StructureProfiler: an all-in-one tool for 3D protein structure profiling. - Agnes Meyder; Stefanie Kampen; Jochen Sieg; Rainer Fährrolfes; Nils-Ole Friedrich; Florian Flachsenberg; Matthias Rarey (Bioinform., 2019)

In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening. - Jochen Sieg; Florian Flachsenberg; Matthias Rarey (J. Chem. Inf. Model., 2019)

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)

Methods for Processing and Analyzing Protein Structure Collections for Data-Driven Structure-Property Relationship Modeling - Jochen Sieg (2023)

Modeling with Alternate Locations in X-ray Protein Structures. - Torben Gutermuth; Jochen Sieg; Tim Stohn; Matthias Rarey (J. Chem. Inf. Model., 2023)

Single mutation protein structure pairs extracted from the PDB with MicroMiner. - Jochen Sieg; Matthias Rarey (UHH-FDR, 2023)

Searching similar local 3D micro-environments in protein structure databases with MicroMiner. - Jochen Sieg; Matthias Rarey (Briefings Bioinform., 2023)

MolPipeline: A Python Package for Processing Molecules with RDKit in Scikit-learn. - Jochen Sieg; Christian Feldmann; Jennifer Hemmerich; Conrad Stork; Frederik Sandfort; Philipp Eiden; Miriam Mathea (J. Chem. Inf. Model., 2024)

Transformers for Molecular Property Prediction: Lessons Learned from the Past Five Years. - Afnan Sultan; Jochen Sieg; Miriam Mathea; Andrea Volkamer (J. Chem. Inf. Model., 2024)