Logo université Nantes

Accueil du site > Publications > Conception de protéines in silico

Publications de l’équipe Conception de protéines in silico


Dhingra S, Sowdhamini R, Sanejouand Y-H, Cadet F, Offmann B Customised fragment libraries for ab initio protein structure prediction using a structural alphabet. . 2020 arXiv preprint arXiv:2005.01696. https://arxiv.org/abs/2005.01696


Richoux F, Servantie C, Borès C, Téletchéa S Comparing two deep learning sequence-based models for protein-protein interaction prediction. 2019 https://arxiv.org/abs/1901.06268

Nagaraja A, Fontaine N, Delsaut M, Charton P, Damour C, Offmann B, Grondin-Perez B, Cadet F Flux prediction using artificial neural network (ANN) for the upper part of glycolysis. PloS one 2019 14(5), e0216178. doi:10.1371/journal.pone.0216178

David B, Arnaud P, Tellier C, Sanejouand Y-H Toward the design of efficient transglycosidases : the case of the GH1 of Thermus thermophilus. Protein engineering, design & selection : PEDS 2019 doi:10.1093/protein/gzz032

Ajjolli Nagaraja A, Fontaine N, Delsaut M, Charton P, Damour C, Offmann B, Grondin-Perez B, Cadet F. Flux prediction using artificial neural network (ANN) for the upper part of glycolysis. PLOS ONE 2019 14:1–15. doi:10.1371/journal.pone.0216178

Ghosh P, Joshi A, Guita N, Offmann B, Sowdhamini R. EcRBPome : a comprehensive database of all known E. coli RNA-binding proteins. BMC genomics 2019 20:403–6. doi:10.1186/s12864-019-5755-5.

Ostafe R, Fontaine N, Frank D, Ng Fuk Chong M, Prodanovic R, Pandjaitan R, Offmann B, Cadet F, Fischer R. One-shot optimization of multiple enzyme parameters : Tailoring glucose oxidase for pH and electron mediators. Biotechnol. Bioeng. 2019, doi:10.1002/bit.27169.

Vetrivel I, de Brevern AG, Cadet F, Srinivasan N, Offmann B. Structural variations within proteins can be as large as variations observed across their homologues. Biochimie 2019, 167:162–170.

Chaaya N, Shahsavarian MA, Maffucci I, Friboulet A, Offmann B, Léger J-B, Rousseau S, Avalle B, Padiolleau-Lefèvre S. Genetic background and immunological status influence B cell repertoire diversity in mice. Scientific reports 2019, 9:14261–7.

Tripathi N, Vetrivel I, Téletchéa S, Jean M, Legembre P, Laurent AD. Investigation of Phospholipase Cγ1 Interaction with SLP76 Using Molecular Modeling Methods for Identifying Novel Inhibitors. Int J Mol Sci. 2019, 20(19). doi:10.3390/ijms20194721.

Gheyouche E, Launay R, Lethiec J, Labeeuw A, Roze C, Amossé A, Téletchéa S. DockNmine, a Web Portal to Assemble and Analyse Virtual and Experimental Interaction Data. Int J Mol Sci. 2019, 20(20). doi:10.3390/ijms20205062.

Le Caignec C, Ory B, Lamoureux F, O’Donohue MF, Orgebin E, Lindenbaum P, Téletchéa S, Saby M, Hurst A, Nelson K, Gilbert SR, Wilnai Y, Zeitlin L, Segev E, Tesfaye R, Nizon M, Cogne B, Bezieau S, Geoffroy L, Hamel A, Mayrargue E, de Courtivron B, Decock-Giraudaud A, Charrier C, Pichon O, Retière C, Redon R, Pepler A, McWalter K, Da Costa L, Toutain A, Gleizes PE, Baud’huin M, Isidor B. RPL13 Variants Cause Spondyloepimetaphyseal Dysplasia with Severe Short Stature. Am J Hum Genet. 2019, 105(5):1040-1047. doi:10.1016/j.ajhg.2019.09.024.

Téletchéa S, Santuz H, Léonard S, Etchebest C. Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (RESPIRE). PLoS ONE 2019, 14(2) : e0211043. doi:10.1371/journal.pone.0211043.


Cadet F, Fontaine N, Li G, Sanchis J, Ng Fuk Chong M, Pandjaitan R, Vetrivel I, Offmann B, Reetz MT. A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes. Sci Rep. . 2018, 8(1):16757. doi:10.1038/s41598-018-35033-y.


Vetrivel I, Mahajan S, Tyagi M, Hoffmann L, Sanejouand Y-H, Srinivasan N, Brevern A, Cadet F, Offmann B Knowledge-based prediction of protein backbone conformation using a structural alphabet. PloS one 2017 12(11), e0186215. doi:10.1371/journal.pone.0186215

Sanejouand Y-H Mutational dynamics of influenza A viruses : a principal component analysis of hemagglutinin sequences of subtype H1. 2017 https://arxiv.org/abs/1710.01594.

Dion J, Advedissian T, Storozhylova N, Dahbi S, Lambert A, Deshayes F, Viguier M, Tellier C, Poirier F, Téletchéa S, Dussouy C, Tateno H, Hirabayashi J, Grandjean C. Development of a Sensitive Microarray Platform for the Ranking of Galectin Inhibitors : Identification of a Selective Galectin-3 Inhibitor. Chembiochem. 2017, 18(24):2428-2440. doi:10.1002/cbic.201700544.

Sanejouand Y-H A singular mutation in the hemagglutinin of the 1918 pandemic virus. Archives of Biochemistry and Biophysics . 2017, 625, 13. DOI : 10.1016/j.abb.2017.05.013

Atmanene, C. ; Ronin, C. ; Gautier, F.-M. ; Djedaïni-Pilard, F. ; Télétchéa, S., Ciesielski, F. ; Vivat, V. ; Grandjean, C. Biophysical and structural characterization of mono/di-arylated lactosamine derivatives interaction with human galectin-3. Biochem Biophys Res Commun . 2017, 489, 281-286.

Mahajan S, Sanejouand, Y-H Jumping between protein conformers using normal modes. JCC 2017, 38(18):1622–1630. https://doi.org/10.1002/jcc.24803

David B, Irague R, Jouanneau D, Daligault F, Czjzek M, Sanejouand Y-H, & Tellier C Internal Water Dynamics Control the Transglycosylation/Hydrolysis Balance in the Agarase (AgaD) of Zobellia galactanivorans. ACS Catalysis 2017, 7:3357–3367. https://doi.org/10.1021/acscatal.7b00348

Labbé P, Faure E, Lecointe S, Le Scouarnec S, Kyndt F, Marrec M, Le Tourneau T, offmann b, Duplaà C, Zaffran S, et al. The alternatively spliced LRRFIP1 Isoform-1 is a key regulator of the Wnt/β-catenin transcription pathway. Biochim. Biophys. Acta. 2017, (Available online 18 March 2017) http://dx.doi.org.gate1.inist.fr/10...

Shahsavarian MA, Chaaya N, Costa N, Boquet D, Atkinson A, Offmann B, Kaveri SV, Lacroix-Desmazes S, Friboulet A, Avalle B, Padiolleau-Lefèvre S. Multitarget selection of catalytic antibodies with β-lactamase activity using phage display. FEBS J. 2017, 284(4):634-653. doi : 10.1111/febs.14012. PubMed PMID : 28075071. (IF 4.237)


Liu G, Ma H, Xie H, Xuan N, Guo X, Fan Z, Rajashekar B, Arnaud P, Offmann B, Picimbon JF. Biotype Characterization, Developmental Profiling, Insecticide Response and Binding Property of Bemisia tabaci Chemosensory Proteins : Role of CSP in Insect Defense. PLoS One. 2016, 11(5):e0154706. doi:10.1371/journal.pone.0154706. PubMed PMID : 27167733 ; PubMed Central PMCID:PMC4864240. (IF 3.54)

Verhaeghe T, De Winter K, Berland M, De Vreese R, D’hooghe M, Offmann B, Desmet T. Converting bulk sugars into prebiotics : semirational design of a transglucosylase with controlled selectivity. CHEMICAL COMMUNICATIONS. 2016, 52(18):3687‑3689 (IF 6.567)


Saumonneau A, Champion E, Peltier-Pain P, Molnar-Gabor D, Hendrickx J, Tran V, Hederos M, Dekany G, Tellier C Design of an α-l-transfucosidase for the synthesis of fucosylated HMOs. Glycobiology 2015 26(3), cwv099. doi:10.1093/glycob/cwv099

Fontaine N, Grondin-Perez B, Cadet F, Offmann B. Modeling of a Cell-Free Synthetic System for Biohydrogen Production. J Comput Sci Syst Biol. 2015, 8:132‑9 (IF 1.62)

Craveur P, Joseph AP, Esque J, Narwani TJ, Noël F, Shinada N, Goguet M, Leonard S, Poulain P, Bertrand O, Faure G, Rebehmed J, Ghozlane A, Swapna LS, Bhaskara RM, Barnoud J, Téletchéa S, Jallu V, Cerny J, Schneider B, Etchebest C, Srinivasan N, Gelly JC, de Brevern AG. Protein flexibility in the light of structural alphabets. Front Mol Biosci. 2015, 2(20)

Mahajan S, Sanejouand Y-H. On the relationship between low-frequency normal modes and the large-scale conformational changes of proteins. Arch Biochem Biophys. 2015, 567C:59‑65 (IF 3.37)

Teze D, Daligault F, Ferriere V, Sanejouand Y-H, Tellier C. Semi-rational approach for converting a GH36 alpha-glycosidase into an alpha-transglycosidase. Glycobiology, 2015, 25:420-427 (IF 3.537)

André-Miral C, Koné FM, Solleux C, Grandjean C, Dion M, Tran V, Tellier C. De novo design of a trans-β-N-acetylglucosaminidase activity from a GH1 β-glycosidase by mechanism engineering. Glycobiology. 2015, 25:394-402 (IF 3.537)

Mahajan S, De Brevern AG, Sanejouand Y-H, Srinivasan N, Offmann B. Use of a structural alphabet to find compatible folds for amino acid sequences. Protein Sci. 2015, 24:145‑53 (IF 2.735)

Le-Bail P, Lorentz C, Pencreac’h G, Soultani-Vigneron S, Pontoire B, Giraldo L, Villeneuve P, Hendrickx J, Tran V. Trapping by amylose of the aliphatic chain grafted onto chlorogenic acid : Importance of the graft position. Carbohydr Polym. 2015, 117:910‑6 (IF 4.074)


Teze D, Hendrickx J, Czjzek M, Ropartz D, Sanejouand Y-H, Tran V, Tellier C, Dion M. Semi-rational approach for converting a GH1 β-glycosidase into a β-transglycosidase. Protein Eng Des Sel. 2014, 27:13‑9 (IF 2.588)

Manoharan M, Fuchs PFJ, Sowdhamini R, Offmann B. Insights on pH-dependent conformational changes of mosquito odorant binding proteins by molecular dynamics simulations. J Biomol Struct Dyn. 2014, 32:1742‑51 (IF 2.983)

Mahajan S, de Brevern AG, Offmann B, Srinivasan N. Correlation between local structural dynamics of proteins inferred from NMR ensembles and evolutionary dynamics of homologues of known structure. J Biomol Struct Dyn. 2014, 32:751‑8 (IF 2.983)

Berland M, Offmann B, André I, Remaud-Siméon M, Charton P. A web-based tool for rational screening of mutants libraries using ProSAR. Protein Eng Des Sel. 2014, 27:375‑81 (IF 2.588)


Teze D, Hendrickx J, Dion M, Tellier C, Woods VL, Tran V, Sanejouand Y-H Conserved water molecules in family 1 glycosidases : a DXMS and molecular dynamics study. Biochemistry. 2013, 52:5900‑10 (IF 3.377)

Manoharan M, Ng Fuk Chong M, Vaïtinadapoulé A, Frumence E, Sowdhamini R, Offmann B. Comparative genomics of odorant binding proteins in Anopheles gambiae, Aedes aegypti, and Culex quinquefasciatus. Genome Biol Evol. 2013, 5:163‑80 (IF 4.759)

Mahajan S, Agarwal G, Iftekhar M, Offmann B, de Brevern AG, Srinivasan N. DoSA : Database of Structural Alignments. Database Oxford. 2013, bat048 (IF 4.457)

Manoharan M, Kannan S, Offmann B, Sowdhamini R, Association of putative members to family of mosquito odorant binding proteins : Scoring scheme using Fuzzy Functional Templates and Cys residue positions. Bioinform Biol Insights. 2013, 7:231-51

Tézé D, Dion M, Daligault F, Tran V, André-Miral C, Tellier C. Alkoxyamino glycoside acceptors for the regioselective synthesis of oligosaccharides using glycosynthases and transglycosidases. Bioorg. Med. Chem Lett. 2013, 23:448-451 (IF 2.338)


Chaput L, Sanejouand Y-H, Balloumi A, Tran V, Graber M. Contribution of both catalytic constant and Michaelis constant to CALB enantioselectivity : Use of FEP calculations for prediction studies. J Mol Catal B-Enzym. 2012, 76:29‑36 (IF 2.823)

Chaput L, Marton Z, Pineau P, Domon L, Tran V, Graber M. Enhancing the enantioselectivity of CALB by substrate imprinting : A combined experimental and molecular dynamics simulation model study. J Mol Catal B-Enzym. 2012, 84:55-61 (IF 2.823)

Paes G, Cortes J, Simeon T, O’Donohue MJ, Tran V. Thumb-loops up for catalysis : a structure/function investigation of a functional loop movement in a GH11 xylanase. Comput Struct Biotechnol J. 2012, 1:1-10 (IF 3.446)


Piazza F, Sanejouand Y-H. Breather-mediated energy transfer in proteins. Discret Contin Dyn S. 2011, 4:1247‑66 (IF 1.195)


Marton Z, Leonard-Nevers V, P.O. Syren PO, Bauer C, Lamarre S, Hult K, Tran V, Graber M. Mutations in the stereospecificity pocket and at the entrance of the active site of Candida antartica lipase B  enhancing enzyme enantioselectivity. J Mol Catal B-Enzym. 2010, 65:11-17 (IF 2.823)

Nommé J, Renodon-Cornière A, Asanomi Y,K. Sakagushi K, Stasiak AZ, Stasiak A, Norden B, Tran V, Takahashi M. Design of Potent Inhibitors of Human RAD51 Recombinase Based on BRC Motifs of BRCA2 Protein  : Modeling and Experimental Validation of a Chimera Peptide. J Med Chem. 2010, 53:5782-5791 (IF 5.614)

Tabrett C, Harrison C.F, Schmidt B, Bellingham S.A, Hardy T, Sanejouand Y-H, Hill A.F, Hogg P.J. Changing the solvent accessibility of the prion protein disulfide bond markedly influences its trafficking and effect on cell function. Biochem. J., 2010, 428:169-182 (IF 4.654)

Tran V, Hoffmann L, Rabiller C, Tellier C, Dion M. Rational design of a GH1 beta-glycosidase to prevent self-condensation during the transglycosylation reaction. Protein Eng Des Sel. 2010, 23:43‑9 (IF 2.588)