Goullieux M, Zoete V, Röhrig UF.
Two-Step Covalent Docking with Attracting Cavities.
J Chem Inf Model. 2023 Dec 25;63(24):7847-7859
Bugnon M, Goullieux M, Röhrig UF, Perez MAS, Daina A, Michielin O, Zoete V.
SwissParam 2023: A Modern Web-Based Tool for Efficient Small Molecule Parametrization.
J Chem Inf Model. 2023 Nov 13;63(21):6469-6475
Röhrig UF, Goullieux M, Bugnon M, Zoete V.
Attracting Cavities 2.0: Improving the Flexibility and Robustness for Small-Molecule Docking.
J Chem Inf Model. 2023 Jun 26;63(12):3925-3940.
Editor(s): Antoine Daina, Michael Przewosny, Vincent Zoete
Open Access Databases and Datasets for Drug Discovery.
WILEY Print ISBN:9783527348398 |Online ISBN:9783527830497
Krebs FS, Moura B, Missiaglia E, Aedo-Lopez V, Michielin O, Tsantoulis P, Bisig B, Trimech M, Zoete V, Homicsko K.
Response and Resistance to Trametinib in MAP2K1-Mutant Triple-Negative Melanoma.
Int J Mol Sci. 2023 Feb 24;24(5):4520
Schmidt J, Chiffelle J, Perez MAS, Magnin M, Bobisse S, Arnaud M, Genolet R, Cesbron J, Barras D, Navarro Rodrigo B, Benedetti F, Michel A, Queiroz L, Baumgaertner P, Guillaume P, Hebeisen M, Michielin O, Nguyen-Ngoc T, Huber F, Irving M, Tissot-Renaud S, Stevenson BJ, Rusakiewicz S, Dangaj Laniti D, Bassani-Sternberg M, Rufer N, Gfeller D, Kandalaft LE, Speiser DE, Zoete V, Coukos G, Harari A.
Neoantigen-specific CD8 T cells with high structural avidity preferentially reside in and eliminate tumors.
Nat Commun. 2023 Jun 6;14(1):3188.
Racle J, Guillaume P, Schmidt J, Michaux J, Larabi A, Lau K, Perez MAS, Croce G, Genolet R, Coukos G, Zoete V, Pojer F, Bassani-Sternberg M, Harari A, Gfeller D.
Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes.
Immunity. 2023 Jun 13;56(6):1359-1375.e13
Álvarez-Prado ÁF, Maas RR, Soukup K, Klemm F, Kornete M, Krebs FS, Zoete V, Berezowska S, Brouland JP, Hottinger AF, Daniel RT, Hegi ME, Joyce JA.
Immunogenomic analysis of human brain metastases reveals diverse immune landscapes across genetically distinct tumors.
Cell Rep Med. 2023 Jan 17;4(1):100900
Mazel-Sanchez B, Niu C, Williams N, Bachmann M, Choltus H, Silva F, Serre-Beinier V, Karenovics W, Iwaszkiewicz J, Zoete V, Kaiser L, Hartley O, Wehrle-Haller B, Schmolke M.
Influenza A virus exploits transferrin receptor recycling to enter host cells.
Proc Natl Acad Sci U S A. 2023 May 23;120(21):e2214936120
Mao K, Borel C, Ansar M, Jolly A, Makrythanasis P, Froehlich C, Iwaszkiewicz J, Wang B, Xu X, Li Q, Blanc X, Zhu H, Chen Q, Jin F, Ankamreddy H, Singh S, Zhang H, Wang X, Chen P, Ranza E, Paracha SA, Shah SF, Guida V, Piceci-Sparascio F, Melis D, Dallapiccola B, Digilio MC, Novelli A, Magliozzi M, Fadda MT, Streff H, Machol K, Lewis RA, Zoete V, Squeo GM, Prontera P, Mancano G, Gori G, Mariani M, Selicorni A, Psoni S, Fryssira H, Douzgou S, Marlin S, Biskup S, De Luca A, Merla G, Zhao S, Cox TC, Groves AK, Lupski JR, Zhang Q, Zhang YB, Antonarakis SE.
FOXI3 pathogenic variants cause one form of craniofacial microsomia
Nat Commun. 2023 Apr 11;14(1):2026
Serey-Gaut M, Cortes M, Makrythanasis P, Suri M, Taylor AMR, Sullivan JA, Asleh AN, Mitra J, Dar MA, McNamara A, Shashi V, Dugan S, Song X, Rosenfeld JA, Cabrol C, Iwaszkiewicz J, Zoete V, Pehlivan D, Akdemir ZC, Roeder ER, Littlejohn RO, Dibra HK, Byrd PJ, Stewart GS, Geckinli BB, Posey J, Westman R, Jungbluth C, Eason J, Sachdev R, Evans CA, Lemire G, VanNoy GE, O'Donnell-Luria A, Mau-Them FT, Juven A, Piard J, Nixon CY, Zhu Y, Ha T, Buckley MF, Thauvin C, Essien Umanah GK, Van Maldergem L, Lupski JR, Roscioli T, Dawson VL, Dawson TM, Antonarakis SE.
Bi-allelic TTI1 variants cause an autosomal-recessive neurodevelopmental disorder with microcephaly.
Am J Hum Genet. 2023 Mar 2;110(3):499-515
Röhrig UF, Majjigapu SR, Vogel P, Reynaud A, Pojer F, Dilek N, Reichenbach P, Ascenção K, Irving M, Coukos G, Michielin O, Zoete V.
Structure-based optimization of type III indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors.
Enzyme Inhib Med Chem. 2022 Dec;37(1):1773-1811
Bragina ME, Daina A, Perez MAS, Michielin O, Zoete V.
The SwissSimilarity 2021 Web Tool: Novel Chemical Libraries and Additional Methods for an Enhanced Ligand-Based Virtual Screening Experience.
Int. J. Mol. Sci., 2022 Jan, 23(2)
Krebs FS, Britschgi C, Pradervand S, Achermann R, Tsantoulis P, Haefliger S, Wicki A, Michielin O, Zoete V.
Structure-based prediction of BRAF mutation classes using machine-learning approaches
Sci Rep. 2022 Jul 22;12(1):12528
Perez MAS, Cuendet MA, Röhrig UF, Michielin O, Zoete V.
Structural Prediction of Peptide-MHC Binding Modes.
Methods Mol Biol. 2022;2405:245-282
Irving M, Zoete V, Bassani-Sternberg M, Coukos G.
A roadmap for driving CAR T cells toward the oncogenic immunopeptidome.
Cancer Cell. 2022 Jan 10;40(1):20-22.
Camviel N, Wolf B, Croce G, Gfeller D, Zoete V, Arber C.
Both APRIL and antibody-fragment-based CAR T cells for myeloma induce BCMA downmodulation by trogocytosis and internalization.
J Immunother Cancer. 2022 Nov;10(11):e005091
Cleary JM, Rouaisnel B, Daina A, Raghavan S, Roller LA, Huffman BM, Singh H, Wen PY, Bardeesy N, Zoete V, Wolpin BM, Losman JA.
Secondary IDH1 resistance mutations and oncogenic IDH2 mutations cause acquired resistance to ivosidenib in cholangiocarcinoma.
NPJ Precis Oncol. 2022 Sep 2;6(1):61
Billault-Chaumartin I, Michon L, Anderson CA, Yde SE, Suarez C, Iwaszkiewicz J, Zoete V, Kovar DR, Martin SG.
Actin assembly requirements of the formin Fus1 to build the fusion focus.
J Cell Sci. 2022 Jul 1;135(13):jcs260289
Meuwissen M, Verstraeten A, Ranza E, Iwaszkiewicz J, Bastiaansen M, Mateiu L, Nemegeer M, Meester JAN, Afenjar A, Amaral M, Ballhausen D, Barnett S, Barth M, Asselbergh B, Spaas K, Heeman B, Bassetti J, Blackburn P, Schaer M, Blanc X, Zoete V, Casas K, Courtin T, Doummar D, Guerry F, Keren B, Pappas J, Rabin R, Begtrup A, Shinawi M, Vulto-van Silfhout AT, Kleefstra T, Wagner M, Ziegler A, Schaefer E, Gerard B, De Bie CI, Holwerda SJB, Abbot MA, Antonarakis SE, Loeys B.
Heterozygous variants in CTR9, which encodes a major component of the PAF1 complex, are associated with a neurodevelopmental disorder.
Genet Med. 2022 Jul;24(7):1583-1591
Cuozzo A, Daina A, Perez MAS, Michielin O, Zoete V.
SwissBioisostere 2021: updated structural, bioactivity and physicochemical data delivered by a reshaped web interface
Nucleic Acids Res., 2022 Jan, 50(D1):D1382-D1390
Krebs FS, Zoete V, Trottet M, Pouchon T, Bovigny C, Michielin O.
Swiss-PO: a new tool to analyze the impact of mutations on protein three-dimensional structures for precision oncology.
NPJ Prec. Oncol., 2021 Mar 18, 5(1):19
Röhrig UF, Majjigapu SR, Reynaud A, Pojer F, Dilek N, Reichenbach P, Ascencao K, Irving M, Coukos G, Vogel P, Michielin O, Zoete V.
Azole-Based Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitors.
J. Med. Chem., 2021 Feb, 64(4):2205-2227
Röhrig UF, Michielin O, Zoete V.
Structure and Plasticity of Indoleamine 2,3-Dioxygenase 1 (IDO1).
J Med Chem., 2021 Dec, 64(24):17690-17705
Merkle PS, Trabjerg E, Hongjian S, Ferber M, Cuendet MA, Jørgensen TJD, Luescher I, Irving M, Zoete V, Michielin O, Rand KD.
Probing the Conformational Dynamics of Affinity-Enhanced T Cell Receptor Variants upon Binding the Peptide-Bound Major Histocompatibility Complex by Hydrogen/Deuterium Exchange Mass Spectrometry.
Biochemistry, 2021 Mar, 60(11):859-872
Cleary JM, Raghavan S, Wu Q, Li YY, Spurr LF, Gupta HV, Rubinson DA, Fetter IJ, Hornick JL, Nowak JA, Siravegna G, Goyal L, Shi L, Brais LK, Loftus M, Shinagare AB, Abrams TA, Clancy TE, Wang J, Patel AK, Brichory F, Vaslin Chessex A, Sullivan RJ, Keller RB, Denning S, Hill ER, Shapiro GI, Pokorska-Bocci A, Zanna C, Ng K, Schrag D, Jänne PA, Hahn WC, Cherniack AD, Corcoran RB, Meyerson M, Daina A, Zoete V, Bardeesy N, Wolpin BM.
FGFR2 Extracellular Domain In-Frame Deletions Are Therapeutically Targetable Genomic Alterations That Function as Oncogenic Drivers in Cholangiocarcinoma.
Cancer Discov., 2021 Oct, 11(10):2488-2505
Hong A, Piva M, Liu S, Hugo W, Lomeli SH, Zoete V, Randolph CE, Yang Z, Wang Y, Lee JJ, Lo SJ, Sun L, Vega-Crespo A, Garcia AJ, Shackelford DB, Dubinett SM, Scumpia PO, Byrum SD, Tackett AJ, Donahue TR, Michielin O, Holmen SL, Ribas A, Moriceau G, Lo RS.
Durable Suppression of Acquired MEK Inhibitor Resistance in Cancer by Sequestering MEK from ERK and Promoting Antitumor T-cell Immunity.
Cancer Discov., 2021 Mar, 11(3):714-735
Waman VP, Sen N, Varadi M, Daina A, Wodak SJ, Zoete V, Velankar S, Orengo C.
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies.
Brief Bioinform., 2021 Mar 22, 22(2):742-768
Antonarakis SE, Holoubek A, Rapti M, Rademaker J, Meylan J, Iwaszkiewicz J, Zoete V, Wilson C, Taylor J, Ansar M, Borel C, Menzel O, Kuzelová K, Santoni FA.
Dominant monoallelic variant in the PAK2 gene causes Knobloch syndrome type 2.
Hum. Mol. Genet., 2021 Dec, 31(1):1-9
Mazel-Sanchez B, Iwaszkiewicz J, Bonifacio JPP, Silva F, Niu C, Strohmeier S, Eletto D, Krammer F, Tan G, Zoete V, Hale BG, Schmolke M.
Influenza A viruses balance ER stress with host protein synthesis shutoff.
Proc. Natl. Acad. Sci. U. S. A., 2021 Sep 7, 118(36):e2024681118
Arnaud M, Chiffelle J, Genolet R, Navarro Rodrigo B, Perez MAS, Huber F, Magnin M, Nguyen-Ngoc T, Guillaume P, Baumgaertner P, Chong C, Stevenson BJ, Gfeller D, Irving M, Speiser DE, Schmidt J, Zoete V, Kandalaft LE, Bassani-Sternberg M, Bobisse S, Coukos G, Harari A.
Sensitive identification of neoantigens and cognate TCRs in human solid tumors.
Nat. Biotechnol., 2021 Nov 15.
Duraiswamy J, Turrini R, Minasyan A, Barras D, Crespo I, Grimm AJ, Casado J, Genolet R, Benedetti F, Wicky A, Ioannidou K, Castro W, Neal C, Moriot A, Renaud-Tissot S, Anstett V, Fahr N, Tanyi JL, Eiva MA, Jacobson CA, Montone KT, Westergaard MCW, Svane IM, Kandalaft LE, Delorenzi M, Sorger PK, Färkkilä A, Michielin O, Zoete V, Carmona SJ, Foukas PG, Powell DJ Jr, Rusakiewicz S, Doucey MA, Dangaj Laniti D, Coukos G.
Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation.
Cancer. Cell., 2021 Dec 13, 39(12):1623-1642.e20
Lanitis E, Kosti P, Ronet C, Cribioli E, Rota G, Spill A, Reichenbach P, Zoete V, Dangaj Laniti D, Coukos G, Irving M.
VEGFR-2 redirected CAR-T cells are functionally impaired by soluble VEGF-A competition for receptor binding.
J. Immunother. Cancer., 2021 Aug, 9(8):e002151.
Waman VP, Sen N, Varadi M, Daina A, Wodak SJ, Zoete V, Velankar S, Orengo C.
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies.
Briefings in Bioinformatics. 2020, in press
Krebs FA, Gérard G, Wicky A, Aedo-Lopez V, Missiaglia E, Bisig B, Trimech M, Michielin O, Homicsko K, Zoete V.
Trametinib Induces the Stabilization of a Dual GNAQ p.Gly48Leu- and FGFR4 p.Cys172Gly-Mutated Uveal Melanoma. The Role of Molecular Modelling in Personalized Oncology.
International Journal Of Molecular Sciences. 2020, in press
Lehal R, Zaric J, Vigolo M, Urech C, Frismantas V, Zangger N, Cao LL , Berger A, Chicote I, Loubery S, Choi SH, Koch U, Blacklow SC, Palmer HG, Bornhauser B, Gonzalez-Gaitan M, Arsenijevic Y, Zoete V, Aster JC, Bourquin JP, Radtke F.
Pharmacological disruption of the Notch transcription factor complex.
PNAS. 2020, 117(28):16292-16301
Orengo C, Velankar S, Wodak S, Zoete V, Bonvin AMJJ, Elofsson A, et al.
A community proposal to integrate structural bioinformatics activities in ELIXIR (3D-Bioinfo Community).
F1000Research, 2020, 9:278
Chiffelle J, Genolet R, Perez MAS, Coukos G, Zoete V, Harari A.
T-cell repertoire analysis and metrics of diversity and clonality.
Chemical Biotechnology - Pharmaceutical Biotechnology, 2020, 65:284-295
Graciotti M, Marino F, Pak H, Baumgaertner P, Thierry AC , Chiffelle J, Perez MAS, Zoete V, Harari A, Bassani-Sternberg M, Kandalaft L.
Deciphering the Mechanisms of Improved Immunogenicity of Hypochlorous Acid-Treated Antigens in Anti-Cancer Dendritic Cell-Based
Vaccines.
Vaccines. 2020, 8(2)
Dheilly E, Battistello E, Katanayeva N, Sungalee S, Michaux J, Duns G, Wehrle S, Sordet-Dessimoz J, Mina M, Racle J, Farinha P, Coukos G, Gfeller D, Mottok A, Kridel R, Correia BE, Steidl C, Bassani-Sternberg M, Ciriello G, Zoete V, Oricchio E.
Cathepsin S Regulates Antigen Processing and T Cell Activity in Non-Hodgkin Lymphoma.
Cancer Cell. 2020, 37 (5):674
Bovay A, Zoete V, Rizkallah PJ, Beck K, Delbreil P, Speiser DE, Cole DK, Marraco SAF.
Identification of a superagonist variant of the immunodominant Yellow fever virus epitope NS4b(214-222) by combinatorial peptide library screening.
Molecular Immunology. 2020, 125:43-50
Spodzieja M, Kuncewicz K, Sieradzan A, Karczynska A, Iwaszkiewicz J, Cesson V, Wegrzyn K, Zhukov, Maszota-Zieleniak M, Michielin O, Speiser DE, Zoete V, Derre L, Rodziewicz-Motowidlo S.
Disulfide-Linked Peptides for Blocking BTLA/HVEM Binding.
International Journal Of Molecular Sciences, 2020, 21 (2)
Ansar M, Ebstein F, Ozkoc H, Paracha SA, Iwaszkiewicz J, Gesemann M, Zoete V, Ranza E, Santoni FA, Sarwar MT, Ahmed J, Kruger E, Bachmann-Gagescu R, Antonarakis SE.
Biallelic variants in PSMB1 encoding the proteasome subunit beta 6 cause impairment of proteasome function, microcephaly, intellectual disability, developmental delay and short stature.
Human Molecular Genetics. 2020, 29(7):1132-1143
Daina A, Michielin O, Zoete V.
SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules.
Nucleic Acids Res. 2019, 47(W1):W357-W364
Daina A, Zoete V.
Application of the SwissDrugDesign Online Resources in Virtual Screening.
Int J Mol Sci. 2019, 20(18). pii: E4612
El Hage K, Zoete V.
Strong Enrichment of Aromatic and Sulfur-Containing Residues in Ligand-Protein Binding Sites.
J Chem Inf Model. 2019, 59(11):4921-4928
Röhrig UF, Reynaud A, Majjigapu SR, Vogel P, Pojer F, Zoete V.
Inhibition Mechanisms of Indoleamine 2,3-Dioxygenase 1 (IDO1).
J Med Chem. 2019, 62(19):8784-8795
Perez MAS, Bassani-Sternberg M, Coukos G, Gfeller D, Zoete V.
Analysis of Secondary Structure Biases in Naturally Presented HLA-I Ligands.
Front Immunol. 2019, 10:2731
Zoete V, Coukos G.
Going Beyond the Sequences: TCR Binding Patterns at the Service of Cancer Detection.
Cancer Res. 2019, 79(7):1299-1301
Bargeton B, Iwaszkiewicz J, Bonifacio G, Roy S, Zoete V, Kellenberger S.
Mutations in the palm domain disrupt modulation of acid-sensing ion channel 1a currents by neuropeptides.
Sci Rep. 2019, 9(1):2599
Bibert S, Piret J, Quinodoz M, Collinet E, Zoete V, Michielin O, Menasria R, Meylan P, Bihl T, Erard V, Fellmann F, Rivolta C, Boivin G, Bochud PY.
Herpes simplex encephalitis in adult patients with MASP-2 deficiency.
PLoS Pathog. 2019, 15(12):e1008168.
Ansar M, Ullah F, Paracha SA, Adams DJ, Lai A, Pais L, Iwaszkiewicz J, Millan F, Sarwar MT, Agha Z, Shah SF, Qaisar AA, Falconnet E, Zoete V, Ranza E, Makrythanasis P, Santoni FA, Ahmed J, Katsanis N, Walsh C, Davis EE, Antonarakis SE.
Bi-allelic Variants in DYNC1I2 Cause Syndromic Microcephaly with Intellectual Disability, Cerebral Malformations, and Dysmorphic Facial Features.
Am J Hum Genet. 2019, 104(6):1073-1087.
Ansar M, Paracha SA, Serretti A, Sarwar MT, Khan J, Ranza E, Falconnet E, Iwaszkiewicz J, Shah SF, Qaisar AA, Santoni FA, Zoete V, Megarbane A, Ahmed J, Colombo R, Makrythanasis P, Antonarakis SE.
Biallelic variants in FBXL3 cause intellectual disability, delayed motor development and short stature.
Hum Mol Genet. 2019, 28(6):972-979.
Daina A, Blatter MC, Gerritsen VB, Zoete V.
Educational Tools to Introduce Computer-Aided Drug Design to Students and to the Public at Large.
Chimia (Aarau). 2018, 72(1):55-61
Daina A, Giuliano G, Pietra C, Wang J, Chi Y, Zou Z, Li F, Yan Z, Zhou Y, Guainazzi A, Rubio SG, Zoete V.
Rational Design, Synthesis and Pharmacological Characterization of Novel Ghrelin Receptor Inverse Agonists as Potential Treatment against Obesity-related Metabolic Diseases.
J. Med. Chem. 2018, 61(24):11039–11060
Kapuria V, Röhrig UF, Waridel P, Lammers F, Borodkin VS, van Aalten DMF, Zoete V, Herr W.
The conserved threonine-rich region of the HCF-1PRO repeat activates promiscuous OGT:UDP-GlcNAc glycosylation and proteolysis activities.
J Biol Chem. 2018, 293(46):17754-17768
Front S, Almeida S, Zoete V, Charollais-Thoenig J, Gallienne E, Marmy C, Pilloud V, Marti R, Wood T, Martin OR, Demotz S.
4-epi-Isofagomine derivatives as pharmacological chaperones for the treatment of lysosomal diseases linked to β-galactosidase mutations: Improved synthesis and biological investigations.
Bioorg Med Chem. 2018 pii: S0968-0896(18):31372-5
Ansar M, Riazuddin S, Sarwar MT, Makrythanasis P, Paracha SA, Iqbal Z, Khan J, Assir MZ, Hussain M, Razzaq A, Polla DL, Taj AS, Holmgren A, Batool N, Misceo D, Iwaszkiewicz J, de Brouwer APM, Guipponi M, Hanquinet S, Zoete V, Santoni FA, Frengen E, Ahmed J, Riazuddin S, van Bokhoven H, Antonarakis SE.
Biallelic variants in LINGO1 are associated with autosomal recessive intellectual disability, microcephaly, speech and motor delay.
Genet Med., 2018, 20(7):778-784.
Battistello E, Katanayeva N, Dheilly E, Tavernari D, Donaldson MC, Bonsignore L, Thome M, Christie AL, Murakami MA, Michielin O, Ciriello G, Zoete V, Oricchio E.
Pan-SRC kinase inhibition blocks B-cell receptor oncogenic signaling in non-Hodgkin lymphoma.
Blood. 2018, 131(21):2345-2356
Tanyi JL, Bobisse S, Ophir E, Tuyaerts S, Roberti A, Genolet R, Baumgartner P, Stevenson BJ, Iseli C, Dangaj D, Czerniecki B, Semilietof A, Racle J, Michel A, Xenarios I, Chiang C, Monos DS, Torigian DA, Nisenbaum HL, Michielin O, June CH, Levine BL, Powell DJ Jr, Gfeller D, Mick R, Dafni U, Zoete V, Harari A, Coukos G, Kandalaft LE.
Personalized cancer vaccine effectively mobilizes antitumor T cell immunity in ovarian cancer.
Sci Transl Med. 2018, 10(436):eaao5931
Bobisse S, Genolet R, Roberti A, Tanyi JL, Racle J, Stevenson BJ, Iseli C, Michel A, Le Bitoux MA, Guillaume P, Schmidt J, Bianchi V, Dangaj D, Fenwick C, Derré L, Xenarios I, Michielin O, Romero P, Monos DS, Zoete V, Gfeller D, Kandalaft LE, Coukos G, Harari A.
Sensitive and frequent identification of high avidity neo-epitope specific CD8 + T cells in immunotherapy-naive ovarian cancer.
Nat Commun. 2018, 9(1):1092
Bovay A, Zoete V, Dolton G, Bulek AM, Cole DK, Rizkallah PJ, Fuller A, Beck K, Michielin O, Speiser DE, Sewell AK, Fuertes Marraco SA.
T cell receptor alpha variable 12-2 bias in the immunodominant response to Yellow fever virus.
Eur J Immunol. 2018, 48(2):258-272
Makrythanasis P, Maroofian R, Stray-Pedersen A, Musaev D, Zaki MS, Mahmoud IG, Selim L, Elbadawy A, Jhangiani SN, Coban Akdemir ZH, Gambin T, Sorte HS, Heiberg A, McEvoy-Venneri J, James KN, Stanley V, Belandres D, Guipponi M, Santoni FA, Ahangari N, Tara F, Doosti M, Iwaszkiewicz J, Zoete V, Backe PH, Hamamy H, Gleeson JG, Lupski JR, Karimiani EG, Antonarakis SE.
Biallelic variants in KIF14 cause intellectual disability with microcephaly.
Eur J Hum Genet. 2018, 26(3):330-339
Daina A, Michielin O, Zoete V.
SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules.
Sci. Rep. 2017, 7:42717
Chaskar P, Zoete V, Röhrig UF.
On-the-Fly QM/MM Docking with Attracting Cavities.
J Chem Inf Model. 2017, 57(1):73-84
Daina A, Blatter M-C, Baillie Gerritsen V, Palagi PM, Marek D, Xenarios I, Schwede T, Michielin O, Zoete V
Drug Design Workshop: A Web-Based Educational Tool To Introduce Computer-Aided Drug Design to the General Public.
J. Chem. Educ., 2017, 94 (3):335–344
Röhrig UF, Zoete V, Michielin O.
The Binding Mode of N-Hydroxyamidines to Indoleamine 2,3-Dioxygenase 1 (IDO1).
Biochemistry. 2017, 56(33):4323-4325
Merkle PS, Irving M, Hongjian S, Ferber M, Jørgensen TJD, Scholten K, Luescher I, Coukos G, Zoete V, Cuendet MA, Michielin O, Rand KD.
The T-Cell Receptor Can Bind to the Peptide-Bound Major Histocompatibility Complex and Uncomplexed β2-Microglobulin through Distinct Binding Sites.
Biochemistry. 2017, 56(30):3945-3961
Spodzieja M, Lach S, Iwaszkiewicz J, Cesson V, Kalejta K, Olive D, Michielin O, Speiser DE, Zoete V, Derré L, Rodziewicz-Motowidło S.
Design of short peptides to block BTLA/HVEM interactions for promoting anticancer T-cell responses.
PLoS One. 2017, 12(6):e0179201
Crippa S, Ancey PB, Vazquez J, Angelino P, Rougemont AL, Guettier C, Zoete V, Delorenzi M, Michielin O, Meylan E.
Mutant CTNNB1 and histological heterogeneity define metabolic subtypes of hepatoblastoma.
EMBO Mol Med. 2017 Nov,9(11):1589-1604
Zoete V, Daina A, Bovigny C, Michielin O.
SwissSimilarity. A web tool for low to ultra high-throughput ligand-based virtual screening.
J Chem Inf Model. 2016 Aug 22;56(8):1399-404.
Daina A., Zoete, V.
A BOILED-Egg to predict gastrointestinal aborption and brain penetration of small molecules.
ChemMedChem 2016, 11(11):1117-21.
Zoete V, Schuepbach T, Bovigny C, Chaskar P, Daina A, Röhrig UF, Michielin O.
Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth
attracting landscape.
J Comput Chem. 2016,37(4):437-47.
Röhrig UF, Majjigapu SR, Caldelari D, Dilek N, Reichenbach P, Ascencao K, Irving M, Coukos G, Vogel P, Zoete
V, Michielin O.
1,2,3-Triazoles as inhibitors of indoleamine 2,3-dioxygenase 2 (IDO2).
Bioorg Med Chem Lett. 2016 Sep 1;26(17):4330-3.
Murone M, Vaslin Chessex A, Attinger A, Ramachandra R, Shetty SJ, Daginakatte G, Sengupta S, Marappan S,
Dhodheri S, Rigotti S, Bachav Y, Brienza S, Traxler P, Lang M, Aguet M, Zoete V, Michielin O, Nicholas C,
Johnson F, Ramachandra M and McAllister A
Debio 0617B Inhibits Growth of STAT3-Driven Solid Tumors through Combined Inhibition of JAK, SRC, and
Class III/V Recept
or Tyrosine Kinases
Mol Cancer Ther. 2016 Oct;15(10):2334-2343.
Kapuria V, Röhrig UF, Bhuiyan T, Borodkin VS, van Aalten DM, Zoete V, Herr W.
Proteolysis of HCF-1 by Ser/Thr glycosylation-incompetent O-GlcNAc transferase:UDP-GlcNAc complexes.
Genes Dev. 2016, 30(8):960-72.
Bensasson RV, Dinkova-Kostova AT, Zheng S, Saito A, Li W, Zoete V, Honda T.
Electron affinity of tricyclic, bicyclic, and monocyclic compounds containing cyanoenones correlates
with their potency as inducers of a cytoprotective enzyme.
Bioorg Med Chem Lett. 2016 Sep 1;26(17):4345-9.
Bonilla X, Parmentier L, King B, Bezrukov F, Kaya G, Zoete V, Seplyarskiy VB, Sharpe HJ, McKee T, Letourneau
A, Ribaux PG, Popadin K, Basset-Seguin N, Chaabene RB, Santoni FA, Andrianova MA, Guipponi M, Garieri M,
Verdan C, Grosdemange K, Sumara O, Eilers M, Aifantis I, Michielin O, de Sauvage FJ, Antonarakis SE,
Nikolaev SI.
Genomic analysis identifies new drivers and progression pathways in skin basal cell carcinoma.
Nat Genet. 2016, 48(4):398-406.
Golay J, Choblet S, Iwaszkiewicz J, Cérutti P, Ozil A, Loisel S, Pugnière M, Ubiali G, Zoete V, Michielin O,
Berthou C, Kadouche J, Mach JP, Duonor-Cérutti M.
Design and Validation of a Novel Generic Platform for the Production of Tetravalent IgG1-like Bispecific
Antibodies.
J Immunol. 2016, 196(7):3199-211.
SIB Swiss Institute of Bioinformatics Members.
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.
Nucleic Acids Res. 2016 Jan 4;44(D1):D27-37.
Baumgaertner P, Costa Nunes C, Cachot A, Maby-El Hajjami H, Cagnon L, Braun M, Derré L, Rivals JP, Rimoldi D,
Gnjatic S, Abed Maillard S, Marcos Mondéjar P, Protti MP, Romano E, Michielin O, Romero P, Speiser DE,
Jandus C.
Vaccination of stage III/IV melanoma patients with long NY-ESO-1 peptide and CpG-B elicits robust CD8+
and CD4+ T-cell responses with multiple specificities including a novel DR7-restricted epitope.
Oncoimmunology. 2016 Sep 9;5(10):e1216290.
Hoeller C, Michielin O, Ascierto PA, Szabo Z, Blank CU.
Systematic review of the use of granulocyte-macrophage colony-stimulating factor in patients with
advanced melanoma.
Cancer Immunol Immunother. 2016 Sep;65(9):1015-34.
Martins F, Orcurto A, Michielin O, Coukos G.
[Principles of adoptive cell therapy based on "Tumor Infiltrating Lymphocytes"].
Rev Med Suisse. 2016 May 18;12(519):989-93. French.
Gonzales C, Yoshihara HA, Dilek N, Leignadier J, Irving M, Mieville P, Helm L, Michielin O, Schwitter J.
In-Vivo Detection and Tracking of T Cells in Various Organs in a Melanoma Tumor Model by 19F-Fluorine
MRS/MRI.
PLoS One. 2016 Oct 13;11(10):e0164557.
Vallois D, Dobay MP, Morin RD, Lemonnier F, Missiaglia E, Juilland M, Iwaszkiewicz J, Fataccioli V, Bisig B,
Roberti A, Grewal J, Bruneau J, Fabiani B, Martin A, Bonnet C, Michielin O, Jais JP, Figeac M, Bernard OA,
Delorenzi M, Haioun C, Tournilhac O, Thome M, Gascoyne RD, Gaulard P, de Leval L.
Activating mutations in genes related to TCR signaling in angioimmunoblastic and other follicular helper
T-cell-derived lymphomas.
Blood. 2016 Sep 15;128(11):1490-502.
Dummer R, Siano M, Hunger RE, Lindenblatt N, Braun R, Michielin O, Mihic-Probst D, von Moos R, Najafi Y,
Guckenberger M, Arnold A.
The updated Swiss guidelines 2016 for the treatment and follow-up of cutaneous melanoma.
Swiss Med Wkly. 2016, 146:w14279
Röhrig UF, Majjigapu SR, Vogel P, Zoete V, Michielin O.
Challenges in the Discovery of Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitors.
J Med Chem. 2015, 58(24):9421-37.
Gfeller D, Zoete V.
Protein homology reveals new targets for bioactive small molecules.
Bioinformatics. 2015, 31(16):2721-7.
Bhuiyan T, Waridel P, Kapuria V, Zoete V, Herr W.
Distinct OGT-Binding Sites Promote HCF-1 Cleavage.
PLoS One. 2015 Aug 25;10(8):e0136636.
Akyuz N, Georgieva ER, Zhou Z, Stolzenberg S, Cuendet MA, Khelashvili G, Altman RB, Terry DS, Freed JH,
Weinstein H, Boudker O, Blanchard SC.
Transport domain unlocking sets the uptake rate of an aspartate transporter.
Nature. 2015, 518(7537):68-73.
Demaria O, De Gassart A, Coso S, Gestermann N, Di Domizio J, Flatz L, Gaide O, Michielin O, Hwu P, Petrova
TV, Martinon F, Modlin RL, Speiser DE, Gilliet M.
STING activation of tumor endothelial cells initiates spontaneous and therapeutic antitumor immunity.
Proc Natl Acad Sci U S A. 2015, in press
Romano E, Kusio-Kobialka M, Foukas PG, Baumgaertner P, Meyer C, Ballabeni P, Michielin O, Weide B, Romero P,
Speiser DE.
Ipilimumab-dependent cell-mediated cytotoxicity of regulatory T cells ex vivo by nonclassical monocytes
in melanoma patients.
Proc Natl Acad Sci USA. 2015, 112(19):6140-5.
Michielin O, Hoeller C.
Gaining momentum: New options and opportunities for the treatment of advanced melanoma.
Cancer Treat Rev. 2015, 41(8):660-70.
Legat A, Maby-El Hajjami H, Baumgaertner P, Cagnon L, Abed-Maillard S, Geldhof C, Iancu EM, Lebon L,
Guillaume P, Dojcinovic D, Michielin O, Romano E, Berthod G, Rimoldi D, Triebel F, Luescher I, Rufer N,
Speiser DE.
Vaccination with LAG-3Ig (IMP321) and peptides induces specific CD4 and CD8 T-cell responses in
metastatic melanoma patients - report of a phase I/IIa clinical trial.
Clin Cancer Res. 2015 Oct 23. pii: clincanres.1212.2015.
Mangana J, Cheng PF, Schindler K, Weide B, Held U, Frauchiger AL, Romano E, Kähler KC, Rozati S, Rechsteiner
M, Moch H, Michielin O, Garbe C, Hauschild A, Hoeller C, Dummer R, Goldinger SM.
Analysis of BRAF and NRAS Mutation Status in Advanced Melanoma Patients Treated with Anti-CTLA-4
Antibodies: Association with Overall Survival?
PLoS One. 2015 Oct 1;10(10):e0139438.
Moura B, Homicsko K, Berthod G, Cerottini JP, Guggisberg D, Gaide O, Maillard MH, Michielin O.
New melanoma immunotherapies: mechanisms of action, efficiency and management of toxicities.
Rev Med Suisse. 2015, 11(475):1108, 1110-4
Daina A, Michielin O, Zoete V.
iLOGP: A Simple, Robust, and Efficient Description of n-Octanol/Water Partition Coefficient for Drug
Design Using the GB/SA Approach.
J Chem Inf Model. 2014, 54(12):3284-301.
Chaskar P, Zoete V, Röhrig UF.
Toward On-The-Fly Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: Development and Benchmark of
a Scoring Function.
J Chem Inf Model. 2014, 54(11):3137-52.
Gfeller D, Grosdidier A, Wirth M, Daina A, Michielin O, Zoete V.
SwissTargetPrediction: a web server for target prediction of bioactive small molecules.
Nucleic Acids Res. 2014, 42(Web Server issue):W32-8
Röhrig UF, Majjigapu SR, Chambon M, Bron S, Pilotte L, Colau D, Van den Eynde BJ, Turcatti G, Vogel P, Zoete
V, Michielin O.
Detailed analysis and follow-up studies of a high-throughput screening for indoleamine 2,3-dioxygenase 1
(IDO1) inhibitors.
Eur J Med Chem. 2014, 12;84:284-301
Stockinger H, Altenhoff AM, Arnold K, Bairoch A, Bastian F, Bergmann S, Bougueleret L, Bucher P, Delorenzi M,
Lane L, Le Mercier P, Lisacek F, Michielin O, Palagi PM, Rougemont J, Schwede T, von Mering C, van Nimwegen
E, Walther D, Xenarios I, Zavolan M, Zdobnov EM, Zoete V, Appel RD.
Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.
Nucleic Acids Res. 2014, 42(Web Server issue):W436-41
Choudhary V, Darwiche R, Gfeller D, Zoete V, Michielin O, Schneiter R.
The caveolin-binding motif of the pathogen-related yeast protein Pry1, a member of the CAP protein
superfamily, is required for in vivo export of cholesteryl acetate.
J Lipid Res. 2014, 55(5):883-94.
Crisante G, Battista L, Iwaszkiewicz J, Nesca V, Mérillat AM, Sergi C, Zoete V, Frateschi S, Hummler E.
The CAP1/Prss8 catalytic triad is not involved in PAR2 activation and protease nexin-1 (PN-1)
inhibition.
FASEB J. 2014, 28(11):4792-805.
Barras D, Chevalier N, Zoete V, Dempsey R, Lapouge K, Olayioye MA, Michielin O, Widmann C.
A WXW Motif Is Required for the Anticancer Activity of the TAT-RasGAP317-326 Peptide.
J Biol Chem. 2014, 289(34):23701-11.
Peters S, Bouchaab H, Zimmerman S, Bucher M, Gaide O, Letovanec I, Homicsko K, Michielin O.
Dramatic response of vemurafenib-induced cutaneous lesions upon switch to dual BRAF/MEK inhibition in a
metastatic melanoma patient.
Melanoma Res. 2014, 24(5):496-500.
Bordry N, Costa-Nunes CM, Cagnon L, Gannon PO, Abed-Maillard S, Baumgaertner P, Murray T, Letovanec I, Lazor
R, Bouchaab H, Rufer N, Romano E, Michielin O, Speiser DE.
Pulmonary Sarcoid-like Granulomatosis after Multiple Vaccinations of a Long-term Surviving Patient with
Metastatic Melanoma.
Cancer Immunol Res. 2014, 2(12):1148-53.
Romano E, Michielin O.
Successes and limitations of targeted cancer therapy in melanoma.
Prog Tumor Res. 2014;41:78-88.
Romano E, Michielin O, Voelter V, Laurent J, Bichat H, Stravodimou A, Romero P, Speiser DE, Triebel F,
Leyvraz S, Harari A.
MART-1 peptide vaccination plus IMP321 (LAG-3Ig fusion protein) in patients receiving autologous PBMCs
after lymphodepletion: results of a Phase I trial.
J Transl Med. 2014, 12:97.
Meyer C, Cagnon L, Costa-Nunes CM, Baumgaertner P, Montandon N, Leyvraz L, Michielin O, Romano E, Speiser DE.
Frequencies of circulating MDSC correlate with clinical outcome of melanoma patients treated with
ipilimumab.
Cancer Immunol Immunother. 2014, 63(3):247-57.
Dummer R, Goldinger SM, Turtschi CP, Eggmann NB, Michielin O, Mitchell L, Veronese L, Hilfiker PR, Felderer
L, Rinderknecht JD.
Vemurafenib in patients with BRAF(V600) mutation-positive melanoma with symptomatic brain metastases:
final results of an open-label pilot study.
Eur J Cancer. 2014, 50(3):611-21.
Kvistborg P, Philips D, Kelderman S, Hageman L, Ottensmeier C, Joseph-Pietras D, Welters MJ, van der Burg S,
Kapiteijn E, Michielin O, Romano E, Linnemann C, Speiser D, Blank C, Haanen JB, Schumacher TN.
Anti-CTLA-4 therapy broadens the melanoma-reactive CD8+ T cell response.
Sci Transl Med. 2014, 6(254):254ra128.
Zoete V, Irving M, Ferber M, Cuendet M, Michielin O.
Structure-based, rational design of T cell receptors.
Frontiers in Immunology, 2013, ;4:268
Ding J, Loizides-Mangold U, Rando G, Zoete V, Michielin O, Reddy JK, Wahli W, Riezman H, Thorens B.
The peroxisomal enzyme L-PBE is required to prevent the dietary toxicity of medium chain fatty acids.
Cell Reports, 2013, 5(1):248-58..
Fagerberg T, Zoete V, Viatte S, Baumgaertner P, Alves PM, Romero P, Speiser DE, Michielin O.
Prediction of cross-recognition of peptide-HLA A2 by
Melan-A-specific CTLs using three-dimensional quantitative structure-activity relationships
PLOS One, 2013, 8(7):e65590.
Wirth M, Volkamer A, Zoete V, Rippmann F, Michielin O, Rarey M, Sauer WH.
Protein pocket and ligand shape comparison and its application in virtual screening.
J Comput Aided Mol Des. 2013, 27(6):511-24.
Gfeller D, Michielin O, Zoete V.
SwissSidechain: a molecular and structural database of non-natural sidechains.
Nucleic Acids Res. 2013, 41(Database issue), D327-32.
Wirth M, Zoete V, Michielin O, Sauer W.
SwissBioisostere: A database of molecular replacements for ligand design.
Nucleic Acids Res. 2013, 41(Database issue), D1137-43.
Chen S, Gfeller D, Buth SA, Michielin O, Leiman PG, Heinis C.
Improving binding affinity and stability of Peptide ligands by substituting glycines with d-amino acids.
Chembiochem. 2013, 14, 1316-22.
Lapouge K, Perozzo R, Iwaszkiewicz J, Bertelli C, Zoete V, Michielin O, Scapozza L, Haas D.
RNA pentaloop structures as effective targets of regulators belonging to the RsmA/CsrA protein family.
RNA Biol. 2013, 10.
Gautschi O, Peters S, Zoete V, Aebersold-Keller F, Strobel K, Schwizer B, Hirschmann A, Michielin O, Diebold
J.
Lung adenocarcinoma with BRAF G469L mutation refractory to vemurafenib.
Lung Cancer. 2013, 82(2):365-7
Romano E, Pradervand S, Paillusson A, Weber J, Harshman K, Muehlethaler K, Speiser DE, Peters S, Rimoldi D,
Michielin O.
Identification of multiple mechanisms of resistance to vemurafenib in a patient with BRAFV600E-mutated
cutaneous melanoma successfully rechallenged after progression.
Clin Cancer Res. 2013, in press.
Demierre N, Zoete V, Michielin O, Stauffer E, Zimmermann DR, Betticher DC, Peters S.
A dramatic lung cancer course in a patient with a rare EGFR germline mutation exon 21 V843I: Is EGFR TKI
resistance predictable?
Lung Cancer. 2013, 80, 81.
Hebeisen M, Baitsch L, Presotto D, Baumgaertner P, Romero P, Michielin O, Speiser DE, Rufer N.
SHP-1 phosphatase activity counteracts increased T cell receptor affinity.
J Clin Invest. 2013, 123, 1044
Peters S, Michielin O, Zimmermann S.
Dramatic Response Induced by Vemurafenib in a BRAF V600E-Mutated Lung Adenocarcinoma.
J Clin Oncol. 2013, 31, e341-4.
Tzika E, Moura B, Romano E, Michielin O.
New therapeutic weapons in stage IV melanoma.
Rev Med Suisse. 2013, 9, 1095
Ferber M, Zoete V, Michielin O.
T-cell receptors binding orientation over peptide/MHC class I is driven by long-range interactions.
PLoS ONE 2012, 2012, 7, e5194
Röhrig UF, Majjigapu SR, Grosdidier A, Bron S, Stroobant V, Pilotte L, Colau D, Vogel P, Van den Eynde
BJ, Zoete V, Michielin O.
Rational Design of 4-Aryl-1,2,3-Triazoles for Indoleamine 2,3-Dioxygenase 1 Inhibition.
J. Med. Chem., 2012, 14, 5270-90.
Irving M, Zoete V, Hebeisen M, Schmid D, Baumgartner P, Guillaume P, Romero P, Speiser D, Luescher I, Rufer
N, Michielin O.
Interplay between T cell receptor binding kinetics and the level of cognate peptide presented by major
histocompatibility complexes governs CD8+ T cell responsiveness.
J. Biol. Chem., 2012, 287, 23068-78.
Gfeller D, Michielin O, Zoete V.
Expanding molecular modeling and design tools to non-natural sidechains.
J. Comput. Chem. 2012, 33, 1525-35.
Johansson MU, Zoete V, Michielin O, Guex N.
Defining and searching for structural motifs using DeepView/Swiss-PdbViewer.
BMC Bioinformatics. 2012, 13, 173.
Buey RM, Sen I, Kortt O, Mohan R, Gfeller D, Veprintsev D, Kretzschmar I, Scheuermann J, Neri D, Zoete V,
Michielin O, de Pereda JM, Akhmanova A, Volkmer R, Steinmetz MO.
Sequence Determinants of a Microtubule Tip Localization Signal (MtLS).
J. Biol. Chem., 2012, 287, 28227-42.
Baitsch L, Legat A, Barba L, Fuertes Marraco SA, Rivals JP, Baumgaertner P, Christiansen-Jucht C, Bouzourene
H, Rimoldi D, Pircher H, Rufer N, Matter M, Michielin O, Speiser DE.
Extended co-expression of inhibitory receptors by human CD8 T-cells depending on differentiation,
antigen-specificity and anatomical localization.
PLoS One., 2012, 7, e30852.
Baumgaertner P, Jandus C, Rivals JP, Derré L, Lövgren T, Baitsch L, Guillaume P, Luescher IF, Berthod G,
Matter M, Rufer N, Michielin O, Speiser DE.
Vaccination-induced functional competence of circulating human tumor-specific CD8 T-cells.
Int. J. Cancer., 2012, 130, 2607-17.
Schraml P, von Teichman A, Mihic-Probst D, Simcock M, Ochsenbein A, Dummer R, Michielin O, Seifert B,
Schläppi M, Moch H, von Moos R.
Predictive value of the MGMT promoter methylation status in metastatic melanoma patients receiving
first-line temozolomide plus bevacizumab in the trial SAKK 50/07.
Oncol Rep. 2012, 28, 654-8.
von Moos R, Seifert B, Simcock M, Goldinger SM, Gillessen S, Ochsenbein A, Michielin O, Cathomas R, Schläppi
M, Moch H, Schraml PH, Mjhic-Probst D, Mamot C, Schönewolf N, Dummer R; Swiss Group for Clinical Cancer
Research (SAKK).
First-line temozolomide combined with bevacizumab in metastatic melanoma: a multicentre phase II trial
(SAKK 50/07).
Ann. Oncol., 2012, 23, 531-6.
Goldinger SM, Dummer R, Baumgaertner P, Mihic-Probst D, Schwarz K, Hammann-Haenni A, Willers J, Geldhof C,
Prior JO, Kündig TM, Michielin O, Bachmann MF, Speiser DE.
Nano-particle vaccination combined with TLR-7 and -9 ligands triggers memory and effector CD8⁺ T-cell
responses in melanoma patients.
Eur J Immunol. 2012, 11, 3049-61.
Berthod G, Lazor R, Letovanec I, Romano E, Noirez L, Mazza Stalder J, Speiser DE, Peters S, Michielin O.
Pulmonary sarcoid-like granulomatosis induced by ipilimumab.
J Clin Oncol. 2012, 30, e156-9.
Nikolaev SI, Rimoldi D, Iseli C, Valsesia A, Robyr D, Gehrig C, Harshman K, Guipponi M, Bukach O, Zoete V,
Michielin O, Muehlethaler K, Speiser D, Beckmann JS, Xenarios I, Halazonetis TD, Jongeneel CV, Stevenson BJ,
Antonarakis SE.
Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma.
Nat Genet., 2011, 44, 133-9.
Grosdidier A, Zoete V, Michielin O.
SwissDock, a protein-small molecule docking web service based on EADock DSS.
Nucleic Acids Res., 2011, 39(Web Server issue), W270-7.
Grosdidier A, Zoete V, Michielin O.
Fast docking using the CHARMM force field with EADock DSS.
J Comput Chem., 2011, 32, 2149–2159.
Zoete V, Cuendet MA, Grosdidier A, Michielin O.
SwissParam: a fast force field generation tool for small organic molecules.
J Comput Chem., 2011, 32, 2359-68.
Cuendet MA, Zoete V, Michielin O.
How T cell receptors interact with peptide-MHCs: a multiple steered molecular dynamics study.
Proteins., 2011, 79, 3007-24.
Leimgruber A, Ferber M, Irving M, Hussain-Kahn H, Wieckowski S, Derré L, Rufer N, Zoete V, Michielin O.
TCRep 3D: an automated in silico approach to study the structural properties of TCR repertoires.
PLoS One., 2011, 6, e26301.
Speiser DE, Wieckowski S, Gupta B, Iancu EM, Baumgaertner P, Baitsch L, Michielin O, Romero P, Rufer N.
Single cell analysis reveals similar functional competence of dominant and nondominant CD8 T-cell
clonotypes.
Proc Natl Acad Sci U S A., 2011, 108, 15318-23.
Rahm N, Yap M, Snoeck J, Zoete V, Muñoz M, Radespiel U, Zimmermann E, Michielin O, Stoye JP, Ciuffi A,
Telenti A.
Unique spectrum of activity of prosimian TRIM5alpha against exogenous and endogenous retroviruses.
J Virol., 2011, 85, 4173-83.
Maillard PV, Zoete V, Michielin O, Trono D.
Homology-based identification of capsid determinants that protect HIV1 from human TRIM5α restriction.
J Biol Chem., 2011, 286, 8128-40.
Sala E, Guasch L, Iwaszkiewicz J, Mulero M, Salvadó MJ, Bladé C, Ceballos M, Valls C, Zoete V, Grosdidier A,
Garcia-Vallvé S, Michielin O, Pujadas G.
Identification of human IKK-2 inhibitors of natural origin (Part II): in Silico prediction of IKK-2
inhibitors in natural extracts with known anti-inflammatory activity.
Eur J Med Chem., 2011, 46, 6098-103.
Strasser B, Iwaszkiewicz J, Michielin O, Mayer A.
The V-ATPase proteolipid cylinder promotes the lipid-mixing stage of SNARE-dependent fusion of yeast
vacuoles.
EMBO J., 2011, 30, 4126-41.
Berthod G, Homicsko K, Bouchaab H, Matter M, Cerottini JP, Guggisberg D, Speiser D, Leyvraz S, Michielin
O.
Melanoma: a new therapeutic era.
Rev Med Suisse., 2011, 7, 1126-30.
Sala E, Guasch L, Iwaszkiewicz J, Mulero M, Salvadó MJ, Pinent M, Zoete V, Grosdidier A, Garcia-Vallvé S,
Michielin O, Pujadas G.
Identification of human IKK-2 inhibitors of natural origin (part I): modeling of the IKK-2 kinase
domain, virtual screening and activity assays.
PLoS One., 2011, 6, e16903.
Röhrig UF, Awad L, Grosdidier A, Larrieu P, Stroobant V, Colau D, Cerundolo V, Simpson AJ,
Vogel P, Van den Eynde BJ, Zoete V, Michielin O.
Rational Design of Indoleamine 2,3-Dioxygenase Inhibitors.
J Med Chem., 2010, 53, 1172-89.
Zoete V, Grosdidier A, Cuendet M, Michielin O
Use of the FACTS solvation model for protein-ligand docking calculations. Application to EADock.
J Mol Recognit., 2010, 23, 457-61.
Schupbach T, Zoete V, Tsakam-Sotche B, Michielin O.
Fourier transform convolution integrals applied to generalized Born molecular volume.
J Comput Chem, 2010, 31, 649-59.
Zoete V, Irving MB, Michielin O.
MM-GBSA binding free energy decomposition and T cell Receptor engineering.
J Mol. Recognition, 2010, 23, 142-52.
Bulliard Y, Narvaiza I, Bertero A, Peddi S, Röhrig UF, Ortiz M, Zoete V, Castro-Díaz N, Turelli P, Telenti A,
Michielin O, Weitzman MD, Trono D.
Structure-Function Analyses Point to a Polynucleotide-Accommodating Groove Essential for APOBEC3A
Restriction Activities.
J Virol. 2010, 85,1765-76.
Maillard PV, Zoete V, Michielin O, Trono D.
Homology-based identification of capsid determinants that protect HIV1 from human TRIM5{alpha}
restriction.
J Biol Chem. 2010, in press.
Liechti LA, Bernèche S, Bargeton B, Iwaszkiewicz J, Roy S, Michielin O, Kellenberger S.
A combined computational and functional approach identifies new residues involved in pH-dependent gating
of ASIC1a.
J Biol Chem. 2010, 285, 16315-29.
Caballero OL, Zhao Q, Rimoldi D, Stevenson BJ, Svobodová S, Devalle S, Röhrig UF, Pagotto A, Michielin O,
Speiser D, Wolchok JD, Liu C, Pejovic T, Odunsi K, Brasseur F, Van den Eynde BJ, Old LJ, Lu X, Cebon J,
Strausberg RL, Simpson AJ.
Frequent MAGE mutations in human melanoma.
PLoS One. 2010, 5, pii: e12773.
Derré L, Rivals JP, Jandus C, Pastor S, Rimoldi D, Romero P, Michielin O, Olive D, Speiser DE.
BTLA mediates inhibition of human tumor-specific CD8+ T cells that can be partially reversed by
vaccination.
J Clin Invest., 2010, 120, 157-67.
Schmid DA, Irving MB, Posevitz V, Hebeisen M, Posevitz-Fejfar A, Sarria JC, Gomez-Eerland R, Thome M,
Schumacher TN, Romero P, Speiser DE, Zoete V, Michielin O, Rufer N.
Evidence for a TCR affinity threshold delimiting maximal CD8 T cell function.
J Immunol. 2010, 184, 4936-46.
Bizzini A, Entenza JM, Michielin O, Arnold I, Erni B, Moreillon P.
A single mutation in enzyme I of the sugar phosphotransferase system confers penicillin tolerance to
Streptococcus gordonii.
Antimicrob Agents Chemother., 2010, 54, 259-66.
Grosdidier A, Zoete, V, Michielin O.
Blind docking of 260 protein-ligand complexes with EADock 2.0.
J Comput Chem, 2009, 30, 2021-2030.
Zoete V, Grosdidier A, Michielin O.
Docking, virtual high throughput screening and in silico fragment-based drug design.
J Cell Mol Med, 2009, 13, 238-48.
Bulliard Y, Turelli P, Röhrig UF, Zoete V, Mangeat B, Michielin O, Trono D.
Functional Analysis and Structural Modeling of Human APOBEC3G Reveals the
Role of Evolutionarily Conserved Elements in HIV-1 and Alu Inhibition.
J Virol, 2009, 83, 12611-21.
Hornitschek P, Lorrain S, Zoete V, Michielin O, Fankhauser C.
HFR1 inhibits the shade avoidance response by heterodimerizing with elongation growth
promoting bHLH class transcription factors.
EMBO J, 2009, 28, 3893-902.
Prior JO, Montemurro M, Orcurto MV, Michielin O, Luthi F,
Benhattar J, Guillou L, Elsig V, Stupp R, Delaloye AB, Leyvraz S.
Early prediction of response to sunitinib after imatinib failure by 18F-fluorodeoxyglucose positron
emission tomography in patients with gastrointestinal stromal tumor.
J Clin Oncol, 2009, 27, 439-445.
Michielin O, Rufer N, Romero P, Laurent J, Cerottini JP, Gugisberg D, Leyvraz S, Speiser DE.
New developments in cancer immunotherapy.
Rev Med Suisse, 2008, 4, 1248-1251.
Capendeguy O, Iwaszkiewicz J, Michielin O, Horisberger JD
The fourth extracellular loop of the alpha subunit of Na,K-ATPase. Functional evidence for close
proximity with the second extracellular loop.
J Biol Chem, 2008, 283, 27850- 27858.
Chodanowski P, Grosdidier A, Feytmans E, Michielin O
Local alignment refinement using structural assessment.
PLoS ONE, 2008, 3, e2645.
Cuendet MA, Michielin O
Protein-Protein Interaction Investigated by Steered Molecular Dynamics: the TCR-pMHC Complex.
Biophys J, 2008, 95, 3575-3590.
Rochat B, Zoete V, Grosdidier A, von Grunigen S, Marull M, Michielin O.
In vitro biotransformation of imatinib by the tumor expressed CYP1A1 and CYP1B1.
Biopharm Drug Dispos 29, 103-118 (2008).
Derre L, Bruyninx M, Baumgaertner P, Ferber M, Schmid D, Leimgruber A, Zoete V,
Romero P, Michielin O, Speiser DE, Rufer N.
Distinct sets of alphabeta TCRs confer similar recognition of tumor antigen NY-ESO-1157-165 by
interacting with its central Met/Trp residues.
Proc Natl Acad Sci U S A, 2008, 105, 15010-15015.
Voelter V, Rufer N, Reynard S, Greub G, Brookes R, Guillaume P, Grosjean F, Fagerberg T, Michielin O,
Rowland-Jones S, Pinilla C, Leyvraz S, Romero P, Appay V.
Characterization of Melan-A reactive memory CD8+ T cells in a healthy donor.
Int Immunol 20, 1087-1096 (2008).
Derré L, Ferber M, Touvrey C, Devevre E, Zoete V, Leimgruber A, Romero P, Michielin O, Lévy F, Speiser
DE.
A novel population of human melanoma-specific CD8 T cells recognizes Melan-AMART-1 immunodominant
nonapeptide but not the corresponding decapeptide.
J Immunol., 2007 Dec 1;179(11):7635-45.
Stupp R, Pica A, Mirimanoff RO, Michielin O.
A practical guide for the management of gliomas
Bull Cancer., 2007, 94(9), 817-22
Michielin O.
Application of molecular modelling to new therapeutic cancer approaches
Bull Cancer. 2007 Sep 1;94(9):763-8
Feige JN, Gelman L, Rossi D, Zoete V, Metivier R, Tudor C, Anghel SI, Grosdidier A, Lathion C, Engelborghs Y,
Michielin O, Wahli W, Desvergne B.
The endocrine disruptor mono-ethyl-hexyl-phthalate is a selective PPARgamma modulator which promotes
adipogenesis
J Biol Chem, 2007, 282(26), 19152-66
Alves PM, Viatte S, Fagerberg T, Michielin O, Bricard G, Bouzourene H, Vuilleumier H, Kruger T, Givel JC,
Lévy F, Speiser DE, Cerottini JC, Romero P.
Immunogenicity of the carcinoembryonic antigen derived peptide 694 in HLA-A2 healthy donors and
colorectal carcinoma patients
Cancer Immunol. Immunother., 2007, 56(11), 1795-805
Zhang KL, Mangeat B, Ortiz M, Zoete V, Trono D, Telenti A, Michielin O.
Model Structure of Human APOBEC3G
PLoS ONE., 2007, 2(4), e378
Zoete V, Grosdidier A, Michielin O.
Peroxisome proliferator-activated receptor structures: Ligand specificity, molecular switch and
interactions with regulators
Biochim. Biophys. Acta, 2007, 1771(8), 915-25
Grosdidier A, Zoete V, Michielin O.
EADock: docking of small molecules into protein active sites with a multiobjective evolutionary
optimization
Proteins, 2007, 67(4): 1010-25
Zoete V, Michielin O.
Comparison between computational alanine scanning and per-residue binding free energy decomposition for
protein-protein association using MM-GBSA: application to the TCR-p-MHC complex
Proteins, 2007, 67(4): 1026-47
Michalik L, Zoete V, Krey G, Grosdidier A, Gelman L, Chodanowski P, Feige JN, Desvergne B, Wahli W, Michielin
O.
Combined simulation and mutagenesis analyses reveal the involvement of key residues for peroxisome
proliferator-activated receptor alpha helix 12 dynamic behavior
J. Biol. Chem., 2007, 282(13): 9666-77
Butticaz C, Michielin O, Wyniger J, Telenti A, Rothenberger S.
Silencing of both beta-TrCP1 and HOS (beta-TrCP2) is required to suppress human immunodeficiency virus
type 1 Vpu-mediated CD4 down-modulation
J. Virol., 2007, 81(3): 1502-5
Colombetti S, Fagerberg T, Baumgartner P, Chapatte L, Speiser DE, Rufer N, Michielin O, Levy F.
Impact of orthologous Melan-A peptide immunizations on the anti-self Melan-A/HLA-A2 T cell
cross-reactivity
J Immunology, 2006, 176 (11): 6560-6567
Aublin A, Ciofani M, Willkomm N, Hamrouni A, Szymczak-Workman AL, Takahashi T, Sandjeu Y, Guillaume P,
Vignali DA, Michielin O, Zúñiga-Pflücker JC, Maryanski JL.
A natural structural variant of the mouse TCR beta-chain displays intrinsic receptor function and
antigen specificity
J Immunology, 2006, 177 (12): 8587-8594
Yip YL, Zoete V, Scheib H, Michielin O.
Structural assessment of single amino acid mutations: Application to TP53 function
Human Mutation, 2006, 27(9): 926-937
Capendeguy O, Chodanowski P, Michielin O, Horisberger JD.
Access of extracellular cations to their binding sites in Na, K-ATPase: Role of the second extracellular
loop of the alpha subunit
J Gen Physiol, 2006, 127(3): 341-352
Fagerberg T, Cerottini JC, Michielin O.
Structural prediction of peptides bound to MHC class I
J Mol Biol, 2006, 356(2): 521-46
Koch M, Schmid F, Zoete V, Meuwly M.
Insulin: a model system for nanomedicine?
Nanomedicine, 2006, 1(3): 373-8
Suarez M, Haenni M, Canarelli S, Fisch F, Chodanowski P, Servis C, Michielin O, Freitag R, Moreillon P,
Mermod N.
Structure-function characterization and optimization of a plant-derived antibacterial peptide
Antimicrob Agents Chemother. 2005, 49(9): 3847-57
De Los Rios P, Cecconi F, Pretre A, Dietler G, Michielin O, Piazza F, Juanico B.
Functional dynamics of PDZ binding domains: a normal-mode analysis
Biophys J, 2005, 89(1): 14-21
Michielin O, Blanchet JS, Fagerberg T, Valmori D, Rubio-Godoy V, Speiser D, Ayyoub M, Alves P, Luescher I,
Gairin JE, Cerottini JC, Romero P.
Tinkering with nature: the tale of optimizing peptide based cancer vaccines
Cancer Treat Res, 2005,123: 267-91
Filges I, Zaman K, Michielin O, Vulliémoz D, Perey L, Stupp R.
Present chemoprevention and future vision
Rev Med Suisse, 2005, 1(20):1343-6, 1349
Cebecauer M, Guillaume P, Mark S, Michielin O, Boucheron N, Bezard M, Meyer BH, Segura JM, Vogel H, Luescher
IF.
CD8+ cytotoxic T lymphocyte activation by soluble major histocompatibility complex-peptide dimmers
J Biol Chem, 2005, 280(25): 23820-8
Li C, Grosdidier A, Crambert G, Horisberger JD, Michielin O, Geering K.
Structural and functional interaction sites between Na,K-ATPase and FXYD proteins
J Biol Chem, 2004, 279(37): 38895-902
Hauert J, Fernandez-Carneado J, Michielin O, Mathieu S, Grell D, Schapira M, Spertini O, Mutter M,
Tuchscherer G, Kovacsovics T.
A template-assembled synthetic protein surface mimetic of the von Willebrand factor A1 domain inhibits
botrocetin-induced platelet aggregation
Chembiochem, 2004, 5(6): 856-64
Horisberger JD, Kharoubi-Hess S, Guennoun S, Michielin O.
The fourth transmembrane segment of the Na,K-ATPase alpha subunit: a systematic mutagenesis study
J Biol Chem, 2004, 279(28): 29542-50