Publications

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

    Preprints

    2024

    • Skrit 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
    (2024). Prospective evaluation of structure-based simulations reveal their ability to predict the impact of kinase mutations on inhibitor binding. bioRxiv. DOI: 10.1101/2024.11.15.623861.
  2. (2024). DockM8: An All-in-One Open-Source Platform for Consensus Virtual Screening in Drug Design. ChemRxiv. DOI: 10.26434/chemrxiv-2024-17k46.
  3. (2024). Analyzing Interfaces, Interactions and Self-Assembly in Soft Matter Simulations with PySoftK. ChemRxiv. DOI: 10.26434/chemrxiv-2024-1lbpg.
  4. (2024). Identification of Novel Smyd1 Inhibitors for Cardiovascular Disease Treatment through Molecular Modelling. ChemRxiv. DOI: 10.26434/chemrxiv-2024-qg66r.

    5. 2023

  5. (2023). TeachOpenCADD goes Deep Learning: Open-source Teaching Platform Exploring Molecular DL Applications. ChemRxiv. DOI: 10.26434/chemrxiv-2023-kz1pb.

    Peer-reviewed publications

    2024

  1. (2024). Benchmarking Cross-Docking Strategies in Kinase Drug Discovery. Journal of Chemical Information and Modeling. DOI: 10.1021/acs.jcim.4c00905.
  2. (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.
  3. (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.
  4. (2024). Reliable Anti-Cancer Drug Sensitivity Prediction and Prioritization. Scientific Reports 14(1). DOI: https://doi.org/10.1038/s41598-024-62956-6.
  5. (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.4c0005.
  6. (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.

    7. 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.
  9. (2023). Hurdles and signposts on the road to virtual control groups—A case study illustrating the influence of anesthesia protocols on electrolyte levels in rats. Frontiers in Pharmacology 14. DOI: 10.3389/fphar.2023.1142534.
  10. (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.

    14. 2022

  14. (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.
  15. (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.
  16. (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.
  17. (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.
  18. (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.
  21. (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.

    22. 2021

  22. (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.
  23. (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.
  24. (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.
  25. (2021). Garcinol from Garcinia indica inhibits HIV‐1 reverse transcriptase‐associated ribonuclease H. Archiv der Pharmazie e2100123. DOI: 10.1002/ardp.202100123.
  26. (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.
  27. (2021). Deep Learning in Virtual Screening: Recent Applications and Developments. International Journal of Molecular Sciences 22(9):4435. DOI: 10.3390/ijms22094435.
  28. (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.
  29. (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.
  30. (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.

    31. 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.
  32. (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.
  34. (2020). Revealing cytotoxic substructures in molecules using deep learning. Journal of Computer-Aided Molecular Design. DOI: 10.1007/s10822-020-00310-4.
  35. (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.

    36. 2019

  36. (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.
  39. (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.
  40. (2019). Advances and Challenges in Computational Target Prediction. Journal of Chemical Information and Modeling 59(5):1728-1742. DOI: 10.1021/acs.jcim.8b00832.
  41. (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.

    42. 2018

  42. (2018). Transition from Academia to Industry and Back. Journal of Chemical Information and Modeling 58(8):1469-1472. DOI: 10.1021/acs.jcim.8b00459.
  43. (2018). Truly Target-Focused Pharmacophore Modeling: A Novel Tool for Mapping Intermolecular Surfaces. Molecules 23(8):1959. DOI: 10.3390/molecules23081959.
  44. (2018). Prediction, Analysis and Comparison of Active Sites. Applied Cheminformatics - Achievements and Future Opportunities. Wiley 2. DOI: 10.1016/bs.armc.2017.08.001.

    45. 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.
  46. (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.
  49. (2017). KinMap: a web-based tool for interactive navigation through human kinome data. BMC Bioinformatics 18(16). DOI: 10.1186/s12859-016-1433-7.