Publications by authors named "Vincent Zoete"

100Publications

T-cell repertoire analysis and metrics of diversity and clonality.

Curr Opin Biotechnol 2020 Sep 1;65:284-295. Epub 2020 Sep 1.

Department of Oncology, Ludwig Institute for Cancer Research Lausanne, Lausanne University Hospital (CHUV) and University of Lausanne (UNIL), Lausanne, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.copbio.2020.07.010DOI Listing
September 2020

Identification of a superagonist variant of the immunodominant Yellow fever virus epitope NS4b by combinatorial peptide library screening.

Mol Immunol 2020 09 6;125:43-50. Epub 2020 Jul 6.

Department of Oncology, Lausanne University Hospital (CHUV), Lausanne, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.molimm.2020.06.025DOI Listing
September 2020

Cathepsin S Regulates Antigen Processing and T Cell Activity in Non-Hodgkin Lymphoma.

Cancer Cell 2020 May 23;37(5):674-689.e12. Epub 2020 Apr 23.

Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, EPFL, Lausanne, 1015 Switzerland; Swiss Cancer Center Leman (SCCL), Lausanne, 1015 Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2020.03.016DOI Listing
May 2020

Herpes simplex encephalitis in adult patients with MASP-2 deficiency.

PLoS Pathog 2019 12 23;15(12):e1008168. Epub 2019 Dec 23.

Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1371/journal.ppat.1008168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6944389PMC
December 2019

Analysis of Secondary Structure Biases in Naturally Presented HLA-I Ligands.

Front Immunol 2019 22;10:2731. Epub 2019 Nov 22.

Computer-Aided Molecular Engineering, Department of Oncology, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.3389/fimmu.2019.02731DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6883762PMC
November 2019

Strong Enrichment of Aromatic and Sulfur-Containing Residues in Ligand-Protein Binding Sites.

J Chem Inf Model 2019 11 12;59(11):4921-4928. Epub 2019 Nov 12.

Computer-Aided Molecular Engineering Group, Department of Fundamental Oncology , University of Lausanne , Ludwig Lausanne Branch, Route de la Corniche 9A , 1066 Epalinges , Switzerland.

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http://dx.doi.org/10.1021/acs.jcim.9b00582DOI Listing
November 2019

Application of the SwissDrugDesign Online Resources in Virtual Screening.

Int J Mol Sci 2019 Sep 18;20(18). Epub 2019 Sep 18.

Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, University of Lausanne, Quartier UNIL-Sorge, Bâtiment Amphipôle, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.3390/ijms20184612DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6770839PMC
September 2019

Inhibition Mechanisms of Indoleamine 2,3-Dioxygenase 1 (IDO1).

J Med Chem 2019 10 26;62(19):8784-8795. Epub 2019 Sep 26.

Molecular Modeling Group , SIB Swiss Institute of Bioinformatics , 1015 Lausanne , Switzerland.

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http://dx.doi.org/10.1021/acs.jmedchem.9b00942DOI Listing
October 2019

SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules.

Nucleic Acids Res 2019 07;47(W1):W357-W364

Molecular Modeling Group, SIB Swiss Institute of Bioinformatics, University of Lausanne, Quartier UNIL-Sorge, Bâtiment Amphipôle, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1093/nar/gkz382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602486PMC
July 2019

Bi-allelic Variants in DYNC1I2 Cause Syndromic Microcephaly with Intellectual Disability, Cerebral Malformations, and Dysmorphic Facial Features.

Am J Hum Genet 2019 06 9;104(6):1073-1087. Epub 2019 May 9.

Department of Genetic Medicine and Development, University of Geneva, 1206 Geneva, Switzerland; Service of Genetic Medicine, University Hospitals of Geneva, 1205 Geneva, Switzerland; iGE3 Institute of Genetics and Genomics of Geneva, 1211 Geneva, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2019.04.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6556908PMC
June 2019

Going Beyond the Sequences: TCR Binding Patterns at the Service of Cancer Detection.

Cancer Res 2019 04;79(7):1299-1301

Ludwig Institute for Cancer Research - Lausanne Branch, University of Lausanne, Lausanne, Épalinges, Switzerland.

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http://dx.doi.org/10.1158/0008-5472.CAN-19-0225DOI Listing
April 2019

Mutations in the palm domain disrupt modulation of acid-sensing ion channel 1a currents by neuropeptides.

Sci Rep 2019 02 22;9(1):2599. Epub 2019 Feb 22.

Department of Pharmacology and Toxicology, University of Lausanne, 1011, Lausanne, Switzerland.

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http://dx.doi.org/10.1038/s41598-018-37426-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6385203PMC
February 2019

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

Blood 2018 05 22;131(21):2345-2356. Epub 2018 Mar 22.

Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.

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http://dx.doi.org/10.1182/blood-2017-10-809210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5969377PMC
May 2018

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

Chimia (Aarau) 2018 Feb;72(1):55-61

Molecular Modeling Group, SIB Swiss Institute of Bioinformatics Bâtiment Génopode, Quartier Sorge, CH-1015 Lausanne, Department of Fundamental Oncology and Ludwig Institute of Cancer Research University of Lausanne, Route de la Corniche 9A, CH-1066 Epalinges;, Email:

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http://dx.doi.org/10.2533/chimia.2018.55DOI Listing
February 2018

Mutant and histological heterogeneity define metabolic subtypes of hepatoblastoma.

EMBO Mol Med 2017 11;9(11):1589-1604

Swiss Institute for Experimental Cancer Research, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland

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http://dx.doi.org/10.15252/emmm.201707814DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5666308PMC
November 2017

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

Biochemistry 2017 08 27;56(33):4323-4325. Epub 2017 Jul 27.

Molecular Modeling Group, SIB Swiss Institute of Bioinformatics , 1015 Lausanne, Switzerland.

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http://pubs.acs.org/doi/10.1021/acs.biochem.7b00586
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http://dx.doi.org/10.1021/acs.biochem.7b00586DOI Listing
August 2017

SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules.

Sci Rep 2017 03 3;7:42717. Epub 2017 Mar 3.

SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1038/srep42717DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5335600PMC
March 2017

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

J Chem Inf Model 2017 01 16;57(1):73-84. Epub 2016 Dec 16.

SIB Swiss Institute of Bioinformatics , Molecular Modeling Group, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1021/acs.jcim.6b00406DOI Listing
January 2017

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

Bioorg Med Chem Lett 2016 09 16;26(17):4330-3. Epub 2016 Jul 16.

Molecular Modeling Group, SIB Swiss Institute for Bioinformatics, CH-1015 Lausanne, Switzerland; Ludwig Center for Cancer Research of the University of Lausanne, CH-1066 Epalinges, Switzerland; Department of Oncology, University of Lausanne and Centre Hospitalier Universitaire Vaudois (CHUV), CH-1011 Lausanne, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.bmcl.2016.07.031DOI Listing
September 2016

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 09 15;26(17):4345-9. Epub 2016 Jul 15.

Department of Chemistry and Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, NY 11794-3400, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bmcl.2016.07.028DOI Listing
September 2016

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

J Chem Inf Model 2016 08 19;56(8):1399-404. Epub 2016 Jul 19.

SIB Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode , CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1021/acs.jcim.6b00174DOI Listing
August 2016

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

ChemMedChem 2016 06 24;11(11):1117-21. Epub 2016 May 24.

SIB Swiss Institute of Bioinformatics, Molecular Modeling Group, Quartier Sorge, Bâtiment Génopode, 1015, Lausanne, Switzerland.

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http://dx.doi.org/10.1002/cmdc.201600182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5089604PMC
June 2016

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

Genes Dev 2016 Apr 7;30(8):960-72. Epub 2016 Apr 7.

Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland;

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http://dx.doi.org/10.1101/gad.275925.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4840301PMC
April 2016

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

J Immunol 2016 Apr 26;196(7):3199-211. Epub 2016 Feb 26.

Centre National de la Recherche Scientifique UPS3044 "Baculovirus et Thérapie," F-30380 Saint-Christol-Lèz Alès, France;

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http://dx.doi.org/10.4049/jimmunol.1501592DOI Listing
April 2016

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

J Comput Chem 2016 Feb 12;37(4):437-47. Epub 2015 Nov 12.

Bâtiment Génopode, SIB Swiss Institute of Bioinformatics, Quartier Sorge, CH-1015 Lausanne, Switzerland.

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http://doi.wiley.com/10.1002/jcc.24249
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http://dx.doi.org/10.1002/jcc.24249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4738475PMC
February 2016

Distinct OGT-Binding Sites Promote HCF-1 Cleavage.

PLoS One 2015 25;10(8):e0136636. Epub 2015 Aug 25.

Center for Integrative Genomics, University of Lausanne, Génopode, Lausanne, Switzerland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0136636PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4549301PMC
May 2016

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

J Med Chem 2015 Dec 26;58(24):9421-37. Epub 2015 May 26.

Molecular Modeling Group, SIB Swiss Institute of Bioinformatics , CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1021/acs.jmedchem.5b00326DOI Listing
December 2015

Protein homology reveals new targets for bioactive small molecules.

Bioinformatics 2015 Aug 21;31(16):2721-7. Epub 2015 Apr 21.

Swiss Institute of Bioinformatics (SIB), Quartier Sorge, Bâtiment Génopode, 1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btv214DOI Listing
August 2015

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 Dec 25;54(12):3284-301. Epub 2014 Nov 25.

Molecular Modeling Group, SIB Swiss Institute of Bioinformatics , Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1021/ci500467kDOI Listing
December 2014

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

J Chem Inf Model 2014 Nov 22;54(11):3137-52. Epub 2014 Oct 22.

Swiss Institute of Bioinformatics , Molecular Modeling Group, Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1021/ci5004152DOI Listing
November 2014

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

Eur J Med Chem 2014 Sep 10;84:284-301. Epub 2014 Jul 10.

Swiss Institute of Bioinformatics, Molecular Modeling Group, Quartier Sorge - Bâtiment Génopode, CH-1015 Lausanne, Switzerland; Department of Oncology, University of Lausanne and Centre Hospitalier Universitaire Vaudois (CHUV), CH-1011 Lausanne, Switzerland; Ludwig Center for Cancer Research of the University of Lausanne, CH-1015 Lausanne, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.ejmech.2014.06.078DOI Listing
September 2014

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

J Biol Chem 2014 Aug 9;289(34):23701-11. Epub 2014 Jul 9.

From the Department of Physiology, University of Lausanne, 1005 Lausanne, Switzerland,

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http://dx.doi.org/10.1074/jbc.M114.576272DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4156047PMC
August 2014

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

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

Swiss Institute of Bioinformatics (SIB), Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland

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http://nar.oxfordjournals.org/content/early/2014/05/03/nar.g
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gku293
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http://dx.doi.org/10.1093/nar/gku293DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4086140PMC
July 2014

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

Bioorg Med Chem Lett 2013 Nov 19;23(22):6068-72. Epub 2013 Sep 19.

Cyclotron Unit, University Hospital of Geneva, Rue Gabrielle Perrte-Gentil 4, Geneva 1211, Switzerland; School of Pharmaceutical Sciences, University of Geneva and University of Lausanne, Quai Ernest Ansermet 30, Geneva 1211, Switzerland.

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http://dx.doi.org/10.1016/j.bmcl.2013.09.031DOI Listing
November 2013

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

Cell Rep 2013 Oct 26;5(1):248-58. Epub 2013 Sep 26.

Center for Integrative Genomics, University of Lausanne, Lausanne 1015, Switzerland.

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http://dx.doi.org/10.1016/j.celrep.2013.08.032DOI Listing
October 2013

Shaping the interaction landscape of bioactive molecules.

Bioinformatics 2013 Dec 17;29(23):3073-9. Epub 2013 Sep 17.

Swiss Institute of Bioinformatics (SIB), Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland, Ludwig Institute for Cancer Research and Pluridisciplinary Center for Clinical Oncology, Centre Hospitalier Universitaire Vaudois, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1093/bioinformatics/btt540DOI Listing
December 2013

Lung adenocarcinoma with BRAF G469L mutation refractory to vemurafenib.

Lung Cancer 2013 Nov 19;82(2):365-7. Epub 2013 Aug 19.

Department of Medical Oncology, Luzerner Kantonsspital, Luzern, Switzerland. Electronic address:

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http://dx.doi.org/10.1016/j.lungcan.2013.08.012DOI Listing
November 2013

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

J Comput Aided Mol Des 2013 Jun 27;27(6):511-24. Epub 2013 Jun 27.

Computational Chemistry, Merck Serono S.A. Geneva, Chemin des Mines 9, 1202 Geneva, Switzerland.

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http://dx.doi.org/10.1007/s10822-013-9659-1DOI Listing
June 2013

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

RNA Biol 2013 Jun 23;10(6):1031-41. Epub 2013 Apr 23.

Département de Microbiologie Fondamentale, Université de Lausanne, Bâtiment Biophore, Lausanne, Switzerland.

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http://dx.doi.org/10.4161/rna.24771DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4111731PMC
June 2013

Recurrent structural motifs in non-homologous protein structures.

Int J Mol Sci 2013 Apr 10;14(4):7795-814. Epub 2013 Apr 10.

Vital-IT Group, SIB Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.3390/ijms14047795DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3645717PMC
April 2013

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 Apr 4;80(1):81-4. Epub 2013 Feb 4.

HFR Fribourg, Hôpital Cantonal, Department of Internal Medicine, Division of Oncology, Fribourg, Switzerland.

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https://linkinghub.elsevier.com/retrieve/pii/S01695002120063
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http://dx.doi.org/10.1016/j.lungcan.2012.11.013DOI Listing
April 2013

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

PLoS One 2012 14;7(12):e51943. Epub 2012 Dec 14.

Multidisciplinary Oncology Center, Lausanne University Hospital (CHUV), Lausanne, Switzerland.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0051943PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3522592PMC
September 2013

SwissBioisostere: a database of molecular replacements for ligand design.

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

Computational Chemistry, Merck Serono S.A., Chemin des Mines, 9, CH-1202 Geneva.

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http://dx.doi.org/10.1093/nar/gks1059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531158PMC
January 2013

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

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

Swiss Institute of Bioinformatics (SIB), Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1093/nar/gks991DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531096PMC
January 2013

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

BMC Bioinformatics 2012 Jul 23;13:173. Epub 2012 Jul 23.

Vital-IT Group, SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
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http://dx.doi.org/10.1186/1471-2105-13-173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3436773PMC
July 2012

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

Chemistry 2012 Jul 13;18(29):8978-86. Epub 2012 Jun 13.

Institut de Science et Ingénierie Supramoléculaires (ISIS-UMR 7006), Université de Strasbourg CNRS, 8 Allée Gaspard Monge, 67000 Strasbourg, France.

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http://dx.doi.org/10.1002/chem.201200546DOI Listing
July 2012

Rational design of 4-aryl-1,2,3-triazoles for indoleamine 2,3-dioxygenase 1 inhibition.

J Med Chem 2012 Jun 22;55(11):5270-90. Epub 2012 May 22.

Ludwig Center for Cancer Research of the University of Lausanne, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1021/jm300260vDOI Listing
June 2012

Expanding molecular modeling and design tools to non-natural sidechains.

J Comput Chem 2012 Jul 14;33(18):1525-35. Epub 2012 Apr 14.

Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode, Lausanne, Switzerland.

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http://doi.wiley.com/10.1002/jcc.22982
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http://dx.doi.org/10.1002/jcc.22982DOI Listing
July 2012

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 Dec 22;46(12):6098-103. Epub 2011 Sep 22.

Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/Marcel·lí Domingo s/n, 43007 Tarragona, Catalonia, Spain.

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http://dx.doi.org/10.1016/j.ejmech.2011.09.022DOI Listing
December 2011

How T cell receptors interact with peptide-MHCs: a multiple steered molecular dynamics study.

Proteins 2011 Nov 30;79(11):3007-24. Epub 2011 Aug 30.

Swiss Institute of Bioinformatics, Génopode, 1015 Lausanne, Switzerland.

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http://doi.wiley.com/10.1002/prot.23104
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http://dx.doi.org/10.1002/prot.23104DOI Listing
November 2011

Potency of inhibition of human DNA topoisomerase I by flavones assessed through physicochemical parameters.

Free Radic Biol Med 2011 Oct 23;51(7):1406-10. Epub 2011 Jun 23.

Molécules de Communication et Adaptation des Microorganismes, Department RDDM, UMR 7245 CNRS/MNHN, Muséum National d'Histoire Naturelle, Paris, France.

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http://dx.doi.org/10.1016/j.freeradbiomed.2011.06.021DOI Listing
October 2011

SwissDock, a protein-small molecule docking web service based on EADock DSS.

Nucleic Acids Res 2011 Jul 29;39(Web Server issue):W270-7. Epub 2011 May 29.

Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkr366DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125772PMC
July 2011

SwissParam: a fast force field generation tool for small organic molecules.

J Comput Chem 2011 Aug 3;32(11):2359-68. Epub 2011 May 3.

Swiss Institute of Bioinformatics, Quartier Sorge-Bâtiment Génopode, Lausanne, Switzerland.

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http://dx.doi.org/10.1002/jcc.21816DOI Listing
August 2011

Fast docking using the CHARMM force field with EADock DSS.

J Comput Chem 2011 Jul 3;32(10):2149-59. Epub 2011 May 3.

Swiss Institute of Bioinformatics (SIB), Quartier Sorge, Bâtiment Génopode, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1002/jcc.21797DOI Listing
July 2011

Unique spectrum of activity of prosimian TRIM5alpha against exogenous and endogenous retroviruses.

J Virol 2011 May 23;85(9):4173-83. Epub 2011 Feb 23.

Institute of Microbiology, University Hospital Center and University of Lausanne, CHUV 1011 Lausanne, Switzerland.

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http://dx.doi.org/10.1128/JVI.00075-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3126249PMC
May 2011

Homology-based identification of capsid determinants that protect HIV1 from human TRIM5α restriction.

J Biol Chem 2011 Mar 17;286(10):8128-40. Epub 2010 Dec 17.

Global Health Institute, School of Life Sciences, and Frontiers in Genetics National Center for Competence in Research, Ecole Polytechnique Fédérale de Lausanne, Switzerland.

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http://dx.doi.org/10.1074/jbc.M110.187609DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048699PMC
March 2011

Potency ranking of triterpenoids as inducers of a cytoprotective enzyme and as inhibitors of a cellular inflammatory response via their electron affinity and their electrophilicity index.

Chem Biol Interact 2010 Jul 28;186(2):118-26. Epub 2010 Apr 28.

Muséum National d'Histoire Naturelle, Molécules de Communication et Adaptation des Microorganismes, Paris, France.

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http://dx.doi.org/10.1016/j.cbi.2010.04.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199116PMC
July 2010

Use of the FACTS solvation model for protein-ligand docking calculations. Application to EADock.

J Mol Recognit 2010 Sep-Oct;23(5):457-61

Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1002/jmr.1012DOI Listing
December 2010

Rational design of indoleamine 2,3-dioxygenase inhibitors.

J Med Chem 2010 Feb;53(3):1172-89

Ludwig Institute for Cancer Research, Lausanne Branch, CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1021/jm9014718DOI Listing
February 2010

Functional analysis and structural modeling of human APOBEC3G reveal the role of evolutionarily conserved elements in the inhibition of human immunodeficiency virus type 1 infection and Alu transposition.

J Virol 2009 Dec 23;83(23):12611-21. Epub 2009 Sep 23.

School of Life Sciences and Frontiers-in-Genetics National Center of Competence in Research, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.

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http://jvi.asm.org/cgi/doi/10.1128/JVI.01491-09
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http://dx.doi.org/10.1128/JVI.01491-09DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2786736PMC
December 2009

Fourier transform convolution integrals applied to generalized Born molecular volume.

J Comput Chem 2010 Feb;31(3):649-59

Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland.

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http://dx.doi.org/10.1002/jcc.21338DOI Listing
February 2010

Docking to heme proteins.

J Comput Chem 2009 Nov;30(14):2305-15

Ludwig Institute for Cancer Research, Ltd., Lausanne, Switzerland.

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http://dx.doi.org/10.1002/jcc.21244DOI Listing
November 2009

Docking, virtual high throughput screening and in silico fragment-based drug design.

J Cell Mol Med 2009 Feb 21;13(2):238-48. Epub 2009 Jan 21.

Swiss Institute of Bioinformatics, Bâtiment Génopode, Quartier Sorge, Lausanne, Switzerland.

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http://dx.doi.org/10.1111/j.1582-4934.2008.00665.xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3823351PMC
February 2009

Blind docking of 260 protein-ligand complexes with EADock 2.0.

J Comput Chem 2009 Oct;30(13):2021-30

Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland.

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http://dx.doi.org/10.1002/jcc.21202DOI Listing
October 2009

Two-step mechanism of induction of the gene expression of a prototypic cancer-protective enzyme by diphenols.

Chem Res Toxicol 2008 Apr 25;21(4):805-12. Epub 2008 Mar 25.

Laboratoire de Chimie des Substances Naturelles, MNHN, USM 0502/UMR 5154 CNRS, Case 54, 63 rue Buffon, F 75005 Paris, France.

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http://dx.doi.org/10.1021/tx7002883DOI Listing
April 2008

In vitro biotransformation of imatinib by the tumor expressed CYP1A1 and CYP1B1.

Biopharm Drug Dispos 2008 Mar;29(2):103-18

Quantitative Mass Spectrometry Facility, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland.

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http://dx.doi.org/10.1002/bdd.598DOI Listing
March 2008