SPICES: a particle-based molecular structure line notation and support library for mesoscopic simulation. - Karina van den Broek; Mirco Daniel; Matthias Epple; Hubert Kuhn; Jonas Schaub; Achim Zielesny (J. Cheminformatics, 2018)

ErtlFunctionalGroupsFinder: automated rule-based functional group detection with the Chemistry Development Kit (CDK). - Sebastian Fritsch; Stefan Neumann 001; Jonas Schaub; Christoph Steinbeck; Achim Zielesny (J. Cheminformatics, 2019)

Too sweet: cheminformatics for deglycosylation in natural products. - Jonas Schaub; Achim Zielesny; Christoph Steinbeck; Maria Sorokina (J. Cheminformatics, 2020)

An algorithm to classify homologous series within compound datasets. - Adelene Lai; Jonas Schaub; Christoph Steinbeck; Emma Schymanski (J. Cheminformatics, 2022)

Scaffold Generator: a Java library implementing molecular scaffold functionalities in the Chemistry Development Kit (CDK). - Jonas Schaub; Julian Zander; Achim Zielesny; Christoph Steinbeck (J. Cheminformatics, 2022)

MORTAR: a rich client application for in silico molecule fragmentation. - Felix Bänsch; Jonas Schaub; Betül Sevindik; Samuel Behr; Julian Zander; Christoph Steinbeck; Achim Zielesny (J. Cheminformatics, 2023)

Cheminformatics Microservice: unifying access to open cheminformatics toolkits. - Venkata Chandrasekhar; Nisha Sharma; Jonas Schaub; Christoph Steinbeck; Kohulan Rajan (J. Cheminformatics, 2023)

PySSA for Windows: End-User Protein Structure Prediction and Visual Analysis with ColabFold and PyMOL. - Hannah Kullik; Martin Urban; Jonas Schaub; Angelika Loidl-Stahlhofen; Achim Zielesny (J. Chem. Inf. Model., 2025)