Andrea Volkamer

32 papers Journal 31

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Chemical Language Models for Natural Products: A State-Space Model Approach. CoRR Ho-Hsuan Wang, Afnan Sultan, Andrea Volkamer, Dietrich Klakow
2025	J	`jnl`	PyPackIT: Automated Research Software Engineering for Scientific Python Applications on GitHub. CoRR Armin Ariamajd, Raquel Lopez-Rios de Castro, Andrea Volkamer
2025	J	`jnl`	Transformers for molecular property prediction: Domain adaptation efficiently improves performance. CoRR Afnan Sultan, Max Rausch-Dupont, Shahrukh Khan, Olga Kalinina, Andrea Volkamer, Dietrich Klakow
2024	J	`jnl`	Benchmarking Cross-Docking Strategies in Kinase Drug Discovery. J. Chem. Inf. Model. David Schaller, Clara D. Christ, John D. Chodera, Andrea Volkamer
2024	J	`jnl`	Guided Docking as a Data Generation Approach Facilitates Structure-Based Machine Learning on Kinases. J. Chem. Inf. Model. Michael Backenköhler, Joschka Groß, Verena Wolf, Andrea Volkamer
2024	J	`jnl`	Transformers for Molecular Property Prediction: Lessons Learned from the Past Five Years. J. Chem. Inf. Model. Afnan Sultan, Jochen Sieg, Miriam Mathea, Andrea Volkamer
2024	J	`jnl`	Transformers for molecular property prediction: Lessons learned from the past five years. CoRR Afnan Sultan, Jochen Sieg, Miriam Mathea, Andrea Volkamer
2022	J	`jnl`	KiSSim: Predicting Off-Targets from Structural Similarities in the Kinome. J. Chem. Inf. Model. Dominique Sydow, Eva Aßmann, Albert J. Kooistra, Friedrich Rippmann, Andrea Volkamer
2022	J	`jnl`	OpenCADD-KLIFS: A Python package to fetch kinase data from the KLIFS database. J. Open Source Softw. Dominique Sydow, Jaime Rodríguez-Guerra, Andrea Volkamer
2022	J	`jnl`	TeachOpenCADD 2022: open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research. Nucleic Acids Res. Dominique Sydow, Jaime Rodríguez-Guerra, Talia B. Kimber, David Schaller, Corey J. Taylor, Yonghui Chen, Mareike Leja, Sakshi Misra, Michele Wichmann, Armin Ariamajd, Andrea Volkamer
2021	J	`jnl`	Assessing the calibration in toxicological in vitro models with conformal prediction. J. Cheminformatics Andrea Morger, Fredrik Svensson, Staffan Arvidsson McShane, Niharika Gauraha, Ulf Norinder, Ola Spjuth, Andrea Volkamer
2021	J	`jnl`	ChemBioSim: Enhancing Conformal Prediction of In Vivo Toxicity by Use of Predicted Bioactivities. J. Chem. Inf. Model. Marina Garcia de Lomana, Andrea Morger, Ulf Norinder, Roland Buesen, Robert Landsiedel, Andrea Volkamer, Johannes Kirchmair, Miriam Mathea
2020	J	`jnl`	Is Structure-Based Drug Design Ready for Selectivity Optimization? J. Chem. Inf. Model. Steven K. Albanese, John D. Chodera, Andrea Volkamer, Simon Keng, Robert Abel, Lingle Wang
2020	J	`jnl`	KinFragLib: Exploring the Kinase Inhibitor Space Using Subpocket-Focused Fragmentation and Recombination. J. Chem. Inf. Model. Dominique Sydow, Paula Schmiel, Jérémie Mortier, Andrea Volkamer
2020	J	`jnl`	KnowTox: pipeline and case study for confident prediction of potential toxic effects of compounds in early phases of development. J. Cheminformatics Andrea Morger, Miriam Mathea, Janosch Achenbach, Antje Wolf, Roland Buesen, Klaus-Jürgen Schleifer, Robert Landsiedel, Andrea Volkamer
2020	J	`jnl`	Revealing cytotoxic substructures in molecules using deep learning. J. Comput. Aided Mol. Des. Henry E. Webel, Talia B. Kimber, Silke Radetzki, Martin Neuenschwander, Marc Nazaré, Andrea Volkamer
2019	J	`jnl`	Advances and Challenges in Computational Target Prediction. J. Chem. Inf. Model. Dominique Sydow, Lindsey Burggraaff, Angelika Szengel, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen, Andrea Volkamer
2019	J	`jnl`	TeachOpenCADD-KNIME: A Teaching Platform for Computer-Aided Drug Design Using KNIME Workflows. J. Chem. Inf. Model. Dominique Sydow, Michele Wichmann, Jaime Rodríguez-Guerra, Daria Goldmann, Gregory A. Landrum, Andrea Volkamer
2019	J	`jnl`	TeachOpenCADD: a teaching platform for computer-aided drug design using open source packages and data. J. Cheminformatics Dominique Sydow, Andrea Morger, Maximilian Driller, Andrea Volkamer
2018	J	`jnl`	Transition from Academia to Industry and Back. J. Chem. Inf. Model. Andrea Volkamer, Sereina Riniker
2017	J	`jnl`	KinMap: a web-based tool for interactive navigation through human kinome data. BMC Bioinform. Sameh Eid, Samo Turk, Andrea Volkamer, Friedrich Rippmann, Simone Fulle
2017	J	`jnl`	ProteinsPlus: a web portal for structure analysis of macromolecules. Nucleic Acids Res. Rainer Fährrolfes, Stefan Bietz, Florian Flachsenberg, Agnes Meyder, Eva Nittinger, Thomas Otto, Andrea Volkamer, Matthias Rarey
2016	J	`jnl`	Identification and Visualization of Kinase-Specific Subpockets. J. Chem. Inf. Model. Andrea Volkamer, Sameh Eid, Samo Turk, Friedrich Rippmann, Simone Fulle
2015	J	`jnl`	Pocketome of Human Kinases: Prioritizing the ATP Binding Sites of (Yet) Untapped Protein Kinases for Drug Discovery. J. Chem. Inf. Model. Andrea Volkamer, Sameh Eid, Samo Turk, Sabrina Jaeger, Friedrich Rippmann, Simone Fulle
2013	—	`—`	COMPASITES - Computer-aided active site analysis of protein structures. Andrea Volkamer
2013	J	`jnl`	Fast Protein Binding Site Comparison via an Index-Based Screening Technology. J. Chem. Inf. Model. Mathias M. von Behren, Andrea Volkamer, Angela M. Henzler, Karen Schomburg, Sascha Urbaczek, Matthias Rarey
2013	J	`jnl`	Protein pocket and ligand shape comparison and its application in virtual screening. J. Comput. Aided Mol. Des. Matthias Wirth, Andrea Volkamer, Vincent Zoete, Friedrich Rippmann, Olivier Michielin, Matthias Rarey, Wolfgang H. B. Sauer
2012	J	`jnl`	Combining Global and Local Measures for Structure-Based Druggability Predictions. J. Chem. Inf. Model. Andrea Volkamer, Daniel Kuhn, Thomas Grombacher, Friedrich Rippmann, Matthias Rarey
2012	J	`jnl`	DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment. Bioinform. Andrea Volkamer, Daniel Kuhn, Friedrich Rippmann, Matthias Rarey
2012	J	`jnl`	Searching for Substructures in Fragment Spaces. J. Chem. Inf. Model. Hans-Christian Ehrlich, Andrea Volkamer, Matthias Rarey
2010	J	`jnl`	Analyzing the Topology of Active Sites: On the Prediction of Pockets and Subpockets. J. Chem. Inf. Model. Andrea Volkamer, Axel Griewel, Thomas Grombacher, Matthias Rarey
2010	J	`jnl`	Where are the boundaries? Automated pocket detection for druggability studies. J. Cheminformatics Andrea Volkamer, Thomas Grombacher, Matthias Rarey