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)

** Publications communes avec d’autres équipes de BFA.

Quartile (Scimago Journal & Country Rank) indiqué à la fin de chaque référence.


Original articles




Karami Y, Murail S, Giribaldi J, Lefranc B, Defontaine F, Lesouhaitier O, Leprince J, de Vries S, Tufféry P. Exploring a Structural Data Mining Approach to Design Linkers for Head-to-Tail Peptide Cyclization. J Chem Inf Model. 2023 Oct 23;63(20):6436-6450. (Q1)


Mermet S, Voisin M, Mordier J, Dubos T, Tutois S, Tuffery P, Baroux C, Tamura K, Probst AV, Vanrobays E, Tatout C. Evolutionarily conserved protein motifs drive interactions between the plant nucleoskeleton and nuclear pores. Plant Cell. 2023 Nov 30;35(12):4284-4303. (Q1)


Barbault F, Brémond E, Rey J, Tufféry P, Maurel F. DockSurf: A Molecular Modeling Software for the Prediction of Protein/Surface Adhesion. J Chem Inf Model. 2023 Aug 28;63(16):5220-5231. (Q1)


Rey J, Murail S, de Vries S, Derreumaux P, Tuffery P. PEP-FOLD4: a pH-dependent force field for peptide structure prediction in aqueous solution. Nucleic Acids Res. 2023 Jul 5;51(W1):W432-W437. (Q1)


Marin GH, Murail S, Andrini L, Garcia M, Loisel S, Tuffery P, Rebollo A. In Silico and In Vivo Studies of a Tumor-Penetrating and Interfering Peptide with Antitumoral Effect on Xenograft Models of Breast Cancer. Pharmaceutics. 2023 Apr 7;15(4):1180. (Q1)


Tufféry P, Derreumaux P. A refined pH-dependent coarse-grained model for peptide structure prediction in aqueous solution. Front Bioinform. 2023 Jan 16;3:1113928.


Ghoula M, Deyawe Kongmeneck A, Eid R, Camproux AC, Moroy G. Comparative Study of the Mutations Observed in the SARS-CoV-2 RBD Variants of Concern and Their Impact on the Interaction with the ACE2 Protein. J Phys Chem B. 2023 Oct 12;127(40):8586-8602. (Q1)


**Postic G, Solarz J, Loubière C, Kandiah J, Sawmynaden J, Adam F, Vilaire M, Léger T, Camadro JM, Victorino DB, Potier MC, Bun E, Moroy G, Kauskot A, Christophe O, Janel N. Over-expression of Dyrk1A affects bleeding by modulating plasma fibronectin and fibrinogen level in mice. J Cell Mol Med. 2023 Aug;27(15):2228-2238. (Q2)


Rasmussen RH, Christensen SL, Calloe K, Nielsen BS, Rehfeld A, Taylor-Clark TE, Haanes KA, Taboureau O, Audouze K, Klaerke DA, Olesen J, Kristensen DM. Xenobiotic Exposure and Migraine-Associated Signaling: A Multimethod Experimental Study Exploring Cellular Assays in Combination with <i>Ex Vivo</i> and <i>In Vivo</i> Mouse Models. Environ Health Perspect. 2023 Nov;131(11):117003. (Q1)


Lazzeri G, Micheletti C, Pasquali S, Faccioli P. RNA folding pathways from all-atom simulations with a variationally improved history-dependent bias. Biophys J. 2023 Aug 8;122(15):3089-3098. (Q1)


**de Thonel A, Ahlskog JK, Daupin K, Dubreuil V, Berthelet J, Chaput C, Pires G, Leonetti C, Abane R, Barris LC, Leray I, Aalto AL, Naceri S, Cordonnier M, Benasolo C, Sanial M, Duchateau A, Vihervaara A, Puustinen MC, Miozzo F, Fergelot P, Lebigot É, Verloes A, Gressens P, Lacombe D, Gobbo J, Garrido C, Westerheide SD, David L, Petitjean M, Taboureau O, Rodrigues-Lima F, Passemard S, Sabéran-Djoneidi D, Nguyen L, Lancaster M, Sistonen L, Mezger V. Author Correction: CBP-HSF2 structural and functional interplay in Rubinstein-Taybi neurodevelopmental disorder. Nat Commun. 2023 Sep 28;14(1):6067. doi: 10.1038/s41467-023-41869-4. Erratum for: Nat Commun. 2022 Nov 16;13(1):7002. (Q1)


Lejal V, Cerisier N, Rouquié D, Taboureau O. Assessment of Drug-Induced Liver Injury through Cell Morphology and Gene Expression Analysis. Chem Res Toxicol. 2023 Sep 18;36(9):1456-1470. (Q1)


Valls-Margarit J, Piñero J, Füzi B, Cerisier N, Taboureau O, Furlong LI. Assessing network-based methods in the context of system toxicology. Front Pharmacol. 2023 Jul 12;14:1225697. (Q1)


Feron F, Amouyal C, Hartemann A, Van GH, Bourron O, Dierick-Gallet A, Michaux C, Santos MD, Baudot M, Devaux G, Taboureau O, Andreelli F. The short-term prognosis of diabetic foot ulceration is independent of nutritional status at admission. J Wound Care. 2023 May 2;32(5):312-317. (Q2)


Cerisier N, Dafniet B, Badel A, Taboureau O. Linking chemicals, genes and morphological perturbations to diseases. Toxicol Appl Pharmacol. 2023 Feb 15;461:116407. (Q1)


Boulcourt S, Badel A, Pionnier R, Neder Y, Ilharreborde B, Simon AL. A gait functional classification of adolescent idiopathic scoliosis (AIS) based on spatio-temporal parameters (STP). Gait Posture. 2023 May;102:50-55. (Q1)




Naceri S, Marc D, Blot R, Flatters D, Camproux AC. Druggable Pockets at the RNA Interface Region of Influenza A Virus NS1 Protein Are Conserved across Sequence Variants from Distinct Subtypes. Biomolecules. 2022 Dec 29;13(1):64. (Q1)


  1. **Villares M, Lourenço N, Berthelet J, Lamotte S, Regad L, Medjkane S, Prina E, Rodrigues-Lima F, Späth G.F & Weitzman J.B. Trifloxystrobin blocks the growth of Theileria Parasites and is a promising drug to treat Buparvaquone resistance, Communication Biology, 2022, 5:1253 . (Q1)


  1. Rebollo A, Fiedele L and Tuffery P. PEP scan: a broad spectrum approach for the characterization of protein-binder interactions. Biomolecules, 2022. 12, 178. (Q2)


  1. Dorgham K, Murail S, Tuffery P, Savier E, Bravo J, & Rebollo A. Binding and Kinetic Analysis of Human Protein Phosphatase PP2A Interactions with Caspase 9 Protein and the Interfering Peptide C9h. Pharmaceutics, 2022, 14(10), 2055. (Q1)
  2. **Liu R, Zhang W, Gou P, Berthelet J, Nian Q, Chevreux G, Legros V, Moroy G, Bui L-C, Wang L, Dupret J-M, Rodrigues Lima, F. Cisplatin causes covalent inhibition of protein-tyrosine phosphatase 1B (PTP1B) through reaction with its active site cysteine: Molecular, cellular and in vivo mice studies. Biomedicine & Pharmacotherapy, 2022, 153, 113372. (Q1)


  1. **Ghoula M, Janel N, Camproux AC, Moroy G. Exploring the Structural Rearrangements of the Human Insulin-Degrading Enzyme through Molecular Dynamics Simulations. Int J Mol Sci. 2022 Feb 3;23(3):1746. (Q1)


  1. El Fessikh M, Elkarhat Z, Flatters D, Camproux AC, Belghiti H, Guerinech H, Bakri Y, Dakka N, El Baghdadi J. Association study of leptin receptor polymorphisms in women with obesity and their impact on protein domains: a case-control study and in silico analyses. Journal of Biomolecular Structure and Dynamics, 2022, 1-13. (Q2)


  1. Nguyen PH, Tuffery P, Derreumaux P. Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations. Methods Mol Biol. 2022;2405:95-113. (Q4)


  1. Binette V, Mousseau N, Tuffery P. A Generalized Attraction-Repulsion Potential and Revisited Fragment Library Improves PEP-FOLD Peptide Structure Prediction. J Chem Theory Comput. 2022 Apr 12;18(4):2720-2736. (Q1)



  1. Naceri S, Marc D, Camproux AC, Flatters D. Influenza A Virus NS1 protein structural flexibility analysis according to its structural polymorphism using computational approaches. Int J Mol Sci. 2022, 23, 1805. (Q1)


  1. Badel A, Breuil L, Laville P, Regad L. Exploration of the Structural Asymmetry Induced by the Intrinsic Flexibility of HIV-2 Protease. Symmetry. 2022, 14, 362. (Q2)


  1. Bertato L, Taboureau O, Chirico N, Papa E. Classification-based QSARs for predicting dietary biomagnification in fish. SAR QSAR environ Res., 2022, 33 (4), 259-271. (Q3)


  1. Guillochon E, Fraering J, Joste V, Kamaliddin C, Vianou B, Houzé L, Baudrin LG, Faucher JF, Aubouy A, Houzé S, Cot M, Argy N, Taboureau O, Bertin GI; NeuroCM group. Transcriptome analysis of Plasmodium falciparum isolates from Benin reveals specific gene expression associated with cerebral malaria. J Infect Dis., 2022, 7, jiac086. (Q1)


  1. 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 O, 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 characterize trends in shared mode of action. Toxicol in Vitro. 2022, 79, 105269. (Q2)


  1. Röder K, Barker AM, Whitehouse A, Pasquali S. Investigating the structural changes due to adenosine methylation of the Kaposi’s sarcoma-associated herpes virus ORF50 transcript. PLOS Computational Biology, PLoS Comput Biol. 2022 May 26;18(5):e1010150. (Q1)


  1. Audouze K, Taboureau O. Emerging bioinformatics methods and resources in Drug toxicology. Methods Mol Biol. 2022, 2425, 133-146. (Q4)


  1. Röder K, Stinermann G, Faccioli P, Pasquali S. Computer-aided comprehensive explorations of RNA structural polymorphism through complementary simulation methods, QRB Discovery, 2022, 3, e21 (Q1)


  1. ** de Thonel A, Ahlskog JK, Daupin K, Dubreuil V, Berthelet J, Chaput C, Pires G, Leonetti C, Abane R, Barris LC, Leray I, Aalto AL, Naceri S, Cordonnier M, Benasolo C, Sanial M, Duchateau A, Vihervaara A, Puustinen MC, Miozzo F, Fergelot P, Lebigot É, Verloes A, Gressens P, Lacombe D, Gobbo J, Garrido C, Westerheide SD, David L, Petitjean M, Taboureau O, Rodrigues-Lima F, Passemard S, Sabéran-Djoneidi D, Nguyen L, Lancaster M, Sistonen L, Mezger V. CBP-HSF2 structural and functional interplay in Rubinstein-Taybi neurodevelopmental disorder. Nat. Commun. 2022, 13, 7002. (Q1)


  1. Achebouche R, Tromelin A, Audouze K, Taboureau O.Application of artificial intelligence to decode the relationships between smell olfactory receptors and small molecules. Sci Rep. 2022, 12, 18817. (Q1)




  1. Savier E, Tuffery P, Bruzzoni-Giovanelli H and Rebollo A. Tumor targeting as new therapeutic approach. Cell penetrating peptides. Methods and protocols, Third Edition. Methods in Molecular Biology. 2021. (Q4)


  1. Savier E, Simon-Gracia L, Charlotte F, Tuffery P, Scatton O and Rebollo A. Bi-functional therapeutic peptides against hepatocellular carcinoma. Pharmaceutics, 2021. 13. 10.3390/pharmaceutics13101631. (Q1)


  1. Rebollo A, Savier E and Tuffery P. PEPscan approach for the identification of protein-protein interfaces: lessons from experiment. Biomolecules. 2021. 11, 772-780. (Q2)


  1. Murail S*, de Vries SJ, Rey J, Moroy G and Tufféry P. SeamDock: An Interactive and Collaborative Online Docking Resource to Assist Small Compound Molecular Docking. Front. Mol. Biosci. (2021). 8:716466. doi: 10.3389/fmolb.2021.716466. (Q1)


  1. 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 a membrane-embedded artificial water channel nanoconstructs. J. Chem. Phys. (2021). 154, 184102. (Q1)


  1. Quignot C, Postic G, Bret H, Rey J, Granger P, Murail S, Chacón P, Andreani J*, Tuffery 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 Research. (2021). 49(W1), W277-W284. (Q1)


  1. **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. (Q1)


  1. Postic G, Andreani J, Marcoux J, Reys V, Guerois R, Rey J, Mouton-Barbosa E, Vandenbrouck Y, Cianferani S, Burlet-Schiltz O, Labesse G, Tuffery P. Proteo3Dnet: a web server for the integration of structural information with interactomics data. Nucleic Acids Res. 2021 Jul 2;49(W1):W567-W572. (Q1)


  1. Laville P, Petitjean M, Regad L. Structural impacts of drug-resistance mutations appearing in HIV-2 protease. Molecules, 2021 Jan ; 26 :611. (Q2)


  1. 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, 9, 763962. (Q1)


  1. 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. 13, 91. (Q1)


  1. Rasmussen HB, Jurgens 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. 23, 13071369. (Q2)


  1. 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, 16, e0252486. (Q2)


  1. 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 & Metabolism. 2021, 47 (5), 101212. (Q1)


  1. Petitjean M. Chirality in Geometric Algebra. Mathematics, MDPI, 2021;9(13):1521. (Q2)


  1. Petitjean M. Global Symmetries, Local Symmetries and Groupoids. Symmetry, MDPI, 2021;13(10):1905. (Q2)


  1. Petitjean M. Symmetry, Antisymmetry, and Chirality: Use and Misuse of Terminology. Symmetry, MDPI, 2021;13(4);603. (Q2)



  1. 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; 21: 46. (Q4)


  1. 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; 38:5014-5026. (Q1)


  1. ** 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, 54, 2360-2369. (Q1)
  2. Abi Hussein H, Geneix C, Cauvin C, Marc D, Flatters D, Camproux AC. Molecular dynamics simulations of influenza A NS1 reveal a remarkably stable RNA-binding domain harboring promisin druggable pockets. Viruses. 2020, 12, 537. (Q2)


  1. ** Ghoula M, Le Marec A, Magnan C, Le Stunff H, Taboureau O. Identification of the interactions interference between the PH and START domain of CERT by limonoid anf HPA inhibitors. Front Mol Biosci. 2020,7,603983. (Q2)


  1. Rasmussen HB, Hansen PR, Taboureau O, Thomsen R, Jürgens G. Pulmonary administration of remdesivir in the treatment of COVID-19. AAPS J. 2020, 22, 121. (Q2)


  1. **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, 58, 102895. (Q1)


  1. 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, 405, 115210. (Q2)


  1. Dafniet B, Cerisier N, Audouze K, Taboureau O. Drug-target-ADR and possible implications of structural variants in adverse events. Mol Inform. 2020, 39, e2000116. (Q2)


  1. 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, 128, 27002. doi: 10.1289/EHP5580. Epub 2020 Feb 7. PMID: 32074470; PMCID: PMC7064318. (Q1)


  1. Elzaiat M, Flatters D, Sierra-Diaz 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. (Q1)


  1. Petitjean M. Chirality in metric spaces. In memoriam Michel Deza. Optimization Letters, Springer Verlag, 2020;14(2):329-338. (Q1)


  1. Petitjean M. Chirality of Dirac Spinors Revisited. Symmetry, MDPI, 2020;12(4):616. (Q3)


  1. Petitjean M. Comment on « Bad Language »: Resolving some Ambiguities about Chirality. Angew Chem Int Ed Engl. 2020 May 11;59(20):7650-7651. (Q1)


  1. Petitjean M. Molecular chirality in classical spacetime: solving the controversy about the spinning cone model of rotating molecules. Chemistry A European Journal. 2020 Aug 21;26(47):10648-10652. (Q1)


  1. Dong CZ, Tuffery P, Parizot C, Dorgham K, Zini JM, Bruzzoni-Giovanelli H and Rebollo A. Identification of PP1/LRRK2 binding sites and design of interfering peptides with potential clinical application. PlosOne. 2020. (Q1)


  1. Glashagen G, de Vries S, Uciechowska U, Samsonov S, Murail S, Tuffery P, Zacharias M. Coarse-grained and atomic resolution biomolecular docking with the ATTRACT approach. Proteins (2020). 1-11 (Q1)
  2. ** Postic G, Janel N, Tuffery P, Moroy G. An information gain-based approach for evaluating protein structure models. Comput Struct Biotechnol J. 2020;18:2228-2236. (Q1)


  1. ** 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® Dietary Supplement: Role of Green Tea Catechins. Int J Mol Sci. 2020 Feb 19;21(4):1404. (Q1)


  1. 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. (Q1)


  1. Tuffery P, de Vries S. The search of sequence variants using a constrained protein evolution simulation approach. Computational and Structural Biotechnology Journal. 2020 Jun 17;18:1790-1799. (Q1)


  1. 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. (Q1)


  1. Postic G, Marcoux J, Reys V, Andreani J, Vandenbrouck Y, Bousquet MP, Mouton-Barbosa E, Cianférani S, Burlet-Schiltz O, Guerois R, Labesse G, Tuffery P. Probing Protein Interaction Networks by Combining MS-Based Proteomics and Structral Data Integration. J Proteome Res. 2020 Jul 2;19(7):2807-2820. (Q1)



  1. 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, 24, 2529. (Q2)


  1. Perrier M, Castain L, Regad L, Todesco E, Landman R, Visseaux B, Yazdanpanah Y, Rodriguez C, Joly V, Calvez V, Marcelin AG, Descamps D, Charpentier C. HIV-1 protease, Gag and gp41 baseline substitutions associated with virological response to a PI-based regimen. J Antimicrob Chemother. 2019 Jun; 74:1679-1692. (Q1)


  1. Petitjean M. About Chirality in Minkowski Spacetime. Symmetry, MDPI, 2019;11(10):1320. (Q3)


  1. 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):662. (Q2)


  1. 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. 2019,37, 4658-4670. (Q1)
  2. Heddar A, Dessen P, Flatters D, Mishrahi M. Novel STAG3 mutations in a Caucasian family with primary ovarian insufficiency. Mol Genet Genomics. 2019 Dec;294(6):1527-1534. (Q2)


  1. Perrier A, Eluard M, Petitjean M, Vanet A. In Silico Design of New Inhibitors Against Hemagglutinin of Influenza. J Phys Chem B. 2019,123, 582-592. (Q3)


  1. 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. 2019,20, 987. (Q1)


  1. 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, 24, 2747. (Q2)


  1. Aguayo-Orozco A, Audouze K, Siggaard T, Barouki R, Brunak S, Taboureau O. sAOP : Linking chemical stressors to adverse outcome pathway network. Bioinformatics. 2019, 35, 5391-5392. (Q1)


  1. Zaffagnini M, Marchand C, Malferrari M, Murail S, Bonacchi S, Genovese S, Montalti M, Venturoli G, Falini G, Baaden M, Lemaire S, Fermani S, Trost P. Glutathionylation primes soluble glyceraldehyde-3-phosphate dehydrogenase for late collapse into insoluble aggregates. Proc. Natl. Acad. Sci. USA. 2019. 116 (51) 26057-26065. (Q1)


  1. Karami Y, Rey J, Postic G, Murail S, Tuffery P, de Vries SJ. DaReUS-Loop: a web server to model loops in homology models. Nucleic Acids Res. 2019. 47, W423-W428. (Q1)


  1. Rey J, Rasolohery I, Tuffery P, Guyon F, Moroy G. PatchSearch: a web server for off-target protein identification. Nucleic Acids Res. 2019 Jul 2;47(W1):W365-W372. (Q1)


  1. 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):987. (Q1)


  1. 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):4648. (Q2)


  1. Stratmann D, Pathmanathan JS, Postic G, Rey J, Chomilier J. TEF 2.0: a graph-based method for decomposing protein structures into closed loops. J Biomol Struct Dyn. 2019 Oct;37(16):4140-4150. (Q2)


2018 (articles published before the team joined BFA)

  1. 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; 8:710. (Q1)


  1. 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;13: e0198854. (Q2)


  1. 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 Nov; 10:644. (Q2)


  1. 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 8:5789. (Q1)


  1. 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, 92, 3517-3533. (Q1)


  1. 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, 9, 396. (Q2)


  1. Kaddurah-Daouk R, Hankemeier T, Scholl EH, Baillie R, Harms A, Stage C, Dalhoff KP, Jűrgens 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, 7, 525-533. (Q1)


  1. 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, 354, 56-63. (Q2)


  1. 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), 209, 125-148. (Q1)


  1. Kocsis I, Sorci M, Vanselous H, Murail S, Sanders S, Licsandru E, Legrand YM, van der Lee A, Baaden M, Petersen P, Belfort G, Barboiu M. Oriented chiral water wires in artificial transmembrane channels. 2018. Science Advances 4: eaao5603. (Q1)


  1. 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. 2018. Bioorg Chem. Dec;81:222-233. doi: 10.1016/j.bioorg.2018.08.016. Epub 2018 Aug 10. PMID: 30153587. (Q3)


  1. 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. 2018. Psychopharmacology (Berl). Jun;235(6):1835-1844. (Q1)


  1. Bourguet E, Ozdarska K, Moroy G, Jeanblanc J, Naassila M. Class I HDAC Inhibitors: Potential New Epigenetic Therapeutics for Alcohol Use Disorder (AUD). 2018. J Med Chem. Mar 8;61(5):1745-1766. (Q1)


  1. Lagarde N, Rey J, Gyulkhandanyan A, Tuffery 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. (Q1)
  2. Quignot C, Rey J, Yu J, Tuffery 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. (Q1)
  3. 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. (Q1)


2017 (articles published before the team joined BFA)

  1. 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. (Q2)


  1. 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 Mar57, 499-516. (Q1)


  1. 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; 24:1134-1137. (Q4)


  1. 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. (Q2)


  1. Borrel A, Camproux AC, Xhaard H. Characterization of Ionizable Groups’ Environments in Proteins and Protein-Ligand Complexes through a Statistical Analysis of the Protein Data Bank. ACS Omega. 2017, 2, 7359-7374. (Q2)


  1. ** 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, 7, e1154. (Q1)


  1. 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; 12:e0182972. (Q2)


  1. 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. (Q2)


  1. 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, 87, 539-544. (Q2)


  1. Petitjean M. A Fast Algorithm to Compute Conical Pockets in Proteins. Application to the Structural Characterization of γ-Carbonic Anhydrases. Mol Inform. 2017,36. (Q2)


  1. Boezio B, Audouze K, Ducrot P, Taboureau O. Network-based approaches in pharmacology. Mol Inform., 2017, 36. (Q2)


  1. Qvortrup K, Jensen JF, Sorensen 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 PPARy partial agonists. PLoS One, 2017, 12, e0162642. (Q2)


  1. Taboureau O, Audouze K. Human environmental disease network: A computational model to assess toxicology of contaminants. ALTEX 2017, 34, 289-300. (Q1)


  1. Bogdan L, Murail S, Poitevin F, Cromer B, Baaden M, Delarue M, Allen T. String method solution of the gating pathways for a pentameric ligand-gated ion channel. Proc. Natl. Acad. Sci. USA. 2017. 114(21):E4158-67. F1000 recommendation. (Q1)


  1. 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. (Q1)


  1. 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. (Q4)


  1. 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 11, 1-21 . (Q1)


  1. 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. (Q3)


  1. 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. (Q1)


  1. Noll C, Kandiah J, Moroy G, Gu Y, Dairou J, Janel N. Catechins as a Potential Dietary Supplementation in Prevention of Comorbidities Linked with Down Syndrome. Nutrients. 2022 May 12;14(10):2039. (Q1)



  1. Aguayo-Orozco A, Taboureau O, Brunak S. The use of systems biology in chemical risk assessment. COTOX. 2019.
  2. Moroy G, Tuffery P. Peptide-Based Strategies Against SARS-CoV-2 Attack: An Updated In Silico Perspective. Frontiers in Drug Discovery 2022 2;899477
  3. **Noll C, Kandiah J, Moroy G, Gu Y, Dairou J, Janel N. Catechins as a Potential Dietary Supplementation in Prevention of Comorbidities Linked with Down Syndrome. Nutrients. 2022 May 12;14(10):2039. doi: 10.3390/nu14102039.

Reviews published before the team joined BFA:

  1. H. Bruzzoni-Giovanelli, V. Alerza, N. Wolff, C.Z. Dong, P. Tuffery and A. Rebollo. Interfering peptides targeting protein/protein interactions: next generation of drugs? Drug Discovery Today. 2018. 23, 272-287.


  1. 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, 22, 404-415.
  2. 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, 91, 3477-3505.