Publications

List of research articles published within the Volkamer Lab during the time at UdS and before at Charité. For additional, individual member’s and earlier publications refer to the Team section and click on any member profile.

    Preprints

    2025

    • Lucas Andersen
    • Max Rausch-Dupont
    • Alejandro Martínez León
    • Andrea Volkamer
    • Jochen S. Hub
    • Dietrich Klakow
    (2025). Accelerating ligand discovery by combining Bayesian optimization with MMGBSA-based binding affinity calculations. bioRxiv. DOI: 10.1101/2025.06.22.660936.
  2. (2025). CustomKinFragLib: Filtering the Kinase-Focused Fragmentation Library. ChemRxiv. DOI: 10.26434/chemrxiv-2025-3gz92.
  3. (2025). Increasing trustworthiness of machine learning-based drug sensitivity prediction with a multivariate random forest approach. ChemRxiv. DOI: 10.26434/chemrxiv-2025-ml78s.
  4. (2025). Evaluation Beyond Goodness of Fit: Biophysical Alignment of AI Models for Kinase-Centric Drug Discovery. ChemRxiv. DOI: 10.26434/chemrxiv-2025-qsw7v.
  5. (2025). Assay-Based Machine Learning: Rethinking Evaluation in Drug Discovery. ChemRxiv. DOI: 10.26434/chemrxiv-2025-zsk6d.
  6. (2025). PyPackIT: Automated Research Software Engineering for Scientific Python Applications on GitHub. arXiv. DOI: https://doi.org/10.48550/arXiv.2503.04921.
  7. (2025). Transformers for molecular property prediction: Domain adaptation efficiently improves performance. arXiv. DOI: https://doi.org/10.48550/arXiv.2503.03360.

    8. 2024

  8. (2024). Lessons learned during the journey of data: from experiment to model for predicting kinase affinity, selectivity, polypharmacology, and resistance. bioRxiv. DOI: 10.1101/2024.09.10.612176.
  9. (2024). DockM8: An All-in-One Open-Source Platform for Consensus Virtual Screening in Drug Design. ChemRxiv. DOI: 10.26434/chemrxiv-2024-17k46.
  10. (2024). Identification of Novel Smyd1 Inhibitors for Cardiovascular Disease Treatment through Molecular Modelling. ChemRxiv. DOI: 10.26434/chemrxiv-2024-qg66r.

    11. 2023

  11. (2023). TeachOpenCADD goes Deep Learning: Open-source Teaching Platform Exploring Molecular DL Applications. ChemRxiv. DOI: 10.26434/chemrxiv-2023-kz1pb.

    Peer-reviewed publications

    2025

    • Sven T. Sowa
    • Murat Kücükdisli
    • Yelena Mostinski
    • David Schaller
    • Carolina S. Vinagreiro
    • Davide Cirillo
    • Chiara Bosetti
    • Shoshy Alam Brinch
    • Kirsten van Laar
    • Anita Wegert
    • Ruben G. G. Leenders
    • Stefan Krauss
    • Jo Waaler
    • Andrea Volkamer
    • Lari Lehtiö
    • Marc Nazaré
    (2025). Deconstruction of Dual-Site Tankyrase Inhibitors Provides Insights into Binding Energetics and Suggests Critical Hotspots for Ligand Optimization. Journal of Medicinal Chemistry 68:7263-7279. DOI: 10.1021/acs.jmedchem.4c02845.
    • Sukrit Singh
    • Vytautas Gapsys
    • Matteo Aldeghi
    • David Schaller
    • Aziz M. Rangwala
    • Jessica B. White
    • Joseph P. Bluck
    • Jenke Scheen
    • William G. Glass
    • Jiaye Guo
    • Sikander Hayat
    • Bert L. de Groot
    • Andrea Volkamer
    • Clara D. Christ
    • Markus A. Seeliger
    • John D. Chodera
    (2025). Prospective Evaluation of Structure-Based Simulations Reveal Their Ability to Predict the Impact of Kinase Mutations on Inhibitor Binding. The Journal of Physical Chemistry B. DOI: https://doi.org/10.1021/acs.jpcb.4c07794.

    3. 2024

    • Fun Man Fung
    • Magdalena Lederbauer
    • Yvonne S.L. Choo
    • Timo Gehring
    • Kevin Maik Jablonka
    • Kjell Jorner
    • Philippe Schwaller
    • Michael B. Sullivan
    • Andrea Volkamer
    • Matthew S. Sigman
    • Kuangbiao Liao
    • Charles Windle
    (2024). Chemical education in digital chemistry. Chem 10:3519–3525. DOI: https://doi.org/10.1016/j.chempr.2024.10.010.
  4. (2024). Benchmarking Cross-Docking Strategies in Kinase Drug Discovery. Journal of Chemical Information and Modeling. DOI: 10.1021/acs.jcim.4c00905.
  5. (2024). Transformers for molecular property prediction: Lessons learned from the past five years. Journal of Chemical Information and Modeling 64:6259−6280. DOI: 10.1021/acs.jcim.4c00747.
  6. (2024). Unleashing the potential of cell painting assays for compound activities and hazards prediction. Frontiers in Toxicology 6(1). DOI: doi.org/10.3389/ftox.2024.1401036.
  7. (2024). Reliable Anti-Cancer Drug Sensitivity Prediction and Prioritization. Scientific Reports 14(1). DOI: https://doi.org/10.1038/s41598-024-62956-6.
  8. (2024). Guided docking as a data generation approach facilitates structure-based machine learning on kinases. Journal of Chemical Information and Modeling. DOI: 10.1021/acs.jcim.4c00055.
  9. (2024). Hit optimization by dynamic combinatorial chemistry on Streptococcus pneumoniae energy-coupling factor transporter ECF-PanT. Chemical Communications. DOI: https://doi.org/10.1039/D3CC04738E.

    10. 2023

    • Melissa L. Boby
    • Daren Fearon
    • Matteo Ferla
    • Mihajlo Filep
    • Lizbé Koekemoer
    • Matthew C. Robinson
    • The COVID Moonshot Consortium
    • (...
    • Jaime Rodríguez-Guerra
    • David Schaller
    • Andrea Volkamer
    • ...)
    • John D. Chodera
    • Alpha A. Lee
    • Nir London
    • Annette von Delft
    • Frank von Delft
    (2023). Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors. Science 382:eabo7201. DOI: 10.1126/science.abo7201.
    • Michael W. Mullowney 
    • Katherine R. Duncan 
    • Somayah S. Elsayed 
    • Neha Garg 
    • Justin J. J. van der Hooft 
    • Nathaniel I. Martin 
    • David Meijer 
    • Barbara R. Terlouw
    • Friederike Biermann
    • Kai Blin 
    • Janani Durairaj 
    • Marina Gorostiola González 
    • Eric J. N. Helfrich 
    • Florian Huber
    • Stefan Leopold-Messer
    • Kohulan Rajan 
    • Tristan de Rond
    • Jeffrey A. van Santen
    • Maria Sorokina 
    • Marcy J. Balunas
    • Mehdi A. Beniddir 
    • Doris A. van Bergeijk 
    • Laura M. Carroll
    • Chase M. Clark 
    • Djork-Arné Clevert
    • Chris A. Dejong
    • Chao Du
    • Scarlet Ferrinho
    • Francesca Grisoni
    • Albert Hofstetter
    • Willem Jespers
    • Olga V. Kalinina
    • Satria A. Kautsar
    • Hyunwoo Kim 
    • Tiago F. Leao
    • Joleen Masschelein
    • Evan R. Rees
    • Raphael Reher
    • Daniel Reker
    • Philippe Schwaller
    • Marwin Segler
    • Michael A. Skinnider 
    • Allison S. Walker
    • Egon L. Willighagen
    • Barbara Zdrazil
    • Nadine Ziemert
    • Rebecca J. M. Goss
    • Pierre Guyomard
    • Andrea Volkamer
    • William H. Gerwick
    • Hyun Uk Kim 
    • Rolf Müller
    • Gilles P. van Wezel
    • Gerard J. P. van Westen
    • Anna K. H. Hirsch
    • Roger G. Linington
    • Serina L. Robinson
    • Marnix H. Medema
    (2023). Artificial intelligence for natural product drug discovery. Nature Reviews Drug Discovery. DOI: 10.1038/s41573-023-00774-7.
  12. (2023). Chemical representation learning for toxicity prediction. Digital Discovery. DOI: https://doi.org/10.1039/D2DD00099G.
    • Florian Perner
    • Eytan M. Stein
    • Daniela V. Wenge
    • Sukrit Singh
    • Jeonghyeon Kim
    • Athina Apazidis
    • Homa Rahnamoun
    • Disha Anand
    • Christian Marinaccio
    • Charlie Hatton
    • Yanhe Wen
    • Richard M. Stone
    • David Schaller
    • Shoron Mowla
    • Wenbin Xiao,
    • Holly A. Gamlen
    • Aaron J. Stonestrom
    • Sonali Persaud
    • Elizabeth Ener
    • Jevon A. Cutler
    • John G. Doench
    • Gerard M. McGeehan
    • Andrea Volkamer
    • John D. Chodera
    • Radosław P. Nowak
    • Eric S. Fischer
    • Ross L. Levine
    • Scott A. Armstrong
    • Sheng F. Cai
    (2023). MEN1 mutations mediate clinical resistance to menin inhibition. Nature. DOI: https://doi.org/10.1038/s41586-023-05755-9.
    • Philipp Jordan
    • Amanda Costa
    • Edgar Specker
    • Oliver Popp
    • Andrea Volkamer
    • Regina Piske
    • Tessa Obrusnik
    • Sabrina Kleissle
    • Kevin Stuke
    • Andre Rex
    • Martin Neuenschwander
    • Jens Peter Von Kries
    • Marc Nazare
    • Phillip Mertins
    • Helmut Kettenmann
    • Susanne A. Wolf
    (2023). Small molecule inhibiting microglial nitric oxide release could become a potential treatment for neuroinflammation. PLoS ONE 18(2). DOI: https://doi.org/10.1371/journal.pone.0278325.
    • Andrea Volkamer
    • Sereina Riniker
    • Eva Nittinger
    • Jessica Lanini
    • Francesca Grisoni
    • Emma Evertsson
    • Raquel Rodríguez-Pérez
    • Nadine Schneider
    (2023). Machine learning for small molecule drug discovery in academia and industry. Artificial Intelligence in the Life Sciences 3:100056. DOI: https://doi.org/10.1016/j.ailsci.2022.100056.

    16. 2022

  16. (2022). Kinase Similarity Assessment Pipeline for Off-Target Prediction [v1.0]. Living Journal of Computational Molecular Science 3(1):1599. DOI: 10.33011/livecoms.3.1.1599.
  17. (2022). KiSSim: Predicting Off-Targets from Structural Similarities in the Kinome. Journal of Chemical Information and Modeling 62(10):2600-2616. DOI: 10.1021/acs.jcim.2c00050.
  18. (2022). TeachOpenCADD 2022: Open Source and FAIR Python Pipelines to Assist in Structural Bioinformatics and Cheminformatics Research. Nucleic Acids Research. DOI: 10.1093/nar/gkac267.
  19. (2022). Studying and mitigating the effects of data drifts on ML model performance at the example of chemical toxicity data. Scientific Reports 12(7244). DOI: 10.1038/s41598-022-09309-3.
  20. (2022). OpenCADD-KLIFS: A Python package to fetch kinase data from the KLIFS database. The Journal of Open Source Software 7(70):3951. DOI: 10.21105/joss.03951.
    • Suzanne Ackloo
    • Rima Al-awar
    • Rommie E. Amaro
    • Cheryl H. Arrowsmith
    • Hatylas Azevedo
    • Robert A. Batey
    • Yoshua Bengio
    • Ulrich A. K. Betz
    • Cristian G. Bologa
    • John D. Chodera
    • Wendy D. Cornell
    • Ian Dunham
    • Gerhard F. Ecker
    • Kristina Edfeldt
    • Aled M. Edwards
    • Michael K. Gilson
    • Claudia R. Gordijo
    • Gerhard Hessler
    • Alexander Hillisch
    • Anders Hogner
    • John J. Irwin
    • Johanna M. Jansen
    • Daniel Kuhn
    • Andrew R. Leach
    • Alpha A. Lee
    • Uta Lessel
    • Maxwell R. Morgan
    • John Moult
    • Ingo Muegge
    • Tudor I. Oprea
    • Benjamin G. Perry
    • Patrick Riley
    • Sophie A. L. Rousseaux
    • Kumar Singh Saikatendu
    • Vijayaratnam Santhakumar
    • Matthieu Schapira
    • Cora Scholten
    • Matthew H. Todd
    • Masoud Vedadi
    • Andrea Volkamer
    • Timothy M. Willson
    (2022). CACHE (Critical Assessment of Computational Hit-finding Experiments): A public–private partnership benchmarking initiative to enable the development of computational methods for hit-finding. Nature Reviews Chemistry. DOI: 10.1038/s41570-022-00363-z.
    • Marina Garcia del Lomana
    • Fredrik Svensson
    • Andrea Volkamer
    • Miriam Mathea
    • Johannes Kirchmair
    (2022). Consideration of predicted small-molecule metabolites in computational toxicology. Digital Discovery. DOI: 10.1039/D1DD00018G.
  23. (2022). Quantitative high-throughput phenotypic screening for environmental estrogens using the E-Morph Screening Assay in combination with in silico predictions. Environment International 158:106947. DOI: https://doi.org/10.1016/j.envint.2021.106947.

    24. 2021

  24. (2021). Maxsmi: Maximizing molecular property prediction performance with confidence estimation using SMILES augmentation and deep learning. Artificial Intelligence in the Life Sciences 1:100014. DOI: 10.1016/j.ailsci.2021.100014.
  25. (2021). Teaching Computer-Aided Drug Design Using TeachOpenCADD. Teaching Programming across the Chemistry Curriculum. ACS Symposium Series 1387. DOI: 10.1021/bk-2021-1387.ch010.
  26. (2021). ChemBioSim: Enhancing Conformal Prediction of In Vivo Toxicity by Use of Predicted Bioactivities. Journal of Chemical Information and Modeling 61(7):3255-3272. DOI: 10.1021/acs.jcim.1c00451.
  27. (2021). Garcinol from Garcinia indica inhibits HIV‐1 reverse transcriptase‐associated ribonuclease H. Archiv der Pharmazie e2100123. DOI: 10.1002/ardp.202100123.
  28. (2021). Assessing the calibration in toxicological in vitro models with conformal prediction. Journal of Cheminformatics 13(1):35. DOI: 10.1186/s13321-021-00511-5.
  29. (2021). Deep Learning in Virtual Screening: Recent Applications and Developments. International Journal of Molecular Sciences 22(9):4435. DOI: 10.3390/ijms22094435.
  30. (2021). New 3-Aryl-2-(2-thienyl)acrylonitriles with High Activity Against Hepatoma Cells. International Journal of Molecular Sciences 22(5):2243. DOI: 10.3390/ijms22052243.
  31. (2021). Analyzing Kinase Similarity in Small Molecule and Protein Structural Space to Explore the Limits of Multi-Target Screening. Molecules 26. DOI: 10.3390/molecules26030629.
  32. (2021). Stability of Smyd1 in endothelial cells is controlled by PML-dependent SUMOylation upon cytokine stimulation. Biochemical Journal 478(1):217–234. DOI: 10.1042/BCJ20200603.

    33. 2020

    • Yelena Mostinski
    • Guus J. J. E. Heynen
    • Maria Pascual López-Alberca
    • Jerome Paul
    • Sandra Miksche
    • Silke Radetzki
    • David Schaller
    • Elena Shanina
    • Carola Seyffarth
    • Yuliya Kolomeets
    • Nandor Ziebart
    • Judith de Schryver
    • Sylvia Oestreich
    • Martin Neuenschwander
    • Yvette Roske
    • Udo Heinemann
    • Christoph Rademacher
    • Andrea Volkamer
    • Jens Peter von Kries
    • Walter Birchmeier
    • Marc Nazaré
    (2020). From Pyrazolones to Azaindoles: Evolution of Active-Site SHP2 Inhibitors Based on Scaffold Hopping and Bioisosteric Replacement. Journal of Medicinal Chemistry 63(23):14780-14804. DOI: 10.1021/acs.jmedchem.0c01265.
  34. (2020). KinFragLib: Exploring the Kinase Inhibitor Space Using Subpocket-Focused Fragmentation and Recombination. Journal of Chemical Information and Modeling. DOI: 10.1021/acs.jcim.0c00839.
    • Steven K. Albanese
    • John D. Chodera
    • Andrea Volkamer
    • Simon Keng
    • Robert Abel
    • Lingle Wang
    (2020). Is Structure-Based Drug Design Ready for Selectivity Optimization?. Journal of Chemical Information and Modeling. DOI: 10.1021/acs.jcim.0c00815.
  36. (2020). Revealing cytotoxic substructures in molecules using deep learning. Journal of Computer-Aided Molecular Design. DOI: 10.1007/s10822-020-00310-4.
  37. (2020). KnowTox: pipeline and case study for confident prediction of potential toxic effects of compounds in early phases of development. Journal of Cheminformatics 12(24). DOI: 10.1186/s13321-020-00422-x.

    38. 2019

  38. (2019). TeachOpenCADD-KNIME: A Teaching Platform for Computer-Aided Drug Design Using KNIME Workflows. Journal of Chemical Information and Modeling 59(10):4083-4086. DOI: 10.1021/acs.jcim.9b00662.
    • Jens Schoene
    • Thais Gazzi
    • Peter Lindemann
    • Mathias Christmann
    • Andrea Volkamer
    • Marc Nazaré
    (2019). Probing 2H-Indazoles as Template for SGK1, Tie2 and SRC Kinase Inhibitors. ChemMedChem 14(16):1514-1527. DOI: 10.1002/cmdc.201900328.
    • Natalia Ernst
    • Konstantin Fackeldey
    • Andrea Volkamer
    • Oliver Opatz
    • Marcus Weber
    (2019). Computation of temperature-dependent dissociation rates of metastable protein-ligand complexes. Molecular Simulation 45(11):904-911. DOI: 10.1080/08927022.2019.1610949.
  41. (2019). TeachOpenCADD: a teaching platform for computer-aided drug design using open source packages and data. Journal of Cheminformatics 11(29). DOI: 10.1186/s13321-019-0351-x.
  42. (2019). Advances and Challenges in Computational Target Prediction. Journal of Chemical Information and Modeling 59(5):1728-1742. DOI: 10.1021/acs.jcim.8b00832.
  43. (2019). Oxazole-Bridged Combretastatin A-4 Derivatives with Tethered Hydroxamic Acids: Structure–Activity Relations of New Inhibitors of HDAC and/or Tubulin Function. International Journal of Molecular Sciences 20(2):338. DOI: 10.3390/ijms20020383.

    44. 2018

  44. (2018). Transition from Academia to Industry and Back. Journal of Chemical Information and Modeling 58(8):1469-1472. DOI: 10.1021/acs.jcim.8b00459.
  45. (2018). Truly Target-Focused Pharmacophore Modeling: A Novel Tool for Mapping Intermolecular Surfaces. Molecules 23(8):1959. DOI: 10.3390/molecules23081959.
  46. (2018). Prediction, Analysis and Comparison of Active Sites. Applied Cheminformatics - Achievements and Future Opportunities. Wiley 2. DOI: 10.1016/bs.armc.2017.08.001.

    47. 2017

    • Stefan Bietz
    • Therese Inhester
    • Florian Lauck
    • Kai Sommer
    • Mathias M. von Behren
    • Rainer Fährrolfes
    • Florian Flachsenberg
    • Agnes Meyder
    • Eva Nittinger
    • Thomas Otto
    • Matthias Hilbig
    • Karen T. Schomburg
    • Andrea Volkamer
    • Matthias Rarey
    (2017). From cheminformatics to structure-based design: Web services and desktop applications based on the NAOMI library. Journal of Biotechnology 261(10):207 - 214. DOI: 10.1016/j.jbiotec.2017.06.004.
  48. (2017). Kinase-Centric Computational Drug Development. Annual Reports in Medicinal Chemistry (Elsevier) 50:197 - 236. DOI: 10.1016/bs.armc.2017.08.001.
    • Rainer Fährrolfes
    • Stefan Bietz
    • Florian Flachsenberg
    • Agnes Meyder
    • Eva Nittinger
    • Thomas Otto
    • Andrea Volkamer
    • Matthias Rarey
    (2017). ProteinsPlus: a web portal for structure analysis of macromolecules. Nucleic Acids Research 45(W1):W337-W343. DOI: 10.1093/nar/gkx333.
    • Annemarie Lang
    • Andrea Volkamer
    • Laura Behm
    • Susanna Röblitz
    • Rainald Ehrig
    • Marlon Schneider
    • Liesbet Geris
    • Joerg Wichard
    • Frank Buttgereit
    (2017). In silico methods – Computational alternatives to animal testing. ALTEX - Alternatives to animal experimentation 35(1):126-128. DOI: 10.14573/altex.1712031.
  51. (2017). KinMap: a web-based tool for interactive navigation through human kinome data. BMC Bioinformatics 18(16). DOI: 10.1186/s12859-016-1433-7.