Where are the boundaries? Automated pocket detection for druggability studies. - Andrea Volkamer; Thomas Grombacher; Matthias Rarey (J. Cheminformatics, 2010)

Analyzing the Topology of Active Sites: On the Prediction of Pockets and Subpockets. - Andrea Volkamer; Axel Griewel; Thomas Grombacher; Matthias Rarey (J. Chem. Inf. Model., 2010)

DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment. - Andrea Volkamer; Daniel Kuhn; Friedrich Rippmann; Matthias Rarey (Bioinform., 2012)

Searching for Substructures in Fragment Spaces. - Hans-Christian Ehrlich; Andrea Volkamer; Matthias Rarey (J. Chem. Inf. Model., 2012)

Combining Global and Local Measures for Structure-Based Druggability Predictions. - Andrea Volkamer; Daniel Kuhn; Thomas Grombacher; Friedrich Rippmann; Matthias Rarey (J. Chem. Inf. Model., 2012)

Protein pocket and ligand shape comparison and its application in virtual screening. - Matthias Wirth; Andrea Volkamer; Vincent Zoete; Friedrich Rippmann; Olivier Michielin; Matthias Rarey; Wolfgang H. B. Sauer (J. Comput. Aided Mol. Des., 2013)

Fast Protein Binding Site Comparison via an Index-Based Screening Technology. - Mathias M. von Behren; Andrea Volkamer; Angela M. Henzler; Karen Schomburg; Sascha Urbaczek; Matthias Rarey (J. Chem. Inf. Model., 2013)

COMPASITES - Computer-aided active site analysis of protein structures. - Andrea Volkamer (2013)

Pocketome of Human Kinases: Prioritizing the ATP Binding Sites of (Yet) Untapped Protein Kinases for Drug Discovery. - Andrea Volkamer; Sameh Eid; Samo Turk; Sabrina Jaeger; Friedrich Rippmann; Simone Fulle (J. Chem. Inf. Model., 2015)

Identification and Visualization of Kinase-Specific Subpockets. - Andrea Volkamer; Sameh Eid; Samo Turk; Friedrich Rippmann; Simone Fulle (J. Chem. Inf. Model., 2016)

KinMap: a web-based tool for interactive navigation through human kinome data. - Sameh Eid; Samo Turk; Andrea Volkamer; Friedrich Rippmann; Simone Fulle (BMC Bioinform., 2017)

ProteinsPlus: a web portal for structure analysis of macromolecules. - Rainer Fährrolfes; Stefan Bietz; Florian Flachsenberg; Agnes Meyder; Eva Nittinger; Thomas Otto; Andrea Volkamer; Matthias Rarey (Nucleic Acids Res., 2017)

Transition from Academia to Industry and Back. - Andrea Volkamer; Sereina Riniker (J. Chem. Inf. Model., 2018)

TeachOpenCADD: a teaching platform for computer-aided drug design using open source packages and data. - Dominique Sydow; Andrea Morger; Maximilian Driller; Andrea Volkamer (J. Cheminformatics, 2019)

Advances and Challenges in Computational Target Prediction. - Dominique Sydow; Lindsey Burggraaff; Angelika Szengel; Herman W. T. van Vlijmen; Adriaan P. IJzerman; Gerard J. P. van Westen; Andrea Volkamer (J. Chem. Inf. Model., 2019)

TeachOpenCADD-KNIME: A Teaching Platform for Computer-Aided Drug Design Using KNIME Workflows. - Dominique Sydow; Michele Wichmann; Jaime Rodríguez-Guerra; Daria Goldmann; Gregory A. Landrum; Andrea Volkamer (J. Chem. Inf. Model., 2019)

Revealing cytotoxic substructures in molecules using deep learning. - Henry E. Webel; Talia B. Kimber; Silke Radetzki; Martin Neuenschwander; Marc Nazaré; Andrea Volkamer (J. Comput. Aided Mol. Des., 2020)

KnowTox: pipeline and case study for confident prediction of potential toxic effects of compounds in early phases of development. - Andrea Morger; Miriam Mathea; Janosch Achenbach; Antje Wolf; Roland Buesen; Klaus-Jürgen Schleifer; Robert Landsiedel; Andrea Volkamer (J. Cheminformatics, 2020)

Is Structure-Based Drug Design Ready for Selectivity Optimization? - Steven K. Albanese; John D. Chodera; Andrea Volkamer; Simon Keng; Robert Abel; Lingle Wang (J. Chem. Inf. Model., 2020)

KinFragLib: Exploring the Kinase Inhibitor Space Using Subpocket-Focused Fragmentation and Recombination. - Dominique Sydow; Paula Schmiel; Jérémie Mortier; Andrea Volkamer (J. Chem. Inf. Model., 2020)

Assessing the calibration in toxicological in vitro models with conformal prediction. - Andrea Morger; Fredrik Svensson; Staffan Arvidsson McShane; Niharika Gauraha; Ulf Norinder; Ola Spjuth; Andrea Volkamer (J. Cheminformatics, 2021)

ChemBioSim: Enhancing Conformal Prediction of In Vivo Toxicity by Use of Predicted Bioactivities. - Marina Garcia de Lomana; Andrea Morger; Ulf Norinder; Roland Buesen; Robert Landsiedel; Andrea Volkamer; Johannes Kirchmair; Miriam Mathea (J. Chem. Inf. Model., 2021)

KiSSim: Predicting Off-Targets from Structural Similarities in the Kinome. - Dominique Sydow; Eva Aßmann; Albert J. Kooistra; Friedrich Rippmann; Andrea Volkamer (J. Chem. Inf. Model., 2022)

OpenCADD-KLIFS: A Python package to fetch kinase data from the KLIFS database. - Dominique Sydow; Jaime Rodríguez-Guerra; Andrea Volkamer (J. Open Source Softw., 2022)

TeachOpenCADD 2022: open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research. - Dominique Sydow; Jaime Rodríguez-Guerra; Talia B. Kimber; David Schaller 002; Corey J. Taylor; Yonghui Chen; Mareike Leja; Sakshi Misra; Michele Wichmann; Armin Ariamajd; Andrea Volkamer (Nucleic Acids Res., 2022)

Guided Docking as a Data Generation Approach Facilitates Structure-Based Machine Learning on Kinases. - Michael Backenköhler; Joschka Groß; Verena Wolf; Andrea Volkamer (J. Chem. Inf. Model., 2024)

Benchmarking Cross-Docking Strategies in Kinase Drug Discovery. - David Schaller 002; Clara D. Christ; John D. Chodera; Andrea Volkamer (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)

Transformers for molecular property prediction: Domain adaptation efficiently improves performance. - Afnan Sultan; Max Rausch-Dupont; Shahrukh Khan; Olga Kalinina; Andrea Volkamer; Dietrich Klakow (CoRR, 2025)

PyPackIT: Automated Research Software Engineering for Scientific Python Applications on GitHub. - Armin Ariamajd; Raquel Lopez-Rios de Castro; Andrea Volkamer (CoRR, 2025)