- 2020. Similarity-Based Methods and Machine Learning Approaches for Target Prediction in Early Drug Discovery: Performance and Scope. International Journal of Molecular Sciences.
- 2020. Scope of 3D shape-based approaches in predicting the macromolecular targets of structurally complex small molecules including natural products and macrocyclic ligands. Journal of Chemical Information and Modeling.
- 2019. Validation strategies for target prediction methods. Briefings in Bioinformatics.
- 2019. Skin Doctor: Machine learning models for skin sensitization prediction that provide estimates and indicators of prediction reliability. International Journal of Molecular Sciences.
- 2019. Phenylethylene glycol-derived LpxC inhibitors with diverse Zn2+-binding groups. Tetrahedron. 486-509.
- 2019. NP-scout: Machine learning approach for the quantification and visualization of the natural product-likeness of small molecules. Biomolecules. 1-17.
- 2019. Hit Dexter 2.0: Machine-Learning Models for the Prediction of Frequent Hitters. Journal of Chemical Information and Modeling. 1030-1043.
- 2019. GLORY: Generator of the structures of likely cytochrome P450 metabolites based on predicted sites of metabolism. Frontiers in Chemistry. 402.
- 2019. FAME 3: Predicting the sites of metabolism in synthetic compounds and natural products for phase 1 and phase 2 metabolic enzymes. Journal of Chemical Information and Modeling. 3400-3412.
- 2019. Cryo-EM structure of pleconaril-resistant rhinovirus-B5 complexed to the antiviral OBR-5-340 reveals unexpected binding site. Proceedings of the National Academy of Sciences of the United States of America. 19109-19115.
- 2019. Conformator: A Novel Method for the Generation of Conformer Ensembles. Journal of Chemical Information and Modeling. 731-742.
- 2019. Analysis of the FLVR motif of SHIP1 and its importance for the protein stability of SH2 containing signaling proteins. Cellular Signalling. 109380.
- 2019. ALADDIN: Docking Approach Augmented by Machine Learning for Protein Structure Selection Yields Superior Virtual Screening Performance. Molecular informatics. 1900103.
- 2018. INH14, a small‐molecule urea derivative, inhibits the IKKα/β‐dependent TLR inflammatory response. ChemBioChem. 710-717.
- 2018. Computational methods and tools to predict cytochrome P450 metabolism for drug discovery. Chemical Biology and Drug Design. 377-386.
- 2018. PAIN(S) relievers for medicinal chemists: How in silico tools can assist in the identification of compounds prone to cause interference in biochemical and cell-based assays.
- 2018. Machine learning models for the prediction of xenobiotic metabolism.
- 2018. In silico prediction of xenobiotic metabolism.
- 2018. Characterization of the chemical space of purchasable natural products.
- 2018. Assessment and prediction of “bad actors” and “frequent hitters”.
- 2018. Computational prediction of xenobiotic metabolism.
- 2018. Computational methods for the prediction of compounds that cause false readouts in biochemical assays.
- 2019. NERDD: A web portal providing access to in silico tools for drug discovery. Bioinformatics.
Academic chapter/article/Conference paper
- 2019. Resources for chemical, biological, and structural data on natural products. 35 pages.
- 2018. Validation strategies for target prediction methods: Scope and limitations.
- 2018. On cytochrome P450 regioselectivity prediction as a stepping stone for the generation of structures of likely metabolites.
- 2018. Machine learning models for guiding protein structure selection lead to a boost in the performance of ensemble docking.
- 2018. Characterization of the readily obtainable natural products space.
Academic literature review
- 2020. Natural products against acute respiratory infections: Strategies and lessons learned. 1-28.
- 2018. Computational approaches for skin sensitization prediction. 738-760.