Exploration of the effect of sequence variations located inside the binding pocket of HIV-1 and HIV-2 proteases.
Triki D , Billot T , Visseaux B, Descamps D, Flatters D , Camproux AC , Regad L .
scientific reports. 10 Avril 2018; 8(1):5789. doi: 10.1038 s41598-018-24124-5..

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

Breast cancer targeting through inhibition of the endoplasmic reticulum-based apoptosis regulator Nrh/BCL2L10
Nougarede A, Popgeorgiev N, Kassem L, Omarjee S, Borel S, Mikaelian I, Lopez J, Gadet R, Marcillat O, Treilleux I,Villoutreix BO, Rimokh R, Gillet G
Cancer Res.. 19 Décembre 2017; in press.

Expression and Functional Characterization of Two Natural Heparin-binding Site Variants of Antithrombin
Dinarvand P, Yang L, Villoutreix BO,Rezaie AR
Journal of Thrombosis and Haemostasis. 2017; in press.

Identification of insulin-sensitizing molecules acting by disrupting the interaction between the Insulin Receptor and Grb14
Gondoin A, Hampe C, Eudes R, Fayolle C, Pierre-Eugene C, Miteva M, Villoutreix BO, Charnay-Pouget F, Aitken DJ, Issad T, Burnol AF
scientific reports. 2017; in press.

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

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

Chirality in metric spaces. In memoriam Michel Deza.
Michel Petitjean
Optim. Letters. 2017; in press.

Class I HDAC Inhibitors: Potential New Epigenetic Therapeutics for Alcohol Use Disorder (AUD).
Bourguet E, Ozdarska K, Moroy G, Jeanblanc J, Naassila M.
J. Med. Chem.. 22 Août 2017; in press.

FAF-Drugs4: Free ADME-Tox Filtering computations for chemical biology and early stages drug discovery
David Lagorce, Lina Bouslama, Jerome Becot, Maria A. Miteva, Bruno O. Villoutreix
Bioinformatics. 2017; in press.

In silico model of the human ClC-Kb chloride channel: pore mapping, biostructural pathology and drug screening.
Louet M, Bitam S, Bakouh N, Bignon Y, Planelles G, Lagorce D, Miteva M, Eladari D, Teulon J, Villoutreix BO.
scientific reports. 07 Juillet 2017; in press.

Statistical profiling of one promiscuous protein binding site: illustrated by urokinase catalytic domain
Natacha Cerisier , Leslie Regad , Dhoha Triki , Michel Petitjean , Delphine Flatters , Anne-Claude Camproux
Molecular Informatics. 29 Juin 2017; 36(10),170040..

The cytochrome P450 3A4 has three major conformations: new clues to drug recognition by this promiscuous enzyme.
Benkaidali L., André F., Moroy G. , Tangour B., Maurel F., Petitjean M.
Molecular Informatics. 2017; 36(10),170044..

Human environmental disease network: a computational model to assess toxicology of contaminants
Taboureau O, Audouze K.
ALTEX. 2017; 34(2):289-300.

A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against
Catharina L, Ribeiro Lima C, Franca A, Ramos Guimarães AC, Alves-Ferreira M, Tuffery P, Derreumaux P, Carels N
Bioinformatics and Biology Insights. 09 Juin 2017; 2017:11 1177932217712471 .

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

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

AMMOS2: a web server for protein ligand-water complexes refinement via molecular mechanics.
Labbé C, Pencheva T, Jereva D, Desvillechabrol D, Becot J, Villoutreix BO, Pajeva I, Miteva MA
Nucleic Acids Research. 09 Mai 2017; in press.

The pepATTRACT web server for blind, large-scale peptide-protein docking.
de Vries SJ, Rey J, Schindler CEM, Zacharias M, Tuffery P.
Nucleic Acids Research. 29 Avril 2017; in press.

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

Peptide Suboptimal Conformation Sampling for the Prediction of Protein-Peptide Interactions.
Lamiable A, Thévenet P, Eustache S, Saladin A, Moroy G, Tuffery P.
Methods Mol Biol. 01 Avril 2017; 2017:1561:21-34..

Computational analysis of calculated physicochemical and ADMET properties of protein-protein interaction inhibitors.
Lagorce D, Douguet D, Miteva MA, Villoutreix BO.
scientific reports. 28 Mars 2017; in press.

Pan-Assay INterference CompoundS that may not be too painful for chemical biology projects.
Lagorce D, Oliveira N, Miteva MA, Villoutreix BO
Drug Discovery Today. 28 Mars 2017; in press.

Gly74Ser mutation in protein C causes thrombosis due to a defect in protein S-dependent anticoagulant function.
Chen, C, Yang L, Villoutreix BO, Wang X, Ding Q, Rezaie AR.
Thromb Haemost.. 28 Mars 2017; in press.

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

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

Structural isosteres of phosphate groups in the Protein Data Bank
Zhang Y, Borrel A , Ghemtio L, Regad L , Boije Af Gennäs G, Camproux AC , Yli-Kauhaluoma J, Xhaard HG.
J. Chem. Inf. Model.. 2017; 57(3):499-516..

Global vision of druggability issues, applications and perspectives
Hiba Abi Hussein , Colette Geneix , Michel Petitjean , Alexandre Borrel , Delphine Flatters , Anne-Claude Camproux
Drug Discovery Today. 2017; 22(2):404-415.

Blockade of the malignant phenotype by β-subunit selective noncovalent inhibition of immuno- and constitutive proteasomes.
Villoutreix B.O, Khatib A.M, Cheng Y, Miteva M.A, Maréchal, X, Vidal J, Reboud-Ravau M.
Oncotarget. 02 Janvier 2017; DOI: 10.18632.

Insights into the interaction of high potency inhibitor IRC-083864 with phosphatase CDC25.
Sarkis M, Miteva M.A, Dasso Lang M.C, Jaouen M, Sari M.A, Galcéra M.O, Ethève-Quelquejeu M, Garbay C,Bertho G, Braud E
Proteins. 05 Décembre 2016; doi: 10.1002.

Design, Synthesis, and Use of MMP-2 Inhibitor-Conjugated Quantum Dots in Functional Biochemical Assays.
Bourguet E, Brazhnik K, Sukhanova A, Moroy G, Brassart-Pasco S, Martin AP, Villena I, Bellon G, Sapi J, Nabiev I.
Bioconjug Chem.. 18 Octobre 2016; 27(4):1067-81..

In silico structural characterization of protein targets for drug development against Trypanosoma cruzi
Ribeiro Lima C , Carels N, Ramos Guimaraes A-C, Tufféry P, Derreumaux P.
J. Mol. Model.. 17 Octobre 2016; in press.

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

Acute genetic ablation of pendrin lowers blood pressure in mice.
Trepiccione F, Soukaseum C, Baudrie V, Kumai Y, Teulon J, Villoutreix BO, Corniere N, Wangemann P, Griffith AJ, Choi BY, Hadchouel J, Chambrey R, Eladari D.
Nephrology Dialysis Transplantation. 06 Octobre 2016; in press.

Effects of common pesticides on prostglandin D2 (PGD2) inhibition in SC5 mouse sertoli cells, evidence of binding at the COX-2 active site, and implications for endocrine disruption.
Kugathas S, Audouze K , Ermler S, Orton F, Rosivatz E, Scholze M, Kortenkamp A.
Environ Health Perspect.. 2016; 124(4):452-9..

Pharmacogenomics of the cytochrome P450 2C family: impacts of amino acid variations on drug metabolism.
Isvoran A, Louet M, Vladoiu DL, Craciun D, Loriot MA, Villoutreix BO, Miteva MA
Drug Discovery Today. 27 Septembre 2016; S1359-6446(16)30339-7.

Pharmacophore Model To Discover OX1 and OX2 Orexin Receptor Ligands
Ainoleena Turku, Alexandre Borrel, Teppo O. Leino, Lasse Karhu, Jyrki P. Kukkonen, and Henri Xhaard
J. Med. Chem.. 22 Septembre 2016; 59(18):8263-75.

A Cell-Penetrating Peptide Targeting AAC-11 Specifically Induces Cancer Cells Death.
Jagot-Lacoussiere L, Kotula E, Villoutreix BO, Bruzzoni-Giovanelli H, Poyet JL.
Cancer Res.. 15 Septembre 2016; 76(18):5479-90..

In silico systems pharmacology to assess drugs therapeutic and toxic effects.
Orozco AA, Audouze K , Brunak S, Taboureau O.
Current Pharmaceutical Design. 06 Septembre 2016; 22(46):6895-6902. .

Discoidin Domains as Emerging Therapeutic Targets.
Villoutreix BO, Miteva MA.
Trends Pharmacol Sci. 01 Août 2016; 37(8):641-59.

Combining bioinformatics, chemoinformatics and experimental approaches to design chemical probes: Applications in the field of blood coagulation.
Villoutreix BO
Ann Pharm Fr. 01 Juillet 2016; 74(4):253-66..

Screening for protein-protein interactions using Förster resonance energy transfer (FRET) and fluorescence lifetime imaging microscopy (FLIM
Margineanu A, Chan JJ, Kelly DJ, Warren SC,Flatters D, Kumar S, Katan M, Dunsby CW, French PM
scientific reports. 24 Juin 2016; 6:28186.

Progress with peptide scanning to study Structure-Activity Relationships: the implications for drug discovery
Eustache S, Leprince J, Tufféry P
Expert Opinion on Drug Discovery. 14 Juin 2016; in press.

A critical assessment of Hidden Markov Model sub-optimal sampling strategies applied to the generation of peptide 3D models.
Lamiable A, Thevenet P, Tuffery P
J. Comput. Chem.. 14 Juin 2016; in press.

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

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

PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex.
Lamiable A, Thévenet P, Rey J, Vavrusa M, Derreumaux P, Tufféry P
Nucleic Acids Research. 29 Avril 2016; in press.

InterEvDock: a docking server to predict the structure of protein-protein interactions using evolutionary information.
Yu J, Vavrusa M, Andreani J, Rey J, Tufféry P, Guerois R.
Nucleic Acids Research. 29 Avril 2016; in press.

In silico characterization of the interaction between LSKL peptide, a LAP-TGF-beta derived peptide, and ADAMTS1.
Laurent MA, Bonnier D, Théret N, Tufféry P, Moroy G
Computational Biology and Chemistry. 21 Avril 2016; 61:155-61.

Binding of phenothiazines into allosteric hydrophobic pocket of human thioredoxin 1.
Philot EA, da Mata Lopes D, de Souza AT, Braz AS, Nantes IL, Rodrigues T, Perahia D, Miteva MA, Scott LP
Eur Biophys J.. 01 Avril 2016; 45(3):279-86.

Effect of cadmium administration in hyperhomocysteinemic mice due to cystathionine beta synthase deficiency.
Ramambason C, Moroy G, Daubigney F, Paul JL, Janel N.
Exp Toxicol Pathol.. 10 Mars 2016; 2016; 68(6):365-70. .

Investigating the impact of missense mutations in hCES1 by in silico structure-based approaches.
Nzabonimpa GS, Rasmussen HB, Brunak S, Taboureau O
Drug Metabol Personal Ther.. 25 Février 2016; in press.

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

Stabilization of protein-protein interaction complexes through small molecules.
Zarzycka B, Kuenemann MA, Miteva MA, Nicolaes GA, Vriend G, Sperandio O.
Drug Discovery Today. 01 Janvier 2016; 21(1):48-57..

iPPI-DB: an online database of modulators of protein-protein interactions.
Labbé CM, Kuenemann MA, Zarzycka B, Vriend G, Nicolaes GA, Lagorce D, Miteva MA, Villoutreix BO, Sperandio O.
Nucleic Acids Research. 01 Janvier 2016; 4;44(D1):D542-7..

Assessment of some pesticides interactions with human cytochrome P450: CYP2C8, CYP2C9 and CYP2C19 by molecular docking approach.
A. Ciorsac, D.Vladoiu, C.Fagnen, M. Louet, MA. Miteva, A.Isvoran
AIP Conference Proceeding Series. 01 Janvier 2016; 1722, 300001.

Computational methods for reproductive and developmental toxicology.
Olivier Taboureau , Karine Audouze , and Søren Brunak
REACH and Environmental Chemicals.. 2015; 3, 23-35..

Exposure to perfluorononanoic acid combined with a low-dose mixture of 14 human-relevant compounds disturbs energy/lipid homeostasis in rats.
Skov K, Kongsbag K, Hadrup N, Frandsen HL, Svingen T, Smedsgaard J, Audouze K , Eklund AC, Vinggaard AM.
Metabolomics. 2015; 11, 1451-1464..

Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis.
G. Moroy, O. Sperandio, S. Rielland, S. Khemka, K. Druart, D. Goyal, D. Perahia, M. A. Miteva
Future Med Chem. 01 Novembre 2015; 7(17):2317-31.

Chemical biology databases : from agregation, curation to représentation.
Audouze K., Taboureau O.
Drug Discovery Today. 2015; 14:25-9.

INDICES Consortium. Individualization of treatments with drugs metabolized by CES1 : combining genetics and metabolomics.
Rasmussen HB, Bjerre D, Linnet K, Jurgens 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, Hugues T, Werge T
Pharmacogenomics. 2015; 16(6):649-65.

Genetic polymorphisms associated with increased risk of developing chronic myelogenous leukemia.
Bruzzoni-Giovanelli H, González J, Sigaux F, Villoutreix BO, Cayuela JM, Guilhot J, Preudhomme C, Guilhot F, Poyet JL and Rousselot P
Oncotarget. 21 Septembre 2015; in press.

Effects of Common Pesticides on Prostaglandin D2 (PGD2) Inhibition in SC5 Mouse Sertoli Cells, Evidence of Binding at the COX2 Active Site, and Implications for Endocrine Disruption.
Kugathas S, Audouze K, Ermler S, Orton F, Rosivatz E, Scholze M, Kortenkamp A.
Environ Health Perspect.. 2015; in press.

Integrated structure- and ligand-based in silico approach to predict inhibition of cytochrome P450 2D6.
Martiny VY, Carbonell P, Chevillard F, Moroy G, Nicot AB, Vayer P, Villoutreix BO, Miteva MA
Bioinformatics. 26 Août 2015; in press.

HHalign-KBest: Exploring sub-optimal alignments for remote homology comparative modeling
Yu J, Picord G, Tuffery P, Guerois R
Bioinformatics. 21 Juillet 2015; in press.

System Biology : a new paradigm for drug discovery
H. Abi Hussein , A. Borrel , L. Regad , D. Flatters , A. Badel , C. Geneix , M. Petitjean , A.-C. Camproux and O. Taboureau
The Practice of Medicinal Chemistry-Fourth Edition . 2015; ISBN : 9780124172050 (Academic Press).

Therapeutic targeting of nuclear gamma-tubulin in RB1-negative tumors.
Lindstrom L, Villoutreix BO, Lehn S, Hellsten R, Nilsson E, Crneta E, Olsson R, Alvarado-Kristensson M.
Molecular Cancer Research. 01 Juillet 2015; 13(7):1073-82.

PockDrug-Server: a new web server for predicting pocket druggability on holo and apo proteins
Hiba Abi Hussein, Alexandre Borrel, Colette Geneix, Michel Petitjean, Leslie Regad, Anne-Claude Camproux
Nucleic Acids Research. 2015; i43(W1):W436-42..

BCSearch: fast structural fragment mining over large collections of protein structures.
Guyon F, Martz F, Vavrusa M, Bécot J, Rey J, Tufféry P.
Nucleic Acids Research. 01 Juillet 2015; 2015 43(W1):W378-82..

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

Analytical algorithms for ligand cone angles calculations. Application to triphenylphosphine palladium complexes.
Petitjean M.
Compt. Rend. Chim.. 05 Juin 2015; 18[6], 678-684.

PockDrug: a model for predicting pocket druggability that overcomes pocket estimation uncertainties
Borrel Alexandre,Regad Leslie, Xhaard Henri, Petitjean Michel, Camproux Anne-Claude
J. Chem. Inf. Model.. 27 Avril 2015; 55(4):882-95.

Theileria parasites secrete a prolyl isomerase which contributes to host leukocyte transformation.
Marsolier J, Perichon M, DeBarry JD, Villoutreix BO, Chluba J, Garrido C, Zhou XZ, Lu KP, Ait-Si-Ali S, Fritsch L, Mhadhbi M, Medjkane S, Weitzman JB.
Nature. 16 Avril 2015; 520(7547):378-82.

Accessing external innovation in drug discovery and development
Tuffery P.
Expert Opinion on Drug Discovery. 10 Avril 2015; in press.

MTiOpenScreen: a web server for structure-based virtual screening.
Labbé C, Rey J, Lagorce D, Vavruša M, Becot J, Sperandio O, Villoutreix B, Tuffery P, Miteva M
Nucleic Acids Research. 03 Avril 2015; 43(W1):W448-54.

FAF-Drugs3: a web-server for compound property calculation and chemical library design.
Lagorce D, Sperandio O, Baell JB, Miteva MA, Villoutreix BO
Nucleic Acids Research. 03 Avril 2015; 43(W1):W200-7.

Prediction of Structural Patterns of Interest from Protein Primary Sequence through Structural Alphabet: Illustration to ATP/GTP Binding Site Prediction
Christelle Reynes, Leslie Regad , Robert Sabatier and Anne-Claude Camproux
Journal of Data Mining in Genomics and Proteomics. 2015; 6:1 .

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

A hot-spot of in-frame duplications activates the oncoprotein AKT1 in juvenile granulosa cell tumors
L. Bessière, A.-L. Todeschini, A. Auguste, S. Sarnacki, D. Flatters, B. Legois, C. Sultan, N. Kalfa, L. Galmiche, R. Veitia
EBioMedicine. 2015; 2(5) : 421- 431.

Computational investigations of hERG channel blockers: New insights and current predictive models.
Villoutreix BO, Taboureau O.
Adv Drug Deliv Rev. 11 Mars 2015; 86:72-82.

In silico design of low molecular weight protein-protein interaction inhibitors: overall concept and recent advances.
Kuenemann MA, Sperandio O, Labbe CM, Lagorce D, Miteva MA, Villoutreix BO
Progress in Biophysics and Molecular Biology. 05 Mars 2015; 119(1):20-32..

Transcriptome profiling of brown adipose tissue during cold exposure reveals extensive regulation of glucose metabolism.
Hao Q, Yadav R, Basse AL, Petersen S, Sonne SB, Rasmussen S, Zhu Q, Lu Z, Wang J, Audouze K, Gupta R, Madsen L, Kristiansen K, Hansen JB.
Am J Physiol Endocrinol Metab.. 01 Mars 2015; 308(5):E380-92.

Les chimiothèques ciblant les interactions protéine-protéine.
Sperandio O, Villoutreix BO, Morelli X, Roche P
Medecine Sciences. 24 Février 2015; Med Sci (Paris) 31, 311-318. .

An exploration of the 3D chemical space has highlighted a specific shape profile for the compounds intended to inhibit protein-protein interactions
Kuenemann M.A., Bourbon L.M., Labbé C.M., Villoutreix B.O., Sperandio O.
BMC Bioinformatics. 13 Février 2015; Volume 16 Suppl 3.

Functional characterization of two novel non-synonymous alterations in CD46 and a Q950H change in factor H found in atypical hemolytic uremic syndrome patients.
Mohlin FC, Nilsson SC, Levart TK, Golubovic E, Rusai K, Muller-Sacherer T, Arbeiter K, Pallinger E, Szarvas N, Csuka D, Szilagyi A, Villoutreix BO, Prohaszka Z, Blom AM
Molecular Immunology. 11 Février 2015; 65(2):367-76.

Tampering with Cell Division by Using Small-Molecule Inhibitors of CDK-CKS Protein Interactions.
Hamdi A, Lesnard A, Suzanne P, Robert T, Miteva MA, Pellerano M, Didier B, Ficko-Blean E, Lobstein A, Hibert M, Rault S, Morris MC, Colas P.
ChemBioChem. 09 Février 2015; 9;16(3):432-9..

The most chiral disphenoid.
Petitjean M.
MATCH Commun. Math. Comput. Chem.. 27 Janvier 2015; 2015, 73[2], 375-384..

DNA Damage-Induced Nuclear Translocation of Apaf-1 is Mediated by Nucleoporin Nup107.
Jagot-Lacoussiere L, Faye A, Villoutreix B, Rain JC, Poyet JL.
Cell Cycle. 27 Janvier 2015; 14(8):1242-51.

Amino acid residues in the laminin G domains of protein S involved in tissue factor pathway inhibitor interaction.
Somajo S, Ahnström J, Fernandez-Recio J, Gierula M, Villoutreix BO, Dahlback B.
Thromb Haemost.. 05 Janvier 2015; 113(5):976-87.

De novo peptide structure prediction: an overview.
Thévenet P, Rey J, Moroy G, Tuffery P.
Methods Mol Biol. 01 Janvier 2015; 1268:1-13..

Tampering with cell division using small-molecule inhibitors of CDK-CKS protein interactions.
A. Hamdi, A. Lesnard, P. Suzanne, T. Robert, M.A. Miteva, M. Pellerano, B. Didier, E. Ficko-Blean, A. Lobstein, M. Hibert, S. Rault, M.C. Morris, P.Colas
ChemBioChem. 01 Décembre 2014; 16(3):432-9.

Biosynthesis of the cyanobacterial neurotoxins anatoxin-a and homoanatoxin-a: From the genome to the metabolites
A. Méjean, R. Mazmouz, G. Paci, K. Moncoq, L. Regad, A. Combes, V. Pichon, O. Ploux
Toxicon. 01 Décembre 2014; Volume 91, 1 December 2014, Pages 166-167.

Rational design of small-molecule stabilizers of spermine synthase dimer by virtual screening and free energy-based approach.
Zhang Z, Martiny V, Lagorce D, Ikeguchi Y, Alexov E, Miteva MA
Plos ONE. 23 Octobre 2014; 9(10):e110884.

BactPepDB: a database of predicted peptides from an exhaustive survey of complete prokaryote genomes
Julien Rey, Patrick Deschavanne , Pierre Tuffery
database. 09 Octobre 2014; bau119. .

Which Three-Dimensional Characteristics Make Efficient Inhibitors of Protein-Protein Interactions?
Kuenemann MA, Bourbon LM, Labbé CM, Villoutreix BO, Sperandio O.
J. Chem. Inf. Model.. 06 Octobre 2014; (Web): October 6, 2014.

Post-docking optimization of protein-ligand interactions involving water molecules.
Jereva D, Pencheva T, Lagorce D, Desvillechabrol D, Pajeva I, Miteva MA
Asian J Physics. 22 Septembre 2014; 23(5)745-756.

The CCA-end of P-tRNA contacts both the human RPL36AL and the A-site bound translation termination factor eRF1 at the peptidyl transferase center of the human 80S ribosome
Codjo Hountondji, Konstantin Bulygin, Jean-Bernard Créchet, Anne Woisard, Pierre Tuffery, Jun-ichi Nakayama, Ludmila Frolova, Knud H. Nierhaus, Galina Karpova, and Soria Baouz
The open biochemistry journal. 25 Août 2014; 11;8:52-67..

Improved PEP-FOLD approach for peptide and miniprotein structure prediction
Yimin Shen , Julien Maupetit , Philippe Derreumaux , and Pierre Tuffery
J. Chem. Theory Comput.. 20 Août 2014; 43(13):4871-93..

VIRAPOPS2 Supports the Influenza Virus Reassortments
Petitjean M., Vanet A.
Source Code Biol Med.. 17 Août 2014; 9:18.

Discovery of novel inhibitors of vascular endothelial growth factor-A-Neuropilin-1 interaction by structure-based virtual screening.
Starzec A, Miteva MA, Ladam P, Villoutreix BO, Perret GY.
Bioorganic Medicinal Chemistry. 01 Août 2014; 1;22(15):4042-8.

A Medicago truncatula rdr6 allele impairs transgene silencing and endogenous phased siRNA production but not development.
Bustos-Sanmamed P1, Hudik E, Laffont C, Reynes C, Sallet E, Wen J, Mysore KS, Camproux AC , Hartmann C, Gouzy J, Frugier F, Crespi M, Lelandais-Brière C.
Plant Biotechnol J.. 24 Juillet 2014; in press.

PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces.
Adrien Saladin, Julien Rey, Pierre Thévenet, Martin Zacharias, Gautier Moroy and Pierre Tufféry
Nucleic Acids Research. 01 Juillet 2014; 42(Web Server issue):W221-6..

Imidazole-derived 2-N-carbamoylmethyl-alkylaminoacetic acids, substrate-dependent modulators of insulin-degrading enzyme in amyloid-β hydrolysis.
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.
European Journal of Medicinal Chemistry. 22 Mai 2014; 79:184-93.

Identification of small inhibitory molecules targeting the Bfl-1 anti-apoptotic protein that alleviate resistance to ABT737.
Mathieu A.L., Sperandio O., Pottiez V., Balzarin S., Herledan A., Elkaim J.O., Fogeron M.L., Piveteau C., Dassonneville S., Deprez B., Villoutreix B.O.,Bonnefoy N. and Leroux F.
Journal of Biomolecular Screening. 2014; 19(7):1035-1046.

Ligand Efficiency Driven Design of New Inhibitors of Mycobacterium tuberculosis Transcriptional Repressor EthR Using Fragment Growing, Merging, and Linking Approaches
Villemagne B., Flipo M., Blondiaux N., Crauste C., Malaquin S., Leroux F., Piveteau C., Villeret V., Brodin P., Villoutreix B.O., Sperandio O., Soror S.H., Wohlkönig A., Wintjens R., Deprez B., Baulard A.R., Willand N.
J. Med. Chem.. 2014; 57(11):4876-88.

Identification of odorant-receptor interactions by global mapping of the human odorome.
Audouze K., Tromelin A., Le Bon A.M., Belloir C., Petersen R.K., Kristiansen K., Brunak S., Taboureau O.
Plos ONE. 29 Avril 2014; (4):e93037.

Identification of novel small molecule inhibitors of activated protein C.
Sperandio O., Wildhagen K.C., Schrijver R., Wielders S., Villoutreix B.O., Nicolaes G.A.
Thromb Res.. 2014; 79:184-93.

Solid-phase synthesis and biological evaluation of N-dipeptido L-homoserine lactones as quorum sensing activators.
Hansen M.R., Le Quement S.T., Jakobsen T.H., Skovstrup S., Taboureau O., Tolker-Nielsen T., Givskov M., Nielsen TE.
ChemBioChem. 10 Février 2014; 15(3):460-5.

Excitation/inhibition balance and learning are modified by Dyrk1a gene dosage
Benoit Souchet, Fayçal Guedj, Ignasi Sahun, Arnaud Duchon, Fabrice Daubigney, Anne Badel, Yuchio Yanagawa, Maria Jose Barallobre, Mara Dierssen, Eugene Yu, Yann Herault, Mariona Arbones, Nathalie Janel, Nicole Creau.
Neurobiology of Disease Manuscript. 2014; 69:65-75.

Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology.
Villoutreix B.O., Kuenemann M.A., Poyet J.L., Bruzzoni-Giovanelli H., Labbe C., Lagorce D., Sperandio O., Miteva M.A.
Molecular Informatics. 2014; 33(6-7):414-437.

The OPEP coarsegrained protein model: from single molecules, amyloid formation, role of macromolecular crowding and hydrodynamics to RNA/DNA complexes
Fabio Sterpone, Simone Melchionna, Pierre Tufféry, Samuela Pasquali, Normand Mousseau, Tristan Cragnolini, Yassmine Chebaro, Jean-Francois Saint-Pierre, Maria Kalimeri, Alessandro Barducci, Yohan Laurin, Alex Tek,Marc Baaden, Phuong Hoang Nguyen, and Philippe Derreumaux
Chem. Soc. Rev.. 2014; 43(13):4871-93..

Editorial: Chirality and Symmetry in the Chemical and PhysicalStructure of Matter.
Borovkov V., Petitjean M.
Symm. Cult. Sci.. 2014; 25[2]-53-54.

Rational design of small molecules targeting the C2 domain of coagulation factor VIII.
Nicolaes G.A., Kulharia M., Voorberg J., Kaijen P.H., Wroblewska A., Wielders S., Schrijver R., Sperandio O., Villoutreix B.O.
Blood. 2014; 123(1):11320.

VIRAPOPS: a Forward Simulator Dedicated to Rapidly Evolved Viral Populations
Petitjean M., Vanet A.
Bioinformatics. 2014; 30[4]- 578580.

Computing cavities, channels, pores and pockets in proteins from nonspherical ligands models.
Benkaidali L., André F., Maouche B., Siregar P., Benyettou M., Maurel F., Petitjean M.
Bioinformatics. 2014; 30[6]- 792800.

Fast protein fragment similarity scoring using a Binet-Cauchy Kernel.
F. Guyon , P. Tufféry
Bioinformatics. 2014; 30 (6): 792-800.

Structure of the prolyl-acyl carrier protein oxidase involved in thebiosynthesis of the cyanotoxin anatoxin-a.
Moncoq K., Regad L., Mann S., Mejean A., Ploux O.
Acta Cryst. D.. 2013; D69 - 2340-2352.

Identification by in silico and in vitro screenings of small organic molecules acting as reversible inhibitors of kallikreins.
Tana X., Bertonati C., Qina L., Furioc L., El Amria C., Hovnanian A., Reboud-Ravaux M., Villoutreix B.O.
European Journal of Medicinal Chemistry. 2013; 70:661-8.

Detecting protein candidate fragments using a structuralalphabet profile comparison approach.
Shen Y., Picord G., Guyon F., Tufféry P.
Plos ONE. 2013; 8(11):e80493.

Aggrecanase-2 inhibitors based on the acylthiosemicarbazide zinc-binding group.
Maingot L., Elbakali J., Dumont J., Bosc D., Cousaert N., Urban A., Deglane G., Villoutreix B.O., Nagase H., Sperandio O., Leroux F., Deprez B., Deprez-Poulain R.
European Journal of Medicinal Chemistry. 2013; 69C:244-261.

The effect of network biology on drug toxicology.
Gautier L., Taboureau O., Audouze K.
Expert Opin Drug Metab Toxicol.. 2013; 9(11):140918.

In silico mechanistic profiling to probe small molecule binding to sulfotransferases.
Martiny V.Y., Carbonell P., Lagorce D., Villoutreix B.O., Moroy G., Miteva M.A.
Plos ONE. 2013; 8(9):e73587.

Physico-chemical characterization of African urban aerosols (Bamako in Mali and Dakar in Senegal) and their toxic effects in human bronchial epithelial cells: description of a worrying situation.
S. Val, C. Liousse, EH. Doumbia, C. Galy-Lacaux, H. Cachier, N. Marchand, A. Badel, E. Gardrat, A. Sylvestre, A. Baeza-Squiban
Part Fibre Toxicol.. 2013; 10(1):10.

Advances in molecular modeling of human cytochrome P450 polymorphism.
Martiny V.Y., Miteva M.A.
J. Mol. Biol.. 2013; 425(21):397892.

Computational analysis of protein-protein interfaces involving an alpha helix: insights for terphenyl-like molecules binding.
Isvoran A., Craciun D., Martiny V.Y., Sperandio O., Miteva M.A.
BMC Pharmacol Toxicol.. 2013; 14(1):31.

Insights into an Original Pocket-Ligand Pair Classification: A Promising Tool for Ligand Profile Prediction
Pérot S. , Regad L. , Reynès C., Sperandio O. , Miteva M.A., Villoutreix B.O., Camproux A-C.
Plos ONE. 2013; 8(6):e63730.

One hundred thousand mouse clicks down the road: a compilation of online resources supporting drug discovery collected over a decade.
Villoutreix B.O., Lagorce D., Labbé C.M., Sperandio O., Miteva M.A.
Drug Discovery Today. 2013; 18(21-22):10819.

1,2,4-triazole derivatives as transient inactivators of kallikreins involved in skin diseases
Tana X., Furio L., Reboud-Ravaux M., Villoutreix B.O., Hovnanian A., El Amri C.
Bioorganic & Medicinal Chemistry Letters. 2013; 23(16):4547-51.

Discovery of a Novel Selective PPARγ Ligand with Partial Agonist Binding Properties by Integrated in Silico/in Vitro Work Flow.
Kouskoumvekaki I, Petersen R.K, Fratev F., Taboureau O., Nielsen T.E., Oprea T.I., Sonne S.B., Flindt E.N., Jónsdóttir S.Ó., Kristiansen K.
J. Chem. Inf. Model.. 2013; 53(4):92337.

HExpoChem: a systems biology resource to explore human exposure to chemicals.
Taboureau O., Jacobsen UP., Kalhauge C., Edsgärd D., Rigina O, Gupta R, Audouze K.
Bioinformatics. 2013; 29(9):12312.

Post-docking Optimization and Analysis of Protein-Ligand Interactions of Estrogen Receptor Alpha using AMMOS Software.
Pencheva T., Jereva D., Miteva M.A., Pajeva I.
Curr Comput Aided Drug Design. 2013; 9(1):83-94.

iPPI-DB: A manually curated and interactive database of small non-peptide inhibitors of protein-protein interactions.
Labbé C.M., Laconde G., Kuenemann M.A., Villoutreix B.O., Sperandio O.
Drug Discovery Today. 2013; 18(19-20):958-68.

Molecular basis of coagulation factor V deficiency caused by the R1698W inter-domain mutation.
Calzavarini S., Villoutreix B.O., Lunghi B., Livaja R., Bernardi F., Dahlbëack B.
Thromb Haemost.. 2013; 110(1):31-8.

A rational free energy-based approach to understanding and targeting disease-causing missense mutations.
Zhang Z., Witham S., Petukh M., Moroy G., Miteva M.A., Ikeguchi Y., Alexov E.
J. Am. Med. Inform. Assoc.. 2013; 20(4):643-51.

Missense mutations in SLC26A8, encoding a sperm-specific activator of the Cystic Fibrosis Transmembrane conductance Regulator.
Dirami T., Rode B., Jollivet M., Da Silva N., Escalier D., Gaitch N., Norez C., Tufféry P., Wolf J.P., Becq F., Ray P.F., Dulioust E., Gacon G., Bienvenu T., and Touré A.
The American Journal of Human Genetics. 2013; 92(5):760-6.

1,2,4-Oxadiazoles identified by virtual screening and their non-covalent inhibition of the human 20S proteasome.
Marechal X., Genin E., Qin L., Sperandio O., Montes M., Basse N., Richy N., Miteva M.A., Reboud-Ravaux M., Vidal J., Villoutreix B.O.
Current Medicinal Chemistry. 2013; 20(18):2351-62.

Comparative analysis of interactions of RASSF1-10
J.J. Chan, D. Flatters, F. Rodrigues-Lima, J. Yan, K. Thalassinos and M. Katan
Advances in Biological Regulation. 2013; 53(2):190-201.

Identification of LasR Ligands through a Virtual Screening Approach.
Skovstrup S, Le Quement ST, Hansen T, Jakobsen TH, Harmsen M, Tolker-Nielsen T, Nielsen TE, Givskov M, Taboureau O.
ChemMedChem. 2013; 8(1):15763.

ChemProt-2.0: visual navigation in a disease chemical biology database.
Kim Kjærulff S, Wich L, Kringelum J, Jacobsen UP, Kouskoumvekaki I, Audouze K, Lund O, Brunak S, Oprea TI, Taboureau O.
Nucleic Acids Research. 2013; 41(D1): D464-D469.

A leap into the chemical space of Protein-Protein Interaction inhibitors. Special Issue : «Toward the design of drugs on Protein-Protein Interaction». Ed. O. Sperandio
Villoutreix B.O., Labbé C.M., Lagorce D., Laconde G., Sperandio O.
Current Pharmaceutical Design. 2012; 18(30):4648-4667. Review.

Analyzing effects of naturally occurring missense mutations.
Zhang Z., Miteva M., Wang L., Alexov E.
Comput Math Methods Med.. 2012; :805827. Review.

Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches.
Tufféry P., Derreumaux P.
Journal of the Royal Society interface. 2012; 9(66):20-33. Review.

AMMOS software: method and application.
Pencheva T, Lagorce D, Pajeva I, Villoutreix BO, Miteva MA.
Methods Mol Biol. 2012; 819:12741.. Review.

Established and emerging trends in computational drug discovery in the structural genomics era.
Taboureau O., Baell J.B., Fernandez-Recio J., Villoutreix B.O.
Chem Biol.. 2012; 19(1):2941. Review.

Design and synthesis of novel bis-thiazolone derivatives as micromolar CDC25 phosphatase inhibitors: Effect of dimerisation on phosphatase inhibition.
Sarkis M., Tran D.N., Kolb S., Miteva M.A., Villoutreix B.O., Garbay C, Braud E.
Bioorganic & Medicinal Chemistry Letters. 2012; 22(24):7345-50.

In silico prediction of aqueous solubility: a multimodel protocol based on chemical similarity.
Chevillard F., Lagorce D., Reynès C., Villoutreix B.O., Vayer P, Miteva M.A.
Mol. Pharm.. 2012; 9:3127-35.

Thymoquinone as an anticancer agent: evidence from inhibition of cancer cells viability and invasion in vitro and tumor growth in vivo.
Attoub S, Sperandio O , Raza H, Arafat K, AlSalam S, Al Sultan MA, Al Safi M, Takahashi T, Adem A.
Fundam Clin Pharmacol.. 2012; 27(5):557-69.

Characterization of Arabidopsis calcium-dependent protein kinases: activated or not by calcium?
Boudsocq M., Droillard M-J., Regad L. Laurière C.
Biochem. J.. 2012; 447, 291-299.

Lys53 of ribosomal protein L36AL and the CCA-end of a tRNA at the P/E hybrid site are in close proximity on the human ribosome.
Hountondji , Bulygin K., Woisard A., Tufféry P., Créchet J-B., Pech M., Nierhaus K.H., Karpova G., and Baouz S.
Biochem. J.. 2012; 13(12):17917.

About the Algebraic Solutions of Smallest Enclosing Cylinders Problems.
Petitjean M.
Appl. Alg. Eng. Comm. Comp.. 2012; 23[3-4], 151164.

Isotype modulates epitope specificity, affinity and the antiviral activities of the anti-HIV human broadly neutralizing 2F5 antibody.
Tudor D, Yu H, Maupetit J., Drillet A-S, Bouceba T, Schwartz-Cornil I, Lopalco L, Tufféry P., Bomsel M.
Proceedings of the National Academy of Sciences USA. 2012; 109(31):12680-5.

PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides.
Thévenet P, Shen Y, Maupetit J, Guyon F, Derreumaux P, Tufféry P.
Nucleic Acids Research. 2012; 40(Web Server issue):W288-93.

Modulation of Soleus H-reflex by spinal DC stimulation in humans.
Lamy JC., Ho C., Badel A., Arrigo RT., Boakye M.
J. Neurophysiol.. 2012; 108(3):90614.

Homozygous CDKN2A deletion is associated with muscle invasion in FGFR3-mutated bladder cancers.
Rebouissou S, Hérault A, Letouzé E, Neuzillet Y, Laplanche A, Ofualuka K, Maillé P, Leroy K, Riou A, Lepage M-L, Vordos D, de la Taille A, Denoux Y, Guyon F, Lebret T, Benhamou S, Allory Y, Radvanyi F.
The Journal of Pathology. 2012; 227(3):315-24.

Gohtam: A website for «Genomic Origin of Horizontal Transfers, Alignment and Metagenomics»
Menigaud S., Mallet L., Picord G., Churlaud C., Borrel A., Deschavanne P.
Bioinformatics. 2012; 28(9):12701271.

Analysis of binding sites on complement factor I using artificial N-linked glycosylation.
Sanchez Gallego I, Groeneveld TW, Krentz S, Nilsson SC, Villoutreix BO, Blom AM
J. Biol. Chem.. 2012; 287(17):13572-83.

Neutrophil Elastase as a Target in Lung Cancer.
Moroy G., Alix AJ, Sapi J, Hornebeck W, Bourguet E.
Anticancer Agents Med Chem.. 2012; 12(6):56579.

Towards in silico structure-based ADMET prediction in drug discovery.
Moroy G., Martiny V., Vayer P., Villoutreix B.O., Miteva M.A.
Drug Discovery Today. 2012; 17(1-2):44-55.

Spheres Unions and Intersections and some of their Applications in Molecular Modeling.
Petitjean M.
Distance Geometry - Theory Methods and Applications. 2012; chap. 4, pp. 61-83. Eds., Springer. ISBN 978-1-461.

Three-dimensional structure generators of drug-like compounds: DG-AMMOS, an open-source package.
Lagorce D., Villoutreix B.O., Miteva M.A.
Expert Opinion on Drug Discovery. 2011; 6(3):339-351.. Review.

Targeting the pro-angiogenic VEGF-VEGFR protein-protein interface with drug-like compounds by in silico and in vitro screening.
Gautier B, Miteva MA. , Goncalves V, Huguenot F, Coric P, Bouaziz S, Seijo B, Gaucher JF, Broutin I, Garbay C, Lesnard A, Rault S, Inguimbert N, Villoutreix BO. , Vidal M.
Chem Biol.. 2011; 18(12):16319.

Protease profiling of liver fibrosis reveals the adam metallopeptidase with thrombospondin type 1 motif, 1 as a central activator of TGF-β
Bourd-Boittin K, Bonnier D, Leyme A, Mari B, Tufféry P, Samson M, Ezan F, Baffet G, Theret N.
Hepatology. 2011; 54(6):217384.

Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs.
Regad L., Martin J., Camproux AC.
BMC Bioinformatics. 2011; 12:247.

SA-Mot: a web server for the identification of motifs of interest extracted from protein loops.
Regad L., Saladin S., Maupetit J., Geneix C., Camproux A-C.
Nucleic Acids Research. 2011; 39(2)(Web server issue):W203-W209.

Tyrosine kinase Syk non-enzymatic inhibitors and potential anti-allergic drug-like compounds discovered by virtual and in vitro screening.
Villoutreix B.O , Laconde G. , Lagorce D. , Martineau P. , Miteva MA. , Dariavach P.
Plos ONE. 2011; 6(6):e21117.

The FAF-Drugs2 server: a multi-step engine to prepare electronic chemical compound collections.
Lagorce D., Maupetit J., Baell J., Sperandio O., Tufféry P., Miteva MA., Galons H., Villoutreix BO.
Bioinformatics. 2011; 27(14):2018-20.

Exploring NMR ensembles of calcium binding proteins: perspectives to design inhibitors of protein-protein interactions
Isvoran A., Badel A., Craescu C T, Miron M. and Miteva M.A.
BMC Structural Biology. 2011; 11(1):24.

Control of peptide nanotube diameter by chemical modifications of an aromatic residue involved in a single close contact.
Tarabout C, Roux S, Gobeaux F, Fay N, Pouget E, Meriadec C, Ligeti M, Thomas D, IJsselstijn M, Besselievre F, Buisson DA, Verbavatz JM, Petitjean M, Valéry C, Perrin L, Rousseau B, Franck Artzner F, Paternostre M, Cintrat JC
Proceedings of the National Academy of Sciences USA. 2011; 108(19):76797684.

Post-docking Optimization and Analysis of Protein-ligand Interactions with AMMOS Free Software.
Pencheva T., Alov P., Jereva D., Pajeva I., Miteva M.A.
Topics in chemistry and Material Science. 2011; 5:4351.

Inhibition of human leukocyte elastase, plasmin and matrix metalloproteinases by oleic acid and oleoyl-galardin derivative(s).
Moroy G, Bourguet E, Decarme M, Sapi J, Alix AJ, Hornebeck W, Lorimier S.
Biochem Pharmacol.. 2011; Mar 181(5):626-35.

Deciphering the shape and deformation of secondary structures through localconformation analysis.
Baussand J., Camproux A.C.
BMC Structural Biology. 2011; 11(1):9.

Targeting AAC-11 in cancer therapy.
Faye A., Poyet J.L.
Expert Opin Ther Targets. 12 Décembre 2010; 14(1):57-65.

Complete regression of a previously untreated melanoma brain metastasis with ipilimumab.
Schartz N. E., Farges C., Madelaine I., Bruzzoni H., Calvo F., Hoos A., Lebbé C.
Melanoma Res.. 2010; 20(3):247-50.