Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors. - Vincent Zoete; Olivier Michielin; Martin Karplus (J. Comput. Aided Mol. Des., 2003)

Blind docking of 260 protein-ligand complexes with EADock 2.0. - Aurélien Grosdidier; Vincent Zoete; Olivier Michielin (J. Comput. Chem., 2009)

Docking to heme proteins. - Ute F. Röhrig; Aurélien Grosdidier; Vincent Zoete; Olivier Michielin (J. Comput. Chem., 2009)

Fourier transform convolution integrals applied to generalized Born molecular volume. - Thierry Schüpbach; Vincent Zoete; Brice Tsakam-Sotché; Olivier Michielin (J. Comput. Chem., 2010)

Fast docking using the CHARMM force field with EADock DSS. - Aurélien Grosdidier; Vincent Zoete; Olivier Michielin (J. Comput. Chem., 2011)

SwissParam: A fast force field generation tool for small organic molecules. - Vincent Zoete; Michel A. Cuendet; Aurélien Grosdidier; Olivier Michielin (J. Comput. Chem., 2011)

SwissDock, a protein-small molecule docking web service based on EADock DSS. - Aurélien Grosdidier; Vincent Zoete; Olivier Michielin (Nucleic Acids Res., 2011)

Defining and searching for structural motifs using DeepView/Swiss-PdbViewer. - Maria U. Johansson; Vincent Zoete; Olivier Michielin; Nicolas Guex (BMC Bioinform., 2012)

Expanding molecular modeling and design tools to non-natural sidechains. - David Gfeller; Olivier Michielin; Vincent Zoete (J. Comput. Chem., 2012)

Shaping the interaction landscape of bioactive molecules. - David Gfeller; Olivier Michielin; Vincent Zoete (Bioinform., 2013)

Protein pocket and ligand shape comparison and its application in virtual screening. - Matthias Wirth; Andrea Volkamer; Vincent Zoete; Friedrich Rippmann; Olivier Michielin; Matthias Rarey; Wolfgang H. B. Sauer (J. Comput. Aided Mol. Des., 2013)

SwissSidechain: a molecular and structural database of non-natural sidechains. - David Gfeller; Olivier Michielin; Vincent Zoete (Nucleic Acids Res., 2013)

SwissBioisostere: a database of molecular replacements for ligand design. - Matthias Wirth; Vincent Zoete; Olivier Michielin; Wolfgang H. B. Sauer (Nucleic Acids Res., 2013)

iLOGP: A Simple, Robust, and Efficient Description of n-Octanol/Water Partition Coefficient for Drug Design Using the GB/SA Approach. - Antoine Daina; Olivier Michielin; Vincent Zoete (J. Chem. Inf. Model., 2014)

SwissTargetPrediction: a web server for target prediction of bioactive small molecules. - David Gfeller; Aurélien Grosdidier; Matthias Wirth; Antoine Daina; Olivier Michielin; Vincent Zoete (Nucleic Acids Res., 2014)

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. - Heinz Stockinger; Adrian M. Altenhoff; Konstantin Arnold; Amos Bairoch; Frederic B. Bastian; Sven Bergmann; Lydie Bougueleret; Philipp Bucher; Mauro Delorenzi; Lydie Lane; Philippe Le Mercier; Frédérique Lisacek; et al. (Nucleic Acids Res., 2014)

Attracting cavities for docking. Replacing the rough energy landscape of the protein by a smooth attracting landscape. - Vincent Zoete; Thierry Schüpbach; Christophe Bovigny; Prasad Chaskar; Antoine Daina; Ute F. Röhrig; Olivier Michielin (J. Comput. Chem., 2016)

SwissSimilarity: A Web Tool for Low to Ultra High Throughput Ligand-Based Virtual Screening. - Vincent Zoete; Antoine Daina; Christophe Bovigny; Olivier Michielin (J. Chem. Inf. Model., 2016)

SwissTargetPrediction: updated data and new features for efficient prediction of protein targets of small molecules. - Antoine Daina; Olivier Michielin; Vincent Zoete (Nucleic Acids Res., 2019)

MedCo: Enabling Secure and Privacy-Preserving Exploration of Distributed Clinical and Genomic Data. - Jean Louis Raisaro; Juan Ramón Troncoso-Pastoriza; Mickaël Misbach; João Sá Sousa; Sylvain Pradervand; Edoardo Missiaglia; Olivier Michielin; Bryan Ford; Jean-Pierre Hubaux (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

A Process Mining Approach to Statistical Analysis: Application to a Real-World Advanced Melanoma Dataset. - Erica Tavazzi; Camille L. Gerard; Olivier Michielin; Alexandre Wicky; Roberto Gatta; Michel A. Cuendet (ICPM Workshops, 2020)

SPHN/PHRT - MedCo in Action: Empowering the Swiss Molecular Tumor Board with Privacy-Preserving and Real-Time Patient Discovery. - Jean Louis Raisaro; Juan Ramón Troncoso-Pastoriza; Sylvain Pradervand; Michel A. Cuendet; Mickaël Misbach; João Sá Sousa; Francesco Marino; Nicolas Freundler; Nicolas Rosat; David Cavin; Alexander B. Leichtle; Jacques Fellay; et al. (MIE, 2020)

Classification of oncology treatment responses from radiology reports with supervised machine learning. - Luc Mottin; Jean-Philippe Goldman; Christoph Jäggli; Rita Achermann; Julien Gobeill; Julien Knafou; Julien Ehrsam; Alexandre Wicky; Camille L. Gerard; Tanja Schwenk; Mélinda Charrier; Petros Tsantoulis; et al. (AMIA, 2022)

SwissBioisostere 2021: updated structural, bioactivity and physicochemical data delivered by a reshaped web interface. - Alessandro Cuozzo; Antoine Daina; Marta A. S. Perez; Olivier Michielin; Vincent Zoete (Nucleic Acids Res., 2022)

Multilingual RECIST classification of radiology reports using supervised learning. - Luc Mottin; Jean-Philippe Goldman; Christoph Jäggli; Rita Achermann; Julien Gobeill; Julien Knafou; Julien Ehrsam; Alexandre Wicky; Camille L. Gerard; Tanja Schwenk; Mélinda Charrier; Petros Tsantoulis; et al. (Frontiers Digit. Health, 2023)

SwissParam 2023: A Modern Web-Based Tool for Efficient Small Molecule Parametrization. - Marine Bugnon; Mathilde Goullieux; Ute F. Röhrig; Marta A. S. Perez; Antoine Daina; Olivier Michielin; Vincent Zoete (J. Chem. Inf. Model., 2023)

HoverFast: an accurate, high-throughput, clinically deployable nuclear segmentation tool for brightfield digital pathology images. - Petros Liakopoulos; Julien Massonnet; Jonatan Bonjour; Medya Tekes Mizrakli; Simon Graham; Michel A. Cuendet; Amanda H. Seipel; Olivier Michielin; Doron Merkler; Andrew Janowczyk (J. Open Source Softw., 2024)