Vincent Zoete

Research interests

Publications

• SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina

  Nucleic Acids Research · 2024 · https://doi.org/10.1093/nar/gkae300

• SwissParam 2023: A Modern Web-Based Tool for Efficient Small Molecule Parametrization

  Journal of Chemical Information and Modeling · 2023 · https://doi.org/10.1021/acs.jcim.3c01053

• Myeloid antigen-presenting cell niches sustain antitumor T cells and license PD-1 blockade via CD28 costimulation

  Cancer Cell · 2021 · https://doi.org/10.1016/j.ccell.2021.10.008

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

  Current Opinion in Biotechnology · 2020 · https://doi.org/10.1016/j.copbio.2020.07.010

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

  Nucleic Acids Research · 2019 · https://doi.org/10.1093/nar/gkz382

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

  Science Translational Medicine · 2018 · https://doi.org/10.1126/scitranslmed.aao5931

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

  Scientific Reports · 2017 · https://doi.org/10.1038/srep42717

• A BOILED‐Egg To Predict Gastrointestinal Absorption and Brain Penetration of Small Molecules

  ChemMedChem · 2016 · https://doi.org/10.1002/cmdc.201600182

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

  Journal of Chemical Information and Modeling · 2016 · https://doi.org/10.1021/acs.jcim.6b00174

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

  Nature Genetics · 2016 · https://doi.org/10.1038/ng.3525

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

  Journal of Medicinal Chemistry · 2015 · https://doi.org/10.1021/acs.jmedchem.5b00326

• iLOGP: A Simple, Robust, and Efficient Description of n -Octanol/Water Partition Coefficient for Drug Design Using the GB/SA Approach

  Journal of Chemical Information and Modeling · 2014 · https://doi.org/10.1021/ci500467k

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

  Nucleic Acids Research · 2014 · https://doi.org/10.1093/nar/gku293

• Shaping the interaction landscape of bioactive molecules

  Bioinformatics · 2013 · https://doi.org/10.1093/bioinformatics/btt540

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

  BMC Bioinformatics · 2012 · https://doi.org/10.1186/1471-2105-13-173

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

  Nucleic Acids Research · 2011 · https://doi.org/10.1093/nar/gkr366

• Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma

  Nature Genetics · 2011 · https://doi.org/10.1038/ng.1026

• Fast docking using the CHARMM force field with EADock DSS

  Journal of Computational Chemistry · 2011 · https://doi.org/10.1002/jcc.21797

• SwissParam: A fast force field generation tool for small organic molecules

  Journal of Computational Chemistry · 2011 · https://doi.org/10.1002/jcc.21816

• Evidence for a TCR Affinity Threshold Delimiting Maximal CD8 T Cell Function

  The Journal of Immunology · 2010 · https://doi.org/10.4049/jimmunol.1000173

• Inhibition of the shade avoidance response by formation of non‐DNA binding bHLH heterodimers

  The EMBO Journal · 2009 · https://doi.org/10.1038/emboj.2009.306

• EADock: Docking of small molecules into protein active sites with a multiobjective evolutionary optimization

  Proteins Structure Function and Bioinformatics · 2007 · https://doi.org/10.1002/prot.21367

• Peroxisome proliferator-activated receptor structures: Ligand specificity, molecular switch and interactions with regulators

  Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids · 2007 · https://doi.org/10.1016/j.bbalip.2007.01.007

• The Endocrine Disruptor Monoethyl-hexyl-phthalate Is a Selective Peroxisome Proliferator-activated Receptor γ Modulator That Promotes Adipogenesis

  Journal of Biological Chemistry · 2007 · https://doi.org/10.1074/jbc.m702724200

• Study of the insulin dimerization: Binding free energy calculations and per‐residue free energy decomposition

  Proteins Structure Function and Bioinformatics · 2005 · https://doi.org/10.1002/prot.20528

Current projects

No projects listed.