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2020 – today
- 2024
[j26]Michael Backenköhler
, Joschka Groß, Verena Wolf, Andrea Volkamer:
Guided Docking as a Data Generation Approach Facilitates Structure-Based Machine Learning on Kinases. J. Chem. Inf. Model. 64(10): 4009-4020 (2024)- [j25]Afnan Sultan, Jochen Sieg, Miriam Mathea, Andrea Volkamer:
Transformers for Molecular Property Prediction: Lessons Learned from the Past Five Years. J. Chem. Inf. Model. 64(16): 6259-6280 (2024) - [i1]Afnan Sultan, Jochen Sieg, Miriam Mathea, Andrea Volkamer:
Transformers for molecular property prediction: Lessons learned from the past five years. CoRR abs/2404.03969 (2024) - 2022
- [j24]Dominique Sydow, Eva Aßmann, Albert J. Kooistra, Friedrich Rippmann, Andrea Volkamer:
KiSSim: Predicting Off-Targets from Structural Similarities in the Kinome. J. Chem. Inf. Model. 62(10): 2600-2616 (2022) - [j23]Dominique Sydow, Jaime Rodríguez-Guerra, Andrea Volkamer:
OpenCADD-KLIFS: A Python package to fetch kinase data from the KLIFS database. J. Open Source Softw. 7(69): 3951 (2022) - [j22]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:
TeachOpenCADD 2022: open source and FAIR Python pipelines to assist in structural bioinformatics and cheminformatics research. Nucleic Acids Res. 50(W1): 753-760 (2022) - 2021
- [j21]Andrea Morger, Fredrik Svensson, Staffan Arvidsson McShane, Niharika Gauraha, Ulf Norinder, Ola Spjuth, Andrea Volkamer:
Assessing the calibration in toxicological in vitro models with conformal prediction. J. Cheminformatics 13(1): 35 (2021) - [j20]Marina Garcia de Lomana, Andrea Morger, Ulf Norinder, Roland Buesen, Robert Landsiedel, Andrea Volkamer, Johannes Kirchmair, Miriam Mathea:
ChemBioSim: Enhancing Conformal Prediction of In Vivo Toxicity by Use of Predicted Bioactivities. J. Chem. Inf. Model. 61(7): 3255-3272 (2021) - 2020
- [j19]Henry E. Webel, Talia B. Kimber, Silke Radetzki, Martin Neuenschwander, Marc Nazaré, Andrea Volkamer:
Revealing cytotoxic substructures in molecules using deep learning. J. Comput. Aided Mol. Des. 34(7): 731-746 (2020) - [j18]Andrea Morger, Miriam Mathea, Janosch Achenbach, Antje Wolf, Roland Buesen, Klaus-Jürgen Schleifer, Robert Landsiedel, Andrea Volkamer:
KnowTox: pipeline and case study for confident prediction of potential toxic effects of compounds in early phases of development. J. Cheminformatics 12(1): 24 (2020) - [j17]Dominique Sydow, Paula Schmiel, Jérémie Mortier, Andrea Volkamer:
KinFragLib: Exploring the Kinase Inhibitor Space Using Subpocket-Focused Fragmentation and Recombination. J. Chem. Inf. Model. 60(12): 6081-6094 (2020) - [j16]Steven K. Albanese, John D. Chodera, Andrea Volkamer, Simon Keng, Robert Abel, Lingle Wang:
Is Structure-Based Drug Design Ready for Selectivity Optimization? J. Chem. Inf. Model. 60(12): 6211-6227 (2020)
2010 – 2019
- 2019
- [j15]Dominique Sydow, Andrea Morger, Maximilian Driller, Andrea Volkamer:
TeachOpenCADD: a teaching platform for computer-aided drug design using open source packages and data. J. Cheminformatics 11(1): 29:1-29:7 (2019) - [j14]Dominique Sydow, Lindsey Burggraaff, Angelika Szengel, Herman W. T. van Vlijmen, Adriaan P. IJzerman, Gerard J. P. van Westen, Andrea Volkamer:
Advances and Challenges in Computational Target Prediction. J. Chem. Inf. Model. 59(5): 1728-1742 (2019) - [j13]Dominique Sydow, Michele Wichmann, Jaime Rodríguez-Guerra, Daria Goldmann, Gregory A. Landrum, Andrea Volkamer:
TeachOpenCADD-KNIME: A Teaching Platform for Computer-Aided Drug Design Using KNIME Workflows. J. Chem. Inf. Model. 59(10): 4083-4086 (2019) - 2018
- [j12]Andrea Volkamer, Sereina Riniker:
Transition from Academia to Industry and Back. J. Chem. Inf. Model. 58(8): 1469-1472 (2018) - 2017
- [j11]Sameh Eid, Samo Turk, Andrea Volkamer, Friedrich Rippmann, Simone Fulle:
KinMap: a web-based tool for interactive navigation through human kinome data. BMC Bioinform. 18(1): 16:1-16:6 (2017) - [j10]Rainer Fährrolfes, Stefan Bietz, Florian Flachsenberg, Agnes Meyder, Eva Nittinger, Thomas Otto, Andrea Volkamer, Matthias Rarey:
ProteinsPlus: a web portal for structure analysis of macromolecules. Nucleic Acids Res. 45(Webserver-Issue): W337-W343 (2017) - 2016
- [j9]Andrea Volkamer, Sameh Eid, Samo Turk, Friedrich Rippmann, Simone Fulle:
Identification and Visualization of Kinase-Specific Subpockets. J. Chem. Inf. Model. 56(2): 335-346 (2016) - 2015
- [j8]Andrea Volkamer, Sameh Eid, Samo Turk, Sabrina Jaeger, Friedrich Rippmann, Simone Fulle:
Pocketome of Human Kinases: Prioritizing the ATP Binding Sites of (Yet) Untapped Protein Kinases for Drug Discovery. J. Chem. Inf. Model. 55(3): 538-549 (2015) - 2013
- [b1]Andrea Volkamer:
COMPASITES - Computer-aided active site analysis of protein structures. University of Hamburg, 2013 - [j7]Matthias Wirth, Andrea Volkamer, Vincent Zoete, Friedrich Rippmann, Olivier Michielin, Matthias Rarey, Wolfgang H. B. Sauer:
Protein pocket and ligand shape comparison and its application in virtual screening. J. Comput. Aided Mol. Des. 27(6): 511-524 (2013) - [j6]Mathias M. von Behren, Andrea Volkamer, Angela M. Henzler, Karen Schomburg, Sascha Urbaczek, Matthias Rarey:
Fast Protein Binding Site Comparison via an Index-Based Screening Technology. J. Chem. Inf. Model. 53(2): 411-422 (2013) - 2012
- [j5]Andrea Volkamer, Daniel Kuhn, Friedrich Rippmann, Matthias Rarey:
DoGSiteScorer: a web server for automatic binding site prediction, analysis and druggability assessment. Bioinform. 28(15): 2074-2075 (2012) - [j4]Andrea Volkamer, Daniel Kuhn, Thomas Grombacher, Friedrich Rippmann, Matthias Rarey:
Combining Global and Local Measures for Structure-Based Druggability Predictions. J. Chem. Inf. Model. 52(2): 360-372 (2012) - [j3]Hans-Christian Ehrlich, Andrea Volkamer, Matthias Rarey:
Searching for Substructures in Fragment Spaces. J. Chem. Inf. Model. 52(12): 3181-3189 (2012) - 2010
- [j2]Andrea Volkamer, Thomas Grombacher, Matthias Rarey:
Where are the boundaries? Automated pocket detection for druggability studies. J. Cheminformatics 2(S-1): 11 (2010) - [j1]Andrea Volkamer, Axel Griewel, Thomas Grombacher, Matthias Rarey:
Analyzing the Topology of Active Sites: On the Prediction of Pockets and Subpockets. J. Chem. Inf. Model. 50(11): 2041-2052 (2010)
Coauthor Index
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