Neuro-explicit AI
for Drug Discovery

@article{grossAssayBasedMachineLearningRethinking2026,
 author = {Groß, Joschka and Backenköhler, Michael and Volkamer, Andrea},
 doi = {10.1039/D6DD00472E},
 eprint = {https://pubs.rsc.org/dd/article-pdf/doi/10.1039/D6DD00472E/15052126/d6dd00472e.pdf},
 issn = {2635-098X},
 journal = {Digital Discovery},
 month = {11},
 title = {Assay-Based Machine Learning: Rethinking Evaluation in Drug Discovery},
 url = {https://doi.org/10.1039/D6DD00472E},
 year = {2026}
}

@article{grossEvaluationBeyondGoodnessOf2026,
 author = {Joschka Groß and Michael Backenköhler and Paula Linh Kramer and Raquel López-Ríos De Castro and Guillermo Pérez-Hernández and Verena Wolf and Andrea Volkamer},
 doi = {10.1016/j.ailsci.2026.100169},
 journal = {Artificial Intelligence in the Life Sciences (AILSCI)},
 month = {6},
 number = {article 100169},
 pages = {1-17},
 publisher = {Elsevier},
 title = {Evaluation beyond goodness of fit: Quantifying biophysical alignment of AI models for kinase-centric drug discovery},
 url = {https://www.sciencedirect.com/science/article/pii/S2667318526000176?via%3Dihub},
 volume = {9},
 year = {2026}
}

@article{linhkramerCustomkinfraglibFilteringTheKinaseFocused2026,
 author = {Linh Kramer, Paula and Buchthal, Katharina and Sydow, Dominique and Sonja Leo, Katharina and Volkamer, Andrea},
 doi = {10.1021/acsomega.5c12231},
 eprint = {https://pubs.acs.org/acsodf/article-pdf/11/10/16369/63264601/ao5c12231.pdf},
 issn = {2470-1343},
 journal = {ACS omega},
 month = {03},
 number = {10},
 pages = {16369--16380},
 publisher = {ACS Publications},
 title = {Customkinfraglib: Filtering the kinase-focused fragmentation library},
 url = {https://doi.org/10.1021/acsomega.5c12231},
 volume = {11},
 year = {2026}
}

@article{castroTheJourneyOfData2025,
 author = {Raquel López-Ríos de Castro and Jaime Rodríguez-Guerra and David Schaller and Talia K Kimber and Corey Taylor and Jessica B White and Michael Backenköhler and Joschka Groß and Alexander M Payne and Benjamin Kaminow and Ivan Pulido and Sukrit Singh and Paula Linh Kramer and Guilermo Pérez-Hernández and Andrea Volkamer and John D Chodera},
 doi = {10.33011/livecoms.6.1.3875},
 editor = {David L. Mobley and Michael R. Shirts and Daniel M. Zuckerman},
 journal = {Living Journal of Computational Molecular Science (LiveCoMS)},
 month = {11},
 number = {1},
 pages = {3875-3875},
 publisher = {University of Colorado Boulder, Boulder, Colorado, USA},
 title = {The Journey of Data: Lessons Learned in Modeling Kinase Affinity, Selectivity, and Resistance [Article v1. 0]},
 url = {https://www.dfki.de/fileadmin/user_upload/import/16917_The_Journey_of_Data_Lessons_Learned_in_Modeling_Ki.pdf},
 volume = {6},
 year = {2025}
}

@article{backenkohlerGuidedDockingAsA2024,
 author = {Michael Backenköhler and Joschka Groß and Verena Wolf and Andrea Volkamer},
 doi = {10.1021/acs.jcim.4c00055},
 journal = {Journal of Chemical Information and Modeling (JCIM)},
 month = {5},
 number = {10},
 pages = {4009-4020},
 publisher = {ACS Publications, Washington DC},
 title = {Guided docking as a data generation approach facilitates structure-based machine learning on kinases},
 url = {https://pubs.acs.org/doi/10.1021/acs.jcim.4c00055},
 volume = {64},
 year = {2024}
}

@inproceedings{backenkohlerStructuralActivityPredictionModels2024,
 author = {Michael Backenköhler and Joschka Groß and Paula Linh Kramer and Verena Wolf and Andrea Volkamer},
 booktitle = {ICML'24 Workshop ML for Life and Material Science: From Theory to Industry Applications. International Conference on Machine Learning (ICML-2024)},
 publisher = {Openreview},
 title = {Structural activity prediction models recover known binding modes (Poster abstract)},
 url = {https://openreview.net/forum?id=9O27GTKm1B},
 year = {2024}
}

@article{caiComputerScienceMethodsFor2023,
 author = {Wentong Cai and  Philipp Andelfinger and  Luca Bortolussi and  Christopher Carothers and  Dong Kevin Jin and  Till Köster and  Michael Lees and  Jason Liu and  Margaret Loper and  Alessandro Pellegrini and  Wen Jun Tan and Verena Wolf},
 journal = {Dagstuhl Reports},
 month = {5},
 number = {10},
 pages = {1-44},
 publisher = {Dagstuhl Reports},
 title = {Computer Science Methods for Effective and Sustainable Simulation Studies},
 volume = {12},
 year = {2023}
}

@article{backenkohlerTeachOpenCADDGoesDeepLearning2023,
 author = {Michael Backenköhler and Paula Linh Kramer and Joschka Groß and Gerrit Großmann and Roman Joeres and Azat Tagirdzhanov and Dominique Sydow and Hamza Ibrahim and Floriane Odje and Verena Wolf and Andrea Volkamer},
 doi = {10.26434/chemrxiv-2023-kz1pb},
 journal = {ChemRxiv},
 month = {5},
 pages = {---},
 publisher = {ChemRxiv.org},
 title = {TeachOpenCADD goes Deep Learning: Open-source Teaching Platform Exploring Molecular DL Applications},
 url = {https://doi.org/10.26434/chemrxiv-2023-kz1pb},
 volume = {ChemRxiv Online},
 year = {2023}
}