Publications

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

    2021

  1. (2021). Garcinol from Garcinia indica inhibits HIV‐1 reverse transcriptase‐associated ribonuclease H. Archiv der Pharmazie e2100123. DOI: 10.1002/ardp.202100123.
  2. (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.
  3. (2021). Deep Learning in Virtual Screening: Recent Applications and Developments. International Journal of Molecular Sciences 22(9):4435. DOI: 10.3390/ijms22094435.
  4. (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.
  5. (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.
  6. (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.
  7. 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.
  8. (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.
  9. (2020). Revealing cytotoxic substructures in molecules using deep learning. Journal of Computer-Aided Molecular Design. DOI: 10.1007/s10822-020-00310-4.
  10. (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.
  11. 2019

  12. (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.
  13. (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.
  14. (2019). Advances and Challenges in Computational Target Prediction. Journal of Chemical Information and Modeling 59(5):1728-1742. DOI: 10.1021/acs.jcim.8b00832.
  15. (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.
  16. 2018

  17. (2018). Transition from Academia to Industry and Back. Journal of Chemical Information and Modeling 58(8):1469-1472. DOI: 10.1021/acs.jcim.8b00459.
  18. (2018). Truly Target-Focused Pharmacophore Modeling: A Novel Tool for Mapping Intermolecular Surfaces. Molecules 23(8):1959. DOI: 10.3390/molecules23081959.
  19. (2018). Prediction, Analysis and Comparison of Active Sites. Applied Cheminformatics - Achievements and Future Opportunities. Wiley 2. DOI: 10.1016/bs.armc.2017.08.001.
  20. 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.
  21. (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.
  22. (2017). KinMap: a web-based tool for interactive navigation through human kinome data. BMC Bioinformatics 18(16). DOI: 10.1186/s12859-016-1433-7.