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Items: 1 to 50 of 107

1.

The conserved threonine-rich region of the HCF-1PRO repeat activates promiscuous OGT:UDP-GlcNAc glycosylation and proteolysis activities.

Kapuria V, Röhrig UF, Waridel P, Lammers F, Borodkin VS, van Aalten DMF, Zoete V, Herr W.

J Biol Chem. 2018 Sep 17. pii: jbc.RA118.004185. doi: 10.1074/jbc.RA118.004185. [Epub ahead of print]

2.

Personalized cancer vaccine effectively mobilizes antitumor T cell immunity in ovarian cancer.

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.

Sci Transl Med. 2018 Apr 11;10(436). pii: eaao5931. doi: 10.1126/scitranslmed.aao5931.

PMID:
29643231
3.

Pan-SRC kinase inhibition blocks B-cell receptor oncogenic signaling in non-Hodgkin lymphoma.

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.

Blood. 2018 May 24;131(21):2345-2356. doi: 10.1182/blood-2017-10-809210. Epub 2018 Mar 22.

4.

Sensitive and frequent identification of high avidity neo-epitope specific CD8 + T cells in immunotherapy-naive ovarian cancer.

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.

Nat Commun. 2018 Mar 15;9(1):1092. doi: 10.1038/s41467-018-03301-0.

5.

Educational Tools to Introduce Computer-Aided Drug Design to Students and to the Public at Large.

Daina A, Blatter MC, Gerritsen VB, Zoete V.

Chimia (Aarau). 2018 Feb 1;72(1):55-61. doi: 10.2533/chimia.2018.55.

PMID:
29490794
6.

Biallelic variants in KIF14 cause intellectual disability with microcephaly.

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.

Eur J Hum Genet. 2018 Mar;26(3):330-339. doi: 10.1038/s41431-017-0088-9. Epub 2018 Jan 17.

7.

T cell receptor alpha variable 12-2 bias in the immunodominant response to Yellow fever virus.

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.

Eur J Immunol. 2018 Feb;48(2):258-272. doi: 10.1002/eji.201747082. Epub 2017 Dec 11.

8.

Mutant CTNNB1 and histological heterogeneity define metabolic subtypes of hepatoblastoma.

Crippa S, Ancey PB, Vazquez J, Angelino P, Rougemont AL, Guettier C, Zoete V, Delorenzi M, Michielin O, Meylan E.

EMBO Mol Med. 2017 Nov;9(11):1589-1604. doi: 10.15252/emmm.201707814.

9.

Biallelic variants in LINGO1 are associated with autosomal recessive intellectual disability, microcephaly, speech and motor delay.

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.

Genet Med. 2018 Jul;20(7):778-784. doi: 10.1038/gim.2017.113. Epub 2017 Aug 24.

PMID:
28837161
10.

The Binding Mode of N-Hydroxyamidines to Indoleamine 2,3-Dioxygenase 1 (IDO1).

Röhrig UF, Zoete V, Michielin O.

Biochemistry. 2017 Aug 22;56(33):4323-4325. doi: 10.1021/acs.biochem.7b00586. Epub 2017 Jul 27.

PMID:
28731684
11.

The T-Cell Receptor Can Bind to the Peptide-Bound Major Histocompatibility Complex and Uncomplexed β2-Microglobulin through Distinct Binding Sites.

Merkle PS, Irving M, Hongjian S, Ferber M, Jørgensen TJD, Scholten K, Luescher I, Coukos G, Zoete V, Cuendet MA, Michielin O, Rand KD.

Biochemistry. 2017 Aug 1;56(30):3945-3961. doi: 10.1021/acs.biochem.7b00385. Epub 2017 Jul 19.

PMID:
28671821
12.

Design of short peptides to block BTLA/HVEM interactions for promoting anticancer T-cell responses.

Spodzieja M, Lach S, Iwaszkiewicz J, Cesson V, Kalejta K, Olive D, Michielin O, Speiser DE, Zoete V, Derré L, Rodziewicz-Motowidło S.

PLoS One. 2017 Jun 8;12(6):e0179201. doi: 10.1371/journal.pone.0179201. eCollection 2017.

13.
14.

On-the-Fly QM/MM Docking with Attracting Cavities.

Chaskar P, Zoete V, Röhrig UF.

J Chem Inf Model. 2017 Jan 23;57(1):73-84. doi: 10.1021/acs.jcim.6b00406. Epub 2016 Dec 16.

PMID:
27983849
15.

1,2,3-Triazoles as inhibitors of indoleamine 2,3-dioxygenase 2 (IDO2).

Röhrig UF, Majjigapu SR, Caldelari D, Dilek N, Reichenbach P, Ascencao K, Irving M, Coukos G, Vogel P, Zoete V, Michielin O.

Bioorg Med Chem Lett. 2016 Sep 1;26(17):4330-3. doi: 10.1016/j.bmcl.2016.07.031. Epub 2016 Jul 16.

PMID:
27469130
16.

Electron affinity of tricyclic, bicyclic, and monocyclic compounds containing cyanoenones correlates with their potency as inducers of a cytoprotective enzyme.

Bensasson RV, Dinkova-Kostova AT, Zheng S, Saito A, Li W, Zoete V, Honda T.

Bioorg Med Chem Lett. 2016 Sep 1;26(17):4345-9. doi: 10.1016/j.bmcl.2016.07.028. Epub 2016 Jul 15.

PMID:
27460172
17.

Debio 0617B Inhibits Growth of STAT3-Driven Solid Tumors through Combined Inhibition of JAK, SRC, and Class III/V Receptor Tyrosine Kinases.

Murone M, Vaslin Chessex A, Attinger A, Ramachandra R, Shetty SJ, Daginakatte G, Sengupta S, Marappan S, Dhodheri S, Rigotti S, Bachhav Y, Brienza S, Traxler P, Lang M, Aguet M, Zoete V, Michielin O, Nicholas C, Johnson FM, Ramachandra M, McAllister A.

Mol Cancer Ther. 2016 Oct;15(10):2334-2343. Epub 2016 Jul 20.

18.

SwissSimilarity: A Web Tool for Low to Ultra High Throughput Ligand-Based Virtual Screening.

Zoete V, Daina A, Bovigny C, Michielin O.

J Chem Inf Model. 2016 Aug 22;56(8):1399-404. doi: 10.1021/acs.jcim.6b00174. Epub 2016 Jul 19.

PMID:
27391578
19.

A BOILED-Egg To Predict Gastrointestinal Absorption and Brain Penetration of Small Molecules.

Daina A, Zoete V.

ChemMedChem. 2016 Jun 6;11(11):1117-21. doi: 10.1002/cmdc.201600182. Epub 2016 May 24.

20.

Proteolysis of HCF-1 by Ser/Thr glycosylation-incompetent O-GlcNAc transferase:UDP-GlcNAc complexes.

Kapuria V, Röhrig UF, Bhuiyan T, Borodkin VS, van Aalten DM, Zoete V, Herr W.

Genes Dev. 2016 Apr 15;30(8):960-72. doi: 10.1101/gad.275925.115. Epub 2016 Apr 7.

21.

Genomic analysis identifies new drivers and progression pathways in skin basal cell carcinoma.

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, Ben Chaabene R, 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.

Nat Genet. 2016 Apr;48(4):398-406. doi: 10.1038/ng.3525. Epub 2016 Mar 7.

PMID:
26950094
22.

Design and Validation of a Novel Generic Platform for the Production of Tetravalent IgG1-like Bispecific Antibodies.

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.

J Immunol. 2016 Apr 1;196(7):3199-211. doi: 10.4049/jimmunol.1501592. Epub 2016 Feb 26.

23.

Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape.

Zoete V, Schuepbach T, Bovigny C, Chaskar P, Daina A, Röhrig UF, Michielin O.

J Comput Chem. 2016 Feb 5;37(4):437-47. doi: 10.1002/jcc.24249. Epub 2015 Nov 12.

24.

Distinct OGT-Binding Sites Promote HCF-1 Cleavage.

Bhuiyan T, Waridel P, Kapuria V, Zoete V, Herr W.

PLoS One. 2015 Aug 25;10(8):e0136636. doi: 10.1371/journal.pone.0136636. eCollection 2015.

25.

Challenges in the Discovery of Indoleamine 2,3-Dioxygenase 1 (IDO1) Inhibitors.

Röhrig UF, Majjigapu SR, Vogel P, Zoete V, Michielin O.

J Med Chem. 2015 Dec 24;58(24):9421-37. doi: 10.1021/acs.jmedchem.5b00326. Epub 2015 May 26. Review.

PMID:
25970480
26.

Protein homology reveals new targets for bioactive small molecules.

Gfeller D, Zoete V.

Bioinformatics. 2015 Aug 15;31(16):2721-7. doi: 10.1093/bioinformatics/btv214. Epub 2015 Apr 21.

PMID:
25900917
27.

iLOGP: a simple, robust, and efficient description of n-octanol/water partition coefficient for drug design using the GB/SA approach.

Daina A, Michielin O, Zoete V.

J Chem Inf Model. 2014 Dec 22;54(12):3284-301. doi: 10.1021/ci500467k. Epub 2014 Nov 25.

PMID:
25382374
28.

Toward on-the-fly quantum mechanical/molecular mechanical (QM/MM) docking: development and benchmark of a scoring function.

Chaskar P, Zoete V, Röhrig UF.

J Chem Inf Model. 2014 Nov 24;54(11):3137-52. doi: 10.1021/ci5004152. Epub 2014 Oct 22.

PMID:
25296988
29.

The CAP1/Prss8 catalytic triad is not involved in PAR2 activation and protease nexin-1 (PN-1) inhibition.

Crisante G, Battista L, Iwaszkiewicz J, Nesca V, Mérillat AM, Sergi C, Zoete V, Frateschi S, Hummler E.

FASEB J. 2014 Nov;28(11):4792-805. doi: 10.1096/fj.14-253781. Epub 2014 Aug 19.

PMID:
25138159
30.

Detailed analysis and follow-up studies of a high-throughput screening for indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors.

Röhrig UF, Majjigapu SR, Chambon M, Bron S, Pilotte L, Colau D, Van den Eynde BJ, Turcatti G, Vogel P, Zoete V, Michielin O.

Eur J Med Chem. 2014 Sep 12;84:284-301. doi: 10.1016/j.ejmech.2014.06.078. Epub 2014 Jul 10.

PMID:
25036789
31.

A WXW motif is required for the anticancer activity of the TAT-RasGAP317-326 peptide.

Barras D, Chevalier N, Zoete V, Dempsey R, Lapouge K, Olayioye MA, Michielin O, Widmann C.

J Biol Chem. 2014 Aug 22;289(34):23701-11. doi: 10.1074/jbc.M114.576272. Epub 2014 Jul 9.

32.

SwissTargetPrediction: a web server for target prediction of bioactive small molecules.

Gfeller D, Grosdidier A, Wirth M, Daina A, Michielin O, Zoete V.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W32-8. doi: 10.1093/nar/gku293. Epub 2014 May 3.

33.

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support.

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.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W436-41. doi: 10.1093/nar/gku380. Epub 2014 May 3.

34.

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.

Choudhary V, Darwiche R, Gfeller D, Zoete V, Michielin O, Schneiter R.

J Lipid Res. 2014 May;55(5):883-94. doi: 10.1194/jlr.M047126. Epub 2014 Mar 5.

35.

Synthesis and in vitro evaluation of a novel radioligand for αvβ3 integrin receptor imaging: [18F]FPPA-c(RGDfK).

Monaco A, Zoete V, Alghisi GC, Rüegg C, Michelin O, Prior J, Scapozza L, Seimbille Y.

Bioorg Med Chem Lett. 2013 Nov 15;23(22):6068-72. doi: 10.1016/j.bmcl.2013.09.031. Epub 2013 Sep 19.

PMID:
24095096
36.

The peroxisomal enzyme L-PBE is required to prevent the dietary toxicity of medium-chain fatty acids.

Ding J, Loizides-Mangold U, Rando G, Zoete V, Michielin O, Reddy JK, Wahli W, Riezman H, Thorens B.

Cell Rep. 2013 Oct 17;5(1):248-58. doi: 10.1016/j.celrep.2013.08.032. Epub 2013 Sep 26.

37.

Structure-Based, Rational Design of T Cell Receptors.

Zoete V, Irving M, Ferber M, Cuendet MA, Michielin O.

Front Immunol. 2013 Sep 12;4:268. doi: 10.3389/fimmu.2013.00268. Review.

38.

Shaping the interaction landscape of bioactive molecules.

Gfeller D, Michielin O, Zoete V.

Bioinformatics. 2013 Dec 1;29(23):3073-9. doi: 10.1093/bioinformatics/btt540. Epub 2013 Sep 17.

PMID:
24048355
39.

Lung adenocarcinoma with BRAF G469L mutation refractory to vemurafenib.

Gautschi O, Peters S, Zoete V, Aebersold-Keller F, Strobel K, Schwizer B, Hirschmann A, Michielin O, Diebold J.

Lung Cancer. 2013 Nov;82(2):365-7. doi: 10.1016/j.lungcan.2013.08.012. Epub 2013 Aug 19.

PMID:
24035431
40.

Monoubiquitination and activity of the paracaspase MALT1 requires glutamate 549 in the dimerization interface.

Cabalzar K, Pelzer C, Wolf A, Lenz G, Iwaszkiewicz J, Zoete V, Hailfinger S, Thome M.

PLoS One. 2013 Aug 19;8(8):e72051. doi: 10.1371/journal.pone.0072051. eCollection 2013.

41.

Prediction of cross-recognition of peptide-HLA A2 by Melan-A-specific cytotoxic T lymphocytes using three-dimensional quantitative structure-activity relationships.

Fagerberg T, Zoete V, Viatte S, Baumgaertner P, Alves PM, Romero P, Speiser DE, Michielin O.

PLoS One. 2013 Jul 16;8(7):e65590. doi: 10.1371/journal.pone.0065590. Print 2013.

42.

Protein pocket and ligand shape comparison and its application in virtual screening.

Wirth M, Volkamer A, Zoete V, Rippmann F, Michielin O, Rarey M, Sauer WH.

J Comput Aided Mol Des. 2013 Jun;27(6):511-24. doi: 10.1007/s10822-013-9659-1. Epub 2013 Jun 27.

PMID:
23807262
43.

RNA pentaloop structures as effective targets of regulators belonging to the RsmA/CsrA protein family.

Lapouge K, Perozzo R, Iwaszkiewicz J, Bertelli C, Zoete V, Michielin O, Scapozza L, Haas D.

RNA Biol. 2013 Jun;10(6):1031-41. doi: 10.4161/rna.24771. Epub 2013 Apr 23.

44.

Recurrent structural motifs in non-homologous protein structures.

Johansson MU, Zoete V, Guex N.

Int J Mol Sci. 2013 Apr 10;14(4):7795-814. doi: 10.3390/ijms14047795.

45.

A dramatic lung cancer course in a patient with a rare EGFR germline mutation exon 21 V843I: Is EGFR TKI resistance predictable?

Demierre N, Zoete V, Michielin O, Stauffer E, Zimmermann DR, Betticher DC, Peters S.

Lung Cancer. 2013 Apr;80(1):81-4. doi: 10.1016/j.lungcan.2012.11.013. Epub 2013 Feb 4.

PMID:
23380224
46.

T-cell receptors binding orientation over peptide/MHC class I is driven by long-range interactions.

Ferber M, Zoete V, Michielin O.

PLoS One. 2012;7(12):e51943. doi: 10.1371/journal.pone.0051943. Epub 2012 Dec 14.

47.

SwissBioisostere: a database of molecular replacements for ligand design.

Wirth M, Zoete V, Michielin O, Sauer WH.

Nucleic Acids Res. 2013 Jan;41(Database issue):D1137-43. doi: 10.1093/nar/gks1059. Epub 2012 Nov 17.

48.

SwissSidechain: a molecular and structural database of non-natural sidechains.

Gfeller D, Michielin O, Zoete V.

Nucleic Acids Res. 2013 Jan;41(Database issue):D327-32. doi: 10.1093/nar/gks991. Epub 2012 Oct 26.

49.

Defining and searching for structural motifs using DeepView/Swiss-PdbViewer.

Johansson MU, Zoete V, Michielin O, Guex N.

BMC Bioinformatics. 2012 Jul 23;13:173. doi: 10.1186/1471-2105-13-173.

50.

Asymmetric synthesis of pochonin E and F, revision of their proposed structure, and their conversion to potent Hsp90 inhibitors.

Karthikeyan G, Zambaldo C, Barluenga S, Zoete V, Karplus M, Winssinger N.

Chemistry. 2012 Jul 16;18(29):8978-86. doi: 10.1002/chem.201200546. Epub 2012 Jun 13.

PMID:
22696415

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