Connected Subgraph Fingerprints: Representing Molecules Using Exhaustive Subgraph Enumeration. - Louis Bellmann; Patrick Penner; Matthias Rarey (J. Chem. Inf. Model., 2019)

A Consistent Scheme for Gradient-Based Optimization of Protein-Ligand Poses. - Florian Flachsenberg; Agnes Meyder; Kai Sommer; Patrick Penner; Matthias Rarey (J. Chem. Inf. Model., 2020)

Shape-Based Descriptors for Efficient Structure-Based Fragment Growing. - Patrick Penner; Virginie Y. Martiny; Arnaud Gohier; Marcus Gastreich; Pierre Ducrot; David Brown; Matthias Rarey (J. Chem. Inf. Model., 2020)

Topological Similarity Search in Large Combinatorial Fragment Spaces. - Louis Bellmann; Patrick Penner; Matthias Rarey (J. Chem. Inf. Model., 2021)

FastGrow: on-the-fly growing and its application to DYRK1A. - Patrick Penner; Virginie Y. Martiny; Louis Bellmann; Florian Flachsenberg; Marcus Gastreich; Isabelle Theret; Christophe Meyer; Matthias Rarey (J. Comput. Aided Mol. Des., 2022)

Comparison of Combinatorial Fragment Spaces and Its Application to Ultralarge Make-on-Demand Compound Catalogs. - Louis Bellmann; Patrick Penner; Marcus Gastreich; Matthias Rarey (J. Chem. Inf. Model., 2022)

The Torsion Library: Semiautomated Improvement of Torsion Rules with SMARTScompare. - Patrick Penner; Wolfgang Guba; Robert Schmidt 002; Agnes Meyder; Martin Stahl; Matthias Rarey (J. Chem. Inf. Model., 2022)

ProteinsPlus: a comprehensive collection of web-based molecular modeling tools. - Katrin Schöning-Stierand; Konrad Diedrich; Christiane Ehrt; Florian Flachsenberg; Joel Graef; Jochen Sieg; Patrick Penner; Martin Poppinga; Annett Ungethüm; Matthias Rarey (Nucleic Acids Res., 2022)

Shape-based methods for Structure-based Fragment Growing - Patrick Penner (2022)

QM assisted ML for 19F NMR chemical shift prediction. - Patrick Penner; Anna Vulpetti (J. Comput. Aided Mol. Des., 2024)