• 2025
  Mareuil F, Torchet R, Ruano LC, Mallet V, Nilges M, Bouvier G, Sperandio O, InDeepNet: a web platform for predicting functional binding sites in proteins using InDeep., Nucleic Acids Res 2025 May; (): .
• 2024
  Alexandra Moine-Franel, Fabien Mareuil, Michael Nilges, Constantin Bogdan Ciambur, Olivier Sperandio, A comprehensive dataset of protein-protein interactions and ligand binding pockets for advancing drug discovery, Scientific Data , 2024, 11 (1), pp.402. ⟨10.1038/s41597-024-03233-z⟩.
• 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.
• 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 2022 Feb; 38(5): 1261-1268.
• 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
  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 Apr; 37(1): 89-96.
• 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;.
• 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.
• 2016
  Kuenemann MA, Labbé CM, Cerdan AH, Sperandio O, Imbalance in chemical space: How to facilitate the identification of protein-protein interaction inhibitors, Sci Rep 2016 Apr;6:23815.
• 2015
  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.
• 2015
  Zarzycka B, Kuenemann MA, Miteva MA, Nicolaes GA, Vriend G, Sperandio O, Stabilization of protein-protein interaction complexes through small molecules, Drug Discov. Today 2016 Jan;21(1):48-57.
• 2015
  Labbé CM, Kuenemann MA, Zarzycka B, Vriend G, Nicolaes GA, Lagorce D, Miteva MA, Villoutreix BO, Sperandio O, iPPI-DB: an online database of modulators of protein-protein interactions, Nucleic Acids Res. 2016 Jan;44(D1):D542-7.
• 2015
  Lagorce D, Sperandio O, Baell JB, Miteva MA, Villoutreix BO, FAF-Drugs3: a web server for compound property calculation and chemical library design, Nucleic Acids Res. 2015 Jul;43(W1):W200-7.
• 2015
  Labbé CM, Rey J, Lagorce D, Vavruša 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;43(W1):W448-54.
• 2015
  Sperandio O, Villoutreix BO, Morelli X, Roche P, [Chemical libraries dedicated to protein-protein interactions], Med Sci (Paris) 2015 Mar;31(3):312-9.
• 2015
  Kuenemann MA, Sperandio O, Labbé CM, Lagorce D, Miteva MA, Villoutreix BO, In silico design of low molecular weight protein-protein interaction inhibitors: Overall concept and recent advances, Prog. Biophys. Mol. Biol. 2015 Oct;119(1):20-32.
• 2014
  Kuenemann MA, Bourbon LM, Labbé CM, Villoutreix BO, Sperandio O, Which three-dimensional characteristics make efficient inhibitors of protein-protein interactions?, J Chem Inf Model 2014 Nov;54(11):3067-79.
• 2014
  Villoutreix BO, Kuenemann MA, Poyet JL, Bruzzoni-Giovanelli H, Labbé C, Lagorce D, Sperandio O, Miteva MA, Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology, Mol Inform 2014 Jun;33(6-7):414-437.
• 2014
  Villemagne B, Flipo M, Blondiaux N, Crauste C, Malaquin S, Leroux F, Piveteau C, Villeret V, Brodin P, Villoutreix BO, Sperandio O, Soror SH, Wohlkönig A, Wintjens R, Deprez B, Baulard AR, Willand N, Ligand efficiency driven design of new inhibitors of Mycobacterium tuberculosis transcriptional repressor EthR using fragment growing, merging, and linking approaches, J. Med. Chem. 2014 Jun;57(11):4876-88.
• 2014
  Mathieu AL, Sperandio O, Pottiez V, Balzarin S, Herlédan A, Elkaïm JO, Fogeron ML, Piveteau C, Dassonneville S, Deprez B, Villoutreix BO, Bonnefoy N, Leroux F, Identification of Small Inhibitory Molecules Targeting the Bfl-1 Anti-Apoptotic Protein That Alleviates Resistance to ABT-737, J Biomol Screen 2014 Aug;19(7):1035-46.
• 2014
  Charton J, Gauriot M, Guo Q, Hennuyer N, Marechal X, Dumont J, Hamdane M, Pottiez V, Landry V, Sperandio O, Flipo M, Buee L, Staels B, Leroux F, Tang WJ, Deprez B, Deprez-Poulain R, Imidazole-derived 2-[N-carbamoylmethyl-alkylamino]acetic acids, substrate-dependent modulators of insulin-degrading enzyme in amyloid-β hydrolysis, Eur J Med Chem 2014 May;79:184-93.
• 2014
  Sperandio O, Wildhagen KC, Schrijver R, Wielders S, Villoutreix BO, Nicolaes GA, Identification of novel small molecule inhibitors of activated protein C, Thromb. Res. 2014 Jun;133(6):1105-14.
• 2013
  Nicolaes GA, Kulharia M, Voorberg J, Kaijen PH, Wroblewska A, Wielders S, Schrijver R, Sperandio O, Villoutreix BO, Rational design of small molecules targeting the C2 domain of coagulation factor VIII, Blood 2014 Jan;123(1):113-20.
• 2013
  Maingot L, Elbakali J, Dumont J, Bosc D, Cousaert N, Urban A, Deglane G, Villoutreix B, Nagase H, Sperandio O, Leroux F, Deprez B, Deprez-Poulain R, Aggrecanase-2 inhibitors based on the acylthiosemicarbazide zinc-binding group, Eur J Med Chem 2013 Nov;69:244-61.
• 2013
  Villoutreix BO, Lagorce D, Labbé CM, Sperandio O, Miteva MA, One hundred thousand mouse clicks down the road: selected online resources supporting drug discovery collected over a decade, Drug Discov. Today 2013 Nov;18(21-22):1081-9.
• 2013
  Pérot S, Regad L, Reynès C, Spérandio O, Miteva MA, Villoutreix BO, Camproux AC, Insights into an original pocket-ligand pair classification: a promising tool for ligand profile prediction, PLoS ONE 2013;8(6):e63730.
• 2013
  Isvoran A, Craciun D, Martiny V, Sperandio O, Miteva MA, Computational analysis of protein-protein interfaces involving an alpha helix: insights for terphenyl-like molecules binding, BMC Pharmacol Toxicol 2013 Jun;14:31.
• 2013
  Labbé CM, Laconde G, Kuenemann MA, Villoutreix BO, Sperandio O, iPPI-DB: a manually curated and interactive database of small non-peptide inhibitors of protein-protein interactions, Drug Discov. Today 2013 Oct;18(19-20):958-68.
• 2013
  Maréchal X, Genin E, Qin L, Sperandio O, Montes M, Basse N, Richy N, Miteva MA, Reboud-Ravaux M, Vidal J, Villoutreix BO, 1,2,4-Oxadiazoles identified by virtual screening and their non-covalent inhibition of the human 20S proteasome, Curr. Med. Chem. 2013;20(18):2351-62.
• 2012
  Attoub S, Sperandio O, Raza H, Arafat K, Al-Salam S, Al Sultan MA, Al Safi M, Takahashi T, Adem A, Thymoquinone as an anticancer agent: evidence from inhibition of cancer cells viability and invasion in vitro and tumor growth in vivo, Fundam Clin Pharmacol 2013 Oct;27(5):557-69.
• 2012
  Sperandio O, Editorial: Toward the design of drugs on protein-protein interactions, Curr. Pharm. Des. 2012;18(30):4585.
• 2012
  Villoutreix BO, Labbé CM, Lagorce D, Laconde G, Sperandio O, A leap into the chemical space of protein-protein interaction inhibitors, Curr. Pharm. Des. 2012;18(30):4648-67.
• 2011
  Lagorce D, Maupetit J, Baell J, Sperandio O, Tufféry P, Miteva MA, Galons H, Villoutreix BO, The FAF-Drugs2 server: a multistep engine to prepare electronic chemical compound collections, Bioinformatics 2011 Jul;27(14):2018-20.
• 2010
  Maingot L, Leroux F, Landry V, Dumont J, Nagase H, Villoutreix B, Sperandio O, Deprez-Poulain R, Deprez B, New non-hydroxamic ADAMTS-5 inhibitors based on the 1,2,4-triazole-3-thiol scaffold, Bioorg. Med. Chem. Lett. 2010 Nov;20(21):6213-6.
• 2010
  Hafizi S, Gustafsson A, Oslakovic C, Idevall-Hagren O, Tengholm A, Sperandio O, Villoutreix BO, Dahlbäck B, Tensin2 reduces intracellular phosphatidylinositol 3,4,5-trisphosphate levels at the plasma membrane, Biochem. Biophys. Res. Commun. 2010 Aug;399(3):396-401.
• 2010
  Pérot S, Sperandio O, Miteva MA, Camproux AC, Villoutreix BO, Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery, Drug Discov. Today 2010 Aug;15(15-16):656-67.
• 2010
  Sperandio O, Mouawad L, Pinto E, Villoutreix BO, Perahia D, Miteva MA, How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis, Eur. Biophys. J. 2010 Aug;39(9):1365-72.
• 2010
  Reynès C, Host H, Camproux AC, Laconde G, Leroux F, Mazars A, Deprez B, Fahraeus R, Villoutreix BO, Sperandio O, Designing focused chemical libraries enriched in protein-protein interaction inhibitors using machine-learning methods, PLoS Comput. Biol. 2010 Mar;6(3):e1000695.
• 2010
  Villoutreix BO, Sperandio O, In silico studies of blood coagulation proteins: from mosaic proteases to nonenzymatic cofactor inhibitors, Curr. Opin. Struct. Biol. 2010 Apr;20(2):168-79.
• 2009
  Sperandio O, Reynès CH, Camproux AC, Villoutreix BO, Rationalizing the chemical space of protein-protein interaction inhibitors, Drug Discov. Today 2010 Mar;15(5-6):220-9.
• 2009
  Quintus F, Sperandio O, Grynberg J, Petitjean M, Tuffery P, Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity, BMC Bioinformatics 2009;10:245.
• 2009
  Sperandio O, Petitjean M, Tuffery P, wwLigCSRre: a 3D ligand-based server for hit identification and optimization, Nucleic Acids Res. 2009 Jul;37(Web Server issue):W504-9.
• 2008
  Sperandio O, Souaille M, Delfaud F, Miteva MA, Villoutreix BO, MED-3DMC: a new tool to generate 3D conformation ensembles of small molecules with a Monte Carlo sampling of the conformational space, Eur J Med Chem 2009 Apr;44(4):1405-9.
• 2008
  Lagorce D, Sperandio O, Galons H, Miteva MA, Villoutreix BO, FAF-Drugs2: free ADME/tox filtering tool to assist drug discovery and chemical biology projects, BMC Bioinformatics 2008;9:396.
• 2008
  Villoutreix BO, Bastard K, Sperandio O, Fahraeus R, Poyet JL, Calvo F, Déprez B, Miteva MA, In silico-in vitro screening of protein-protein interactions: towards the next generation of therapeutics, Curr Pharm Biotechnol 2008 Apr;9(2):103-22.
• 2008
  Sperandio O, Miteva MA, Segers K, Nicolaes GA, Villoutreix BO, Screening Outside the Catalytic Site: Inhibition of Macromolecular Inter-actions Through Structure-Based Virtual Ligand Screening Experiments, Open Biochem J 2008;2:29-37.
• 2007
  Villoutreix BO, Renault N, Lagorce D, Sperandio O, Montes M, Miteva MA, Free resources to assist structure-based virtual ligand screening experiments, Curr. Protein Pept. Sci. 2007 Aug;8(4):381-411.
• 2007
  Segers K, Sperandio O, Sack M, Fischer R, Miteva MA, Rosing J, Nicolaes GA, Villoutreix BO, Design of protein membrane interaction inhibitors by virtual ligand screening, proof of concept with the C2 domain of factor V, Proc. Natl. Acad. Sci. U.S.A. 2007 Jul;104(31):12697-702.
• 2007
  Sperandio O, Andrieu O, Miteva MA, Vo MQ, Souaille M, Delfaud F, Villoutreix BO, MED-SuMoLig: a new ligand-based screening tool for efficient scaffold hopping, J Chem Inf Model 2007 May-Jun;47(3):1097-110.
• 2006
  Sperandio O, Miteva MA, Delfaud F, Villoutreix BO, Receptor-based computational screening of compound databases: the main docking-scoring engines, Curr. Protein Pept. Sci. 2006 Oct;7(5):369-93.
• 2002
  Sperandio O, Fan BT, Zakrzewska K, Jia ZJ, Zheng RL, Panaye A, Doucet JP, El Fassi N, Theoretical study of fast repair of DNA damage by cistanoside C and analogs: mechanism and docking, SAR QSAR Environ Res 2002 Mar;13(2):243-60.