. ⟨10.3390/sym13101905⟩. ⟨hal-03381876⟩

Petitjean M. Symmetry, Antisymmetry, and Chirality: Use and Misuse of Terminology. Symmetry, MDPI, 2021, 13 (4), pp.603. ⟨10.3390/sym13040603⟩.

Laville P, Petitjean M, Regad L. Structural Impacts of Drug-Resistance Mutations Appearing in HIV-2 Protease. Molecules, MDPI, 2021, 26 (3), pp.611. ⟨10.3390/molecules26030611⟩.

Ghoula M, Le Marec A, Magnan C, Le Stunff H, Taboureau O. Identification of the Interactions Interference Betwe en the PH and START Domain of CERT by Limonoid and HPA Inhibitors. Front Mol Biosci. 2020 Nov 27;7:603983. doi: 10.3389/fmolb.2020.603983. PMID: 33330630; PMCID: PMC7729066.

Khamassi M, Xu L, Rey J, Duchemin M, Bouceba T, Tuffery P, Tudor D, Bomsel M. The CH1α domain of mucosal gp41 IgA contributes to antibody specificity and antiviral functions in HIV-1 highly exposed Sero-Negative individuals. PLoS Pathog. 2020 Dec 14;16(12):e1009103. doi: 10.1371/journal.ppat.1009103. PMID: 33315937; PMCID: PMC7802955.

Dong CZ, Bruzzoni-Giovanelli H, Yu Y, Dorgham K, Parizot C, Zini JM, Brossas JY, Tuffery P, Rebollo A. Identification of peptides interfering with the LRRK2/PP1 interaction. PLoS One. 2020 Aug 13;15(8):e0237110. doi: 10.1371/journal.pone.0237110. PMID: 32790695; PMCID: PMC7425875.

Postic G, Marcoux J, Reys V, Andreani J, Vandenbrouck Y, Bousquet MP, Mouton-Barbosa E, Cianférani S, Burlet-Schiltz O, Guerois R, Labesse G, Tufféry P. Probing Protein Interaction Networks by Combining MS-Based Proteomics and Structural Data Integration. J Proteome Res. 2020 Jul 2;19(7):2807-2820. doi: 10.1021/acs.jproteome.0c00066. Epub 2020 May 7. PMID: 32338910.

Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, Feenstra KA, Gerloff DL, Hamelryck T, Hancock JM, Helmer-Citterich M, Hospital A, Orozco M, Perrakis A, Rarey M, Soares C, Sussman JL, Thornton JM, Tuffery P, Tusnady G, Wierenga R, Salminen T, Schneider B. A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community). F1000Res. 2020 Apr 22;9:ELIXIR-278. doi: 10.12688/f1000research.20559.1. PMID: 32566135; PMCID: PMC7284151.

Postic G, Janel N, Tufféry P, Moroy G. An information gain-based approach for evaluating protein structure models. Comput Struct Biotechnol J. 2020;18:2228-2236. doi: 10.1016/j.csbj.2020.08.013. Epub 2020 Aug 18. PMID: 32837711; PMCID: PMC7431362.

Tufféry P, de Vries S. The search of sequence variants using a constrained protein evolution simulation approach. Comput Struct Biotechnol J. 2020 Jun 17;18:1790-1799. doi: 10.1016/j.csbj.2020.06.018. PMID: 32695271; PMCID: PMC7355721.

Crobeddu B, Baudrimont I, Deweirdt J, Sciare J, Badel A, Camproux AC, Bui LC, Baeza-Squiban A. Lung Antioxidant Depletion: A Predictive Indicator of Cellular Stress Induced by Ambient Fine Particles. Environ Sci Technol. 2020 Feb 18;54(4):2360-2369. doi: 10.1021/acs.est.9b05990. Epub 2020 Jan 30. PMID: 31961142.

Abi Hussein H, Geneix C, Cauvin C, Marc D, Flatters D, Camproux AC. Molecular Dynamics Simulations of Influenza A Virus NS1 Reveal a Remarkably Stable RNA-Binding Domain Harboring Promising Druggable Pockets. Viruses. 2020 May 14;12(5):537. doi: 10.3390/v12050537. PMID: 32422922; PMCID: PMC7290946.

Triki D, Kermarrec M, Visseaux B, Descamps D, Flatters D, Camproux AC, Regad L. Exploration of the effects of sequence variations between HIV-1 and HIV-2 proteases on their three-dimensional structures. J Biomol Struct Dyn. 2020 Oct;38(17):5014-5026. doi: 10.1080/07391102.2019.1704877. Epub 2019 Dec 27. PMID: 31830870.

Laville P, Fartek S, Cerisier N, Flatters D, Petitjean M, Regad L. Impacts of drug resistance mutations on the structural asymmetry of the HIV-2 protease. BMC Mol Cell Biol. 2020 Jun 23;21(1):46. doi: 10.1186/s12860-020-00290-1. PMID: 32576133; PMCID: PMC7310402.

Elzaiat M, Flatters D, Sierra-Díaz DC, Legois B, Laissue P, Veitia RA. DHH pathogenic variants involved in 46,XY disorders of sex development differentially impact protein self-cleavage and structural conformation. Hum Genet. 2020 Nov;139(11):1455-1470. doi: 10.1007/s00439-020-02189-5. Epub 2020 Jun 5. PMID: 32504121.

Gu Y, Moroy G, Paul JL, Rebillat AS, Dierssen M, de la Torre R, Cieuta-Walti C, Dairou J, Janel N. Molecular Rescue of Dyrk1A Overexpression Alterations in Mice with Fontup<sup>®</sup> Dietary Supplement: Role of Green Tea Catechins. Int J Mol Sci. 2020 Feb 19;21(4):1404. doi: 10.3390/ijms21041404. PMID: 32092951; PMCID: PMC7073110.

Amouyal C, Castel J, Guay C, Lacombe A, Denom J, Migrenne-Li S, Rouault C, Marquet F, Georgiadou E, Stylianides T, Luquet S, Le Stunff H, Scharfmann R, Clément K, Rutter GA, Taboureau O, Magnan C, Regazzi R, Andreelli F. A surrogate of Roux-en-Y gastric bypass (the enterogastro anastomosis surgery) regulates multiple beta-cell pathways during resolution of diabetes in ob/ob mice. EBioMedicine. 2020 Aug;58:102895. doi: 10.1016/j.ebiom.2020.102895. Epub 2020 Jul 30. PMID: 32739864; PMCID: PMC7393530.

Rasmussen HB, Hansen PR, Taboureau O, Thomsen R, Jürgens G. Pulmonary administration of remdesivir in the treatment of COVID-19. AAPS J. 2020 Sep 17;22(6):121. doi: 10.1208/s12248-020-00506-4. PMID: 32944838; PMCID: PMC7498113.

Taboureau O, El M’Selmi W, Audouze K. Integrative systems toxicology to predict human biological systems affected by exposure to environmental chemicals. Toxicol Appl Pharmacol. 2020 Oct 15;405:115210. doi: 10.1016/j.taap.2020.115210. Epub 2020 Aug 27. PMID: 32860831.

Dafniet B, Cerisier N, Audouze K, Taboureau O. Drug-target-ADR Network and Possible Implications of Structural Variants in Adverse Events. Mol Inform. 2020 Dec;39(12):e2000116. doi: 10.1002/minf.202000116. Epub 2020 Aug 28. PMID: 32725965.

Mansouri K, Kleinstreuer N, Abdelaziz AM, Alberga D, Alves VM, Andersson PL, Andrade CH, Bai F, Balabin I, Ballabio D, Benfenati E, Bhhatarai B, Boyer S, Chen J, Consonni V, Farag S, Fourches D, García-Sosa AT, Gramatica P, Grisoni F, Grulke CM, Hong H, Horvath D, Hu X, Huang R, Jeliazkova N, Li J, Li X, Liu H, Manganelli S, Mangiatordi GF, Maran U, Marcou G, Martin T, Muratov E, Nguyen DT, Nicolotti O, Nikolov NG, Norinder U, Papa E, Petitjean M, Piir G, Pogodin P, Poroikov V, Qiao X, Richard AM, Roncaglioni A, Ruiz P, Rupakheti C, Sakkiah S, Sangion A, Schramm KW, Selvaraj C, Shah I, Sild S, Sun L, Taboureau O, Tang Y, Tetko IV, Todeschini R, Tong W, Trisciuzzi D, Tropsha A, Van Den Driessche G, Varnek A, Wang Z, Wedebye EB, Williams AJ, Xie H, Zakharov AV, Zheng Z, Judson RS. CoMPARA: Collaborative Modeling Project for Androgen Receptor Activity. Environ Health Perspect. 2020 Feb;128(2):27002. doi: 10.1289/EHP5580. Epub 2020 Feb 7. PMID: 32074470; PMCID: PMC7064318.

Petitjean M. Chirality in metric spaces. In memoriam Michel Deza. Optimization Letters, Springer Verlag, 2020, 14 (2), pp.329-338. ⟨10.1007/s11590-017-1189-7⟩.

Petitjean M. Chirality of Dirac Spinors Revisited. Symmetry, MDPI, 2020, 12 (4), pp.616. ⟨10.3390/sym12040616⟩.

Petitjean M., Comment on « Bad Language »: Resolving some Ambiguities about Chirality. Angew. Chem. Int. Ed., 2020, 59[20], 7650–7651. DOI 10.1002/anie.201904314, hal-02567126 (Angew. Chem. 2020, \underline{132}[20], 7722–7723. DOI 10.1002/ange.201904314

Petitjean M., Molecular chirality in classical spacetime: solving the controversy about the spinning cone model of rotating molecules. Chem. Eur. J., 2020, 26[47] 10648–10652. DOI 10.1002/chem.201904247

Petitjean M., Extreme asymmetry and chirality. A challenging quantification. Symmetry Cult. Sci., 2020, DOI 10.26830/symmetry_2020_4_439

Glashagen G, de Vries S, Uciechowska-Kaczmarzyk U, Samsonov SA, Murail S, Tuffery P, Zacharias M. Coarse-grained and atomic resolution biomolecular docking with the ATTRACT approach. Proteins. 2020 Aug;88(8):1018-1028. doi: 10.1002/prot.25860. Epub 2019 Dec 13. PMID: 31785163.

Lagarde N, Goldwaser E, Pencheva T, Jereva D, Pajeva I, Rey J, Tuffery P, Villoutreix BO, Miteva MA. A Free Web-Based Protocol to Assist Structure-Based Virtual Screening Experiments. Int J Mol Sci. 2019 Sep 19;20(18).

Rey J, Rasolohery I, Tufféry P, Guyon F, Moroy G. PatchSearch: a web server for off-target protein identification. Nucleic Acids Res. 2019 Jul2;47(W1):W365-W372.

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 Jul 2;47(W1):W423-W428.

Cerisier N, Petitjean M, Regad L, Bayard Q, Réau M, Badel A, Camproux AC. High Impact: The Role of Promiscuous Binding Sites in Polypharmacology. Molecules. 2019 Jul 10;24(14).

Benkaidali L, André F, Moroy G, Tangour B, Maurel F, Petitjean M. Four Major Channels Detected in the Cytochrome P450 3A4: A Step toward Understanding Its Multispecificity. Int J Mol Sci. 2019 Feb 25;20(4).

Perrier A, Eluard M, Petitjean M, Vanet A. In Silico Design of New Inhibitors Against Hemagglutinin of Influenza. J Phys Chem B. 2019 Jan 24;123(3):582-592.

Petitjean M. About Chirality in Minkowski Spacetime. Symmetry, MDPI, 2019, 11 (10), pp.1320.

Ozeel V, Perrier A, Vanet A, Petitjean M. The Symmetric Difference Distance: A New Way to Evaluate the Evolution of Interfaces along Molecular Dynamics Trajectories; Application to Influenza Hemagglutinin. Symmetry, MDPI, 2019, 11 (5), pp.662.

Triki D, Fartek S, Visseaux B, Descamps D, Camproux AC, Regad L. Characterizing the structural variability of HIV-2 protease upon the binding of diverse ligands using a structural alphabet approach. J Biomol Struct Dyn. 2019 Oct;37(17):4658-4670.

Briand E, Thomsen R, Linnet K, Rasmussen HB, Brunak S, Taboureau O. Combined Ensemble Docking and Machine Learning in Identification of Therapeutic Agents with Potential Inhibitory Effect on Human CES1. Molecules. 2019 Jul 29;24(15).

Aguayo-Orozco A, Audouze K, Siggaard T, Barouki R, Brunak S, Taboureau O. sAOP: Linking chemical stressors to Adverse Outcomes Pathway Networks. Bioinformatics. 2019 Jul 22.

Aguayo-Orozco A, Bois FY, Brunak S, Taboureau O. Analysis of Time-Series Gene Expression Data to Explore Mechanisms of Chemical-Induced Hepatic Steatosis Toxicity. Front Genet. 2018 Sep 18;9:396.

Allam I, Flatters D, Caumes G, Regad L, Delos V, Nuel G, Camproux AC. SAFlex: A structural alphabet extension to integrate protein structural flexibility and missing data information. PLoS One. 2018 Jul 5;13(7):e0198854.

Audouze K, Taboureau O, Grandjean P. A systems biology approach to predictive developmental neurotoxicity of a larvicide used in the prevention of Zika virus transmission. Toxicol Appl Pharmacol. 2018 Sep 1;354:56-63.

Bouissou C, Petitjean M. Asymmetric Exchanges. J Interd Method Iss Sci. 2018;4:1-18.

Bourguet E, Ozdarska K, Moroy G, Jeanblanc J, Naassila M. Class I HDAC Inhibitors: Potential New Epigenetic Therapeutics for Alcohol Use Disorder (AUD). J Med Chem. 2018 Mar 8;61(5):1745-1766.

Bruzzoni-Giovanelli H, Alezra V, Wolff N, Dong CZ, Tuffery P, Rebollo A. Interfering peptides targeting protein-protein interactions: the next generation of drugs? Drug Discov Today. 2018 Feb;23(2):272-285.

Grinberg M, Stöber RM, Albrecht W, Edlund K, Schug M, Godoy P, Cadenas C, Marchan R, Lampen A, Braeuning A, Buhrke T, Leist M, Oberemm A, Hellwig B, Kamp H, Gardner I, Escher S, Taboureau O, Aguayo-Orozco A, Sachinidis A, Ellinger-Ziegelbauer H, Rahnenführer J, Hengstler JG. Toxicogenomics directory of rat hepatotoxicants in vivo and in cultivated hepatocytes. Arch Toxicol. 2018 Dec;92(12):3517-3533.

Jeanblanc J, Bourguet E, Sketriené D, Gonzalez C, Moroy G, Legastelois R, Létévé M, Trussardi-Régnier A, Naassila M. Interest of new alkylsulfonylhydrazide-type compound in the treatment of alcohol use disorders. Psychopharmacology (Berl). 2018 Jun;235(6):1835-1844.

Kaddurah-Daouk R, Hankemeier T, Scholl EH, Baillie R, Harms A, Stage C, Dalhoff KP, Jürgens G, Taboureau O, Nzabonimpa GS, Motsinger-Reif AA, Thomsen R, Linnet K, Rasmussen HB; INDICES Consortium; Pharmacometabolomics Research Network. Pharmacometabolomics Informs About Pharmacokinetic Profile of Methylphenidate. CPT Pharmacometrics Syst Pharmacol. 2018 Aug;7(8):525-533.

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 12;8(1):13673.

Kocsis I, Sorci M, Vanselous H, Murail S, Sanders SE, Licsandru E, Legrand YM, van der Lee A, Baaden M, Petersen PB, Belfort G, Barboiu M. Oriented chiral water wires in artificial transmembrane channels. Sci Adv. 2018 Mar 23;4(3):eaao5603.

Lagarde N, Rey J, Gyulkhandanyan A, Tufféry P, Miteva MA, Villoutreix BO. Online structure-based screening of purchasable approved drugs and natural compounds: retrospective examples of drug repositioning on cancer targets. Oncotarget. 2018 Aug 17;9(64):32346-32361.

Létévé M, Gonzalez C, Moroy G, Martinez A, Jeanblanc J, Legastelois R, Naassila M, Sapi J, Bourguet E. Unexpected effect of cyclodepsipeptides bearing a sulfonylhydrazide moiety towards histone deacetylase activity. Bioorg Chem. 2018 Dec;81:222-233.

Murail S, Vasiliu T, Neamtu A, Barboiu M, Sterpone F, Baaden M. Water permeation across artificial I-quartet membrane channels: from structure to disorder. Faraday Discuss. 2018 Sep 28;209(0):125-148.

Ollitrault G, Fartek S, Descamps D, Camproux AC, Visseaux B, Regad L. Characterization of HIV-2 Protease Structure by Studying Its Asymmetry at the Different Levels of Protein Description. Symmetry. 2018;10(11);644.

Quignot C, Rey J, Yu J, Tufféry P, Guerois R, Andreani J. InterEvDock2: an expanded server for protein docking using evolutionary and biological information from homology models and multimeric inputs. Nucleic Acids Res. 2018 Jul 2;46(W1):W408-W416.

Sutherland GA, Grayson KJ, Adams NBP, Mermans DMJ, Jones AS, Robertson AJ, Auman DB, Brindley AA, Sterpone F, Tuffery P, Derreumaux P, Dutton PL, Robinson C, Hitchcock A, Hunter CN. Probing the quality control mechanism of the Escherichia coli twin-arginine translocase with folding variants of a de novo-designed heme protein. J Biol Chem. 2018 May 4;293(18):6672-6681.

Triki D, Billot T, Visseaux B, Descamps D, Flatters D, Camproux AC, Regad L. Exploration of the effect of sequence variations located inside the binding pocket of HIV-1 and HIV-2 proteases. Sci Rep. 2018 Apr 10;8(1):5789.

Triki D, Cano Contreras ME, Flatters D, Visseaux B, Descamps D, Camproux AC, Regad L. Analysis of the HIV-2 protease’s adaptation to various ligands: characterization of backbone asymmetry using a structural alphabet. Sci Rep. 2018 Jan 15;8(1):710.

Abi Hussein H, Geneix C, Petitjean M, Borrel A, Flatters D, Camproux AC. Global vision of druggability issues: applications and perspectives. Drug Discov Today. 2017 Feb;22(2):404-415.

Benkaidali L, André F, Moroy G, Tangour B, Maurel F, Petitjean M. The cytochrome P450 3A4 has three major conformations: new clues to drug recognition by this promiscuous enzyme. Mol Inform. 2017;36(10):1700044.

Boezio B, Audouze K, Ducrot P, Taboureau O. Network-based Approaches in Pharmacology. Mol Inform. 2017 Oct;36(10).

Catharina L, Lima CR, Franca A, Guimarães ACR, Alves-Ferreira M, Tuffery P, Derreumaux P, Carels N. A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against Leishmania major. Bioinform Biol Insights. 2017 Jun 12;11:1177932217712471.

Caumes G, Borrel A, Abi Hussein H, Camproux AC, Regad L. Investigating the Importance of the Pocket-estimation Method in Pocket-based Approaches: An Illustration Using Pocket-ligand Classification. Mol Inform. 2017 Sep;36(9).

Cerisier N, Regad L, Triki D, Camproux AC, Petitjean M. Cavity Versus Ligand Shape Descriptors: Application to Urokinase Binding Pockets. J Comput Biol. 2017 Nov;24(11):1134-1137.

Cerisier N, Regad L, Triki D, Petitjean M, Flatters D, Camproux AC. Statistical Profiling of One Promiscuous Protein Binding Site: Illustrated by Urokinase Catalytic Domain. Mol Inform. 2017 Oct;36(10).

de Vries SJ, Rey J, Schindler CEM, Zacharias M, Tuffery P. The pepATTRACT web server for blind, large-scale peptide-protein docking. Nucleic Acids Res. 2017 Jul 3;45(W1):W361-W364.

de Vries SJ, Zacharias M. Fast and accurate grid representations for atom-based docking with partner flexibility. J Comput Chem. 2017 Jun 30;38(17):1538-46.

Eustache S, Créchet JB, Bouceba T, Nakayama JI, Tanaka M, Suzuki M, Woisard A, Tuffery P, Baouz S, Hountondji C. A Functional Role for the Monomethylated Gln-51 and Lys-53 Residues of the 49GGQTK53 Motif of eL42 from Human 80S Ribosomes. Open Biochem J. 2017 Mar 31;11:8-26.

Janel N, Alexopoulos P, Badel A, Lamari F, Camproux AC, Lagarde J, Simon S, Feraudet-Tarisse C, Lamourette P, Arbones M, Paul JL, Dubois B, Potier MC, Sarazin M, Delabar JM. Combined assessment of DYRK1A, BDNF and homocysteine levels as diagnostic marker for Alzheimer’s disease. Transl Psychiatry. 2017 Jun 20;7(6):e1154.

Lamiable A, Thévenet P, Eustache S, Saladin A, Moroy G, Tuffery P. Peptide Suboptimal Conformation Sampling for the Prediction of Protein-Peptide Interactions. Methods Mol Biol. 2017;1561:21-34.

Leist M, Ghallab A, Graepel R, Marchan R, Hassan R, Bennekou SH, Limonciel A, Vinken M, Schildknecht S, Waldmann T, Danen E, van Ravenzwaay B, Kamp H, Gardner I, Godoy P, Bois FY, Braeuning A, Reif R, Oesch F, Drasdo D, Höhme S, Schwarz M, Hartung T, Braunbeck T, Beltman J, Vrieling H, Sanz F, Forsby A, Gadaleta D, Fisher C, Kelm J, Fluri D, Ecker G, Zdrazil B, Terron A, Jennings P, van der Burg B, Dooley S, Meijer AH, Willighagen E, Martens M, Evelo C, Mombelli E, Taboureau O, Mantovani A, Hardy B, Koch B, Escher S, van Thriel C, Cadenas C, Kroese D, van de Water B, Hengstler JG. Adverse outcome pathways: opportunities, limitations and open questions. Arch Toxicol. 2017 Nov;91(11):3477-3505.

Lev B, Murail S, Poitevin F, Cromer BA, Baaden M, Delarue M, Allen TW. String method solution of the gating pathways for a pentameric ligand-gated ion channel. Proc Natl Acad Sci U S A. 2017 May 23;114(21):E4158-E4167.

Murail S. Simulation of Ligand Binding to Membrane Proteins. Methods Mol Biol. 2017;1635:359-381.

Paris F, Flatters D, Caburet S, Legois B, Servant N, Lefebvre H, Sultan C, Veitia RA. A novel variant of DHH in a familial case of 46,XY disorder of sex development: Insights from molecular dynamics simulations. Clin Endocrinol (Oxf). 2017 Nov;87(5):539-544.

Petitjean M. A fast algorithm to compute conical pockets in proteins. Application to the structural characterization of $\gamma$-carbonic anhydrases. Mol Inform. 2017;36(10):1600155.

Qvortrup K, Jensen JF, Sørensen MS, Kouskoumvekaki I, Petersen RK, Taboureau O, Kristiansen K, Nielsen TE. Synthesis and biological evaluation of dihydropyrano-[2,3-c]pyrazoles as a new class of PPARγ partial agonists. PLoS One. 2017 Feb 28;12(2):e0162642.

Rasolohery I, Moroy G, Guyon F. PatchSearch: A Fast Computational Method for Off-Target Detection. J Chem Inf Model. 2017 Apr 24;57(4):769-777.

Regad L, Chéron JB, Triki D, Senac C, Flatters D, Camproux AC. Exploring the potential of a structural alphabet-based tool for mining multiple target conformations and target flexibility insight. PLoS One. 2017 Aug 17;12(8):e0182972.

Sasse A, de Vries SJ, Schindler CE, de Beauchêne IC, Zacharias M. Rapid Design of Knowledge-Based Scoring Potentials for Enrichment of Near-Native Geometries in Protein-Protein Docking. PloS one. 2017;12(1):e0170625.

Schindler CEM, Beauchêne IC de, Vries SJ de, Zacharias M. Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI. Proteins: Structure, Function, and Bioinformatics. 2017 Mar 1;85(3):391-8.

Taboureau O, Audouze K. Human Environmental Disease Network: A computational model to assess toxicology of contaminants. ALTEX. 2017;34(2):289-300.

Zhang Y, Borrel A, Ghemtio L, Regad L, Boije Af Gennäs G, Camproux AC, Yli-Kauhaluoma J, Xhaard H. Structural Isosteres of Phosphate Groups in the Protein Data Bank. J Chem Inf Model. 2017 Mar 27;57(3):499-516.

Aguayo-Orozco A, Audouze K, Brunak S, Taboureau O. In Silico Systems Pharmacology to Assess Drug’s Therapeutic and Toxic Effects. Curr Pharm Des. 2016;22(46):6895-6902.

de Beauchene IC, de Vries SJ, Zacharias M. Fragment-based modelling of single stranded RNA bound to RNA recognition motif containing proteins. Nucleic acids research. 2016;44(10):4565-4580.

de Beauchene IC, de Vries SJ, Zacharias M. Binding site identification and flexible docking of single stranded RNA to proteins using a fragment-based approach. PLoS computational biology. 2016;12(1):e1004697.

Bourguet E, Brazhnik K, Sukhanova A, Moroy G, Brassart-Pasco S, Martin AP, Villena I, Bellon G, Sapi J, Nabiev I. Design, Synthesis, and Use of MMP-2 Inhibitor-Conjugated Quantum Dots

de Vries SJ, de Beauchêne IC, Schindler CE, Zacharias M. Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling. Biophysical journal. 2016;110(4):785-797.

Diudea M.V, Petitjean M. Chiral Multitori as Snub Derivatives. Rev Roum Chim. 2016;61(4-5):327-335.

Eustache S, Leprince J, Tufféry P. Progress with peptide scanning to study structure-activity relationships: the implications for drug discovery. Expert Opin Drug Discov. 2016 Aug;11(8):771-84.

Kringelum J, Kjaerulff SK, Brunak S, Lund O, Oprea TI, Taboureau O. ChemProt-3.0: a global chemical biology diseases mapping. Database (Oxford). 2016 Feb 13;2016.

Lamiable A, Thévenet P, Rey J, Vavrusa M, Derreumaux P, Tufféry P. PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex. Nucleic Acids Res. 2016 Jul 8;44(W1):W449-54.

Lamiable A, Thevenet P, Tufféry P. A critical assessment of hidden markov model sub-optimal sampling strategies applied to the generation of peptide 3D models. J Comput Chem. 2016 Aug 5;37(21):2006-16.

Lima CR, Carels N, Guimaraes AC, Tufféry P, Derreumaux P. In silico structural characterization of protein targets for drug development against Trypanosoma cruzi. J Mol Model. 2016 Oct;22(10):244.

Laurent B, Murail S, Shahsavar A, Sauguet L, Delarue M, Baaden M. Sites of Anesthetic Inhibitory Action on a Cationic Ligand-Gated Ion Channel. Structure. 2016 Apr 5;24(4):595-605.

Laurent MA, Bonnier D, Théret N, Tufféry P, Moroy G. In silico characterization of the interaction between LSKL peptide, a LAP-TGF-beta derived peptide, and ADAMTS1. Comput Biol Chem. 2016 Apr;61:155-61.

Licsandru E, Kocsis I, Shen YX, Murail S, Legrand YM, van der Lee A, Tsai D, Baaden M, Kumar M, Barboiu M. Salt-Excluding Artificial Water Channels Exhibiting Enhanced Dipolar Water and Proton Translocation. J Am Chem Soc. 2016 Apr 27;138(16):5403-9.

Margineanu A, Chan JJ, Kelly DJ, Warren SC, Flatters D, Kumar S, Katan M, Dunsby CW, French PM. Corrigendum: Screening for protein-protein interactions using Förster resonance energy transfer (FRET) and fluorescence lifetime imaging microscopy (FLIM). Sci Rep. 2016 Sep 22;6:33621.

Nzabonimpa GS, Rasmussen HB, Brunak S, Taboureau O; INDICES Consortium. Investigating the impact of missense mutations in hCES1 by in silico structure-based approaches. Drug Metab Pers Ther. 2016.

Petitjean M, Camproux A.-C. Book Review: In Silico Medicinal Chemistry: Computational Methods to Support Drug Design, Edited by Nathan Brown. ChemMedChem. 2016;11(13):1480-1481.

Ramambason C, Moroy G, Daubigney F, Paul JL, Janel N. Effect of cadmium administration in hyperhomocysteinemic mice due to cystathionine beta synthase deficiency. Exp Toxicol Pathol. 2016 Jun;68(6):365-70.

Schindler CE, de Vries SJ, Sasse A, Zacharias M. SAXS Data Alone can Generate High-Quality Models of Protein-Protein Complexes. Structure. 2016;24(8):1387-1397.

Sun H, Yue PY, Wang SR, Huo L, Zhao Y, Xie S, Kringelum JV, Lund O, Taboureau O, Zhou J, Wong RN, Fang WS. Synthesis and Biological Evaluations of Cytotoxic and Antiangiogenic Triterpenoids-Jacaranone Conjugates. Med Chem. 2016;12(8):775-785.

Van Zundert GCP, Rodrigues J, Trellet M, Schmitz C, Kastritis PL, Karaca E, et al. The HADDOCK2. 2 web server: user-friendly integrative modeling of biomolecular complexes. Journal of molecular biology. 2016;428(4):720-725.

Yu J, Vavrusa M, Andreani J, Rey J, Tufféry P, Guerois R. InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information. Nucleic Acids Res. 2016 Jul 8;44(W1):W542-9.

Audouze K, Taboureau O. Chemical biology databases: from aggregation, curation to representation. Drug Discov Today Technol. 2015 Jul;14:25-9.

Bessière L, Todeschini AL, Auguste A, Sarnacki S, Flatters D, Legois B, Sultan C, Kalfa N, Galmiche L, Veitia RA. A Hot-spot of In-frame Duplications Activates the Oncoprotein AKT1 in Juvenile Granulosa Cell Tumors. EBioMedicine. 2015 Mar 6;2(5):421-31.

Borrel A, Regad L, Xhaard H, Petitjean M, Camproux AC. PockDrug: A Model for Predicting Pocket Druggability That Overcomes Pocket Estimation Uncertainties. J Chem Inf Model. 2015 Apr 27;55(4):882-95.

de Vries SJ, Schindler CE, de Beauchêne IC, Zacharias M. A web interface for easy flexible protein-protein docking with ATTRACT. Biophysical journal. 2015;108(3):462-465.

Dueholm B, Krieger C, Drew D, Olry A, Kamo T, Taboureau O, Weitzel C, Bourgaud F, Hehn A, Simonsen HT. Evolution of substrate recognition sites (SRSs) in cytochromes P450 from Apiaceae exemplified by the CYP71AJ subfamily. BMC Evol Biol. 2015 Jun 26;15:122.

Guyon F, Martz F, Vavrusa M, Bécot J, Rey J, Tufféry P. BCSearch: fast structural fragment mining over large collections of protein structures. Nucleic Acids Res. 2015 Jul 1;43(W1):W378-82.

Hussein HA, Borrel A, Geneix C, Petitjean M, Regad L, Camproux AC. PockDrug-Server: a new web server for predicting pocket druggability on holo and apo proteins. Nucleic Acids Res. 2015 Jul 1;43(W1):W436-42.

Labbé CM, Rey J, Lagorce D, Vavru?a M, Becot J, Sperandio O, Villoutreix BO, Tufféry P, Miteva MA. MTiOpenScreen: a web server for structure-based virtual screening. Nucleic Acids Res. 2015 Jul 1;43(W1):W448-54.

Martiny VY, Carbonell P, Chevillard F, Moroy G, Nicot AB, Vayer P, Villoutreix BO, Miteva MA. Integrated structure- and ligand-based in silico approach to predict inhibition of cytochrome P450 2D6. Bioinformatics. 2015 Dec 15;31(24):3930-7.

Moraga-Cid G, Sauguet L, Huon C, Malherbe L, Girard-Blanc C, Petres S, Murail S, Taly A, Baaden M, Delarue M, Corringer PJ. Allosteric and hyperekplexic mutant phenotypes investigated on an ?1 glycine receptor transmembrane structure. Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):2865-70.

Moroy G, Sperandio O, Rielland S, Khemka S, Druart K, Goyal D, Perahia D, Miteva MA. Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis. Future Med Chem. 2015;7(17):2317-31.

Petitjean M. The most Chiral Disphenoid. MATCH Commun Math Comput Chem. 2015;73(2):375-384.

Petitjean M. Analytical Algorithms for Ligand Cone Angles Calculations. Application to Triphenylphosphine Palladium Complexes. Compt Rend Chim. 2015;18(6):678-684.

Petitjean M, Badel A, Veitia R.A, Vanet A. Synthetic Lethals in HIV: Ways to Avoid Drug Resistance. Biology Direct. 2015 Apr 17;10:17.

Rasmussen HB, Bjerre D, Linnet K, Jürgens G, Dalhoff K, Stefansson H, Hankemeier T, Kaddurah-Daouk R, Taboureau O, Brunak S, Houmann T, Jeppesen P, Pagsberg AK, Plessen K, Dyrborg J, Hansen PR, Hansen PE, Hughes T, Werge T; INDICES Consortium. Individualization of treatments with drugs metabolized by CES1: combining genetics and metabolomics. Pharmacogenomics. 2015;16(6):649-65.

Schindler CE, de Vries SJ, Zacharias M. iATTRACT: Simultaneous global and local interface optimization for protein-protein docking refinement. Proteins: Structure, Function, and Bioinformatics. 2015;83(2):248-258.

Schindler CE, de Vries SJ, Zacharias M. Fully blind peptide-protein docking with pepattract. Structure. 2015;23(8):1507-1515.

Thomsen R, Nielsen LM, Holm NB, Rasmussen HB, Linnet K; INDICES Consortium. Synthetic cannabimimetic agents metabolized by carboxylesterases. Drug Test Anal. 2015 Jul;7(7):565-576.

Thévenet P, Rey J, Moroy G, Tuffery P. De novo peptide structure prediction: an overview. Methods Mol Biol. 2015;1268:1-13.

Tufféry P. Accessing external innovation in drug discovery and development. Expert Opin Drug Discov. 2015 Jun;10(6):579-589.

Villoutreix BO, Taboureau O. Computational investigations of hERG channel blockers: New insights and current predictive models. Adv Drug Deliv Rev. 2015 Jun 23;86:72-82.

Yu J, Picord G, Tuffery P, Guerois R. HHalign-Kbest: exploring sub-optimal alignments for remote homology comparative modeling. Bioinformatics. 2015 Dec 1;31(23):3850-3852.