2025
MITE: the Minimum Information about a Tailoring Enzyme database for capturing specialized metabolite biosynthesis
Nucleic Acids Research (2025)
Nucleic Acids Research (2025)
Generative Modeling of Full-Atom Protein Conformations using Latent Diffusion on Graph Embeddings
arXiv, accepted at NeurIPS 2025 (2025)
arXiv, accepted at NeurIPS 2025 (2025)
Commit: Reaction classification and yield prediction using the differential reaction fingerprint DRFP
Digital Discovery (2025)
Digital Discovery (2025)
To Bin or not to Bin: Alternative Representations of Mass Spectra
arXiv, accepted at LMRL@ICLR 2025 (2025)
arXiv, accepted at LMRL@ICLR 2025 (2025)
Implicit Neural Representations of Molecular Vector-Valued Functions
arXiv, accepted at LMRL@ICLR 2025 (2025)
arXiv, accepted at LMRL@ICLR 2025 (2025)
2024
Language models can identify enzymatic active sites in protein sequences
Computational and Structural Biotechnology Journal 23, 1929–1937 (2024)
Computational and Structural Biotechnology Journal 23, 1929–1937 (2024)
2023
EnzymeMap: curation, validation and data-driven prediction of enzymatic reactions
Chemical Science 14, 14229–14242 (2023)
Chemical Science 14, 14229–14242 (2023)
Quantum chemical data generation as fill-in for reliability enhancement of machine-learning reaction and retrosynthesis planning
Digital Discovery 2, 663–673 (2023)
Digital Discovery 2, 663–673 (2023)
An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification
Journal of Cheminformatics 15 (2023)
Journal of Cheminformatics 15 (2023)
2022
Reaction classification and yield prediction using the differential reaction fingerprint DRFP
Digital Discovery 1, 91–97 (2022)
Digital Discovery 1, 91–97 (2022)
2021
Mapping the space of chemical reactions using attention-based neural networks
Nature Machine Intelligence 3, 144–152 (2021)
Nature Machine Intelligence 3, 144–152 (2021)
2020
One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome
Journal of Cheminformatics 12 (2020)
Journal of Cheminformatics 12 (2020)
Time is of the essence: containment of the SARS-CoV-2 epidemic in Switzerland from February to May 2020
medRxiv (2020)
medRxiv (2020)
Visualization of very large high-dimensional data sets as minimum spanning trees
Journal of Cheminformatics 12 (2020)
Journal of Cheminformatics 12 (2020)
2019
Optimizing TRPM4 inhibitors in the MHFP6 chemical space
European Journal of Medicinal Chemistry 166, 167–177 (2019)
European Journal of Medicinal Chemistry 166, 167–177 (2019)
2018
A probabilistic molecular fingerprint for big data settings
Journal of Cheminformatics 10, 144–152 (2018)
Journal of Cheminformatics 10, 144–152 (2018)
Exploring DrugBank in Virtual Reality Chemical Space
Journal of Chemical Information and Modeling 58, 1731–1735 (2018)
Journal of Chemical Information and Modeling 58, 1731–1735 (2018)
Deep Learning Invades Drug Design and Synthesis: Medical Chemistry and Chemical Biology Highlights
CHIMIA 72, 70 (2018)
CHIMIA 72, 70 (2018)
SmilesDrawer: Parsing and Drawing SMILES-Encoded Molecular Structures Using Client-Side JavaScript
Journal of Chemical Information and Modeling 58, 1–7 (2018)
Journal of Chemical Information and Modeling 58, 1–7 (2018)
2017
FUn: a framework for interactive visualizations of large, high-dimensional datasets on the web
Bioinformatics 34, 1433–1435 (2017)
Bioinformatics 34, 1433–1435 (2017)
Design, crystal structure and atomic force microscopy study of thioether ligated D,L-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa
Chemical Science 8, 643–649 (2017)
Chemical Science 8, 643–649 (2017)
Chemical space guided discovery of antimicrobial bridged bicyclic peptides against Pseudomonas aeruginosa and its biofilms
Chemical Science 8, 6784–6798 (2017)
Chemical Science 8, 6784–6798 (2017)
WebMolCS: A Web-Based Interface for Visualizing Molecules in Three-Dimensional Chemical Spaces
Journal of Chemical Information and Modeling 57, 643–649 (2017)
Journal of Chemical Information and Modeling 57, 643–649 (2017)