Industry + academic experience
Experience spanning pharmaceutical R&D, computational chemistry and academic research.
Alessio Prunotto
Computational Chemist · Chemical Data Scientist
Zurich, Switzerland · Email · LinkedIn · GitHub · Google Scholar
Download CVResearch interests
- Computational Chemistry
- Chemoinformatics
- Machine Learning
- Drug Discovery
- Molecular Design
Highlights
Chemical AI / automation
Development of predictive and automated computational workflows.
Drug discovery
Experience across molecular modeling, docking, molecular dynamics and computational screening.
9 publications
Peer-reviewed research in computational chemistry and drug discovery.
Work Experience
Chemical Data Scientist — Synple Chem Aug 2025 – Present
Zurich, Switzerland
- Build and validate predictive models for chemical reactivity and solubility, physics-based and ML-based
- Integrate model outputs into automated synthesis workflows
Drug Hunter / Computational Chemist — Aqemia Feb 2022 – Jul 2025
Paris, France
- Contributed to early-stage drug discovery programs using protein modeling, molecular docking and molecular dynamics
- Led initiatives to automate and scale computational analyses, including MD trajectory analysis and ligand-pose assessment
- Developed computational workflows for evaluating protein–ligand interactions and ligand binding poses
Postdoctoral Researcher Nov 2020 – Jan 2022
Computer-aided Molecular Engineering group · Lausanne, Switzerland · Supervisor: Prof. Vincent Zoete
- Developed interaction-fingerprint methods to post-process docking outputs and assess ligand-pose quality
- Built a Rosetta-based scoring method for pMHC specificity towards T-cell receptors
Graduate Researcher Jul 2015 – Oct 2020
Laboratory for Biomolecular Modeling, EPFL · Lausanne, Switzerland · Supervisor: Prof. Matteo Dal Peraro
- Characterized membrane-binding mechanisms of two peripheral membrane proteins (NDM-1, Golph3), identifying candidate allosteric sites
- Proposed experimentally testable hypotheses from simulation data across several collaborative projects
Research Assistant Jan 2015 – Jun 2015
Laboratory for Biomolecular Modeling, EPFL · Lausanne, Switzerland
Supervisor: Prof. Matteo Dal Peraro
- Characterized aggregating properties of
Research Assistant Jan 2013 – Dec 2014
Computational Biophysics group, University of Applied Sciences and Arts of Southern Switzerland · Lugano, Switzerland · Supervisor: Prof. Andrea Danani
- Contributed to multiple structure-based drug discovery projects, including TLR7 mechanism-of-action studies
- Supervised a potency-optimization project for a GHS-R inverse agonist
Visiting Student Apr 2012 – Oct 2012
Li Ka Shing Institute of Virology, University of Alberta · Edmonton, Canada · Supervisors: Prof. Michael Houghton, Prof. Jack Tuszynski
- Automated the search for NS5B (hepatitis C polymerase) inhibitors via docking, homology modelling, MD and free-energy calculations (Master’s final project)
Education
Ph.D.
Computational Biology / Computational Chemistry
EPFL · Lausanne, Switzerland
M.Sc.
Biomedical Engineering
Polytechnic University of Turin · Turin, Italy
B.Sc.
Biomedical Engineering
Polytechnic University of Turin · Turin, Italy
Expertise
Computational chemistry
- Molecular docking
- Molecular dynamics
- Protein modeling
- Structure-based drug design
Cheminformatics & data science
- Chemical data analysis
- Molecular representations
- Machine learning
- Predictive modeling
Drug discovery
- Virtual screening
- Protein–ligand interactions
- Molecular design
Programming & tools
- Python
- RDKit
- PyTorch
- scikit-learn
- pandas
- NumPy
- AutoDock Vina
- GROMACS
- Rosetta
- Git
- Linux
- SLURM