Publications

2026

  1. Arka Som, Marion V. F. Quijano Rincon, Nikolai Hempel, Lisa Johannknecht, Moritz L. Obenauer, Paul Czodrowski, Tanja Weil, Pol Besenius. Cucurbit[8]uril Couples Enzymatic and Supramolecular Reaction Networks for Peptide Isomerization and Recognition in Gain-of-Function Hydrogels ChemRxiv

2025

  1. Julien Hazemann, Thierry Kimmerlin, A. Mac Sweeney, Geoffroy Bourquin, Roland Lange, Daniel Ritz, Sylvia Richard‐Bildstein, Sylvain Regeon, Paul Czodrowski. Accelerating the Hit-To-Lead Optimization of a SARS-CoV-2 Mpro Inhibitor Series by Combining High-Throughput Medicinal Chemistry and Computational Simulations Journal of Medicinal Chemistry, 68(8), 8269–8294
  2. Son V. Ha, Steffen Jaensch, Maciej M. Kańduła, Dorota Herman, Paul Czodrowski, Hugo Ceulemans. Cross modality learning of cell painting and transcriptomics data improves mechanism of action clustering and bioactivity modelling Scientific Reports, 15(1), 23010
  3. Cruz C., Arsenio N., Pham, Thanh Huy, Zimmer, Collin, Massei, Riccardo, Sun, Yi, Czodrowski, Paul. From Cells to Morphological Profiles A FAIR cloud processing pipeline using Galaxy Zenodo (CERN European Organization for Nuclear Research)
  4. Anna Santura, J. J. Müller, Madita Wolter, Ina-Charlotte Tutzschky, Moritz Ruf, A. Metz, Anna Sandner, Stefan Merkl, Gerhard Klebe, Serghei Glinca et al.. Natural Product-like Fragments Unlock Novel Chemotypes for a Kinase Target─Exploring Options beyond the Flatland Journal of Chemical Information and Modeling, 66(4), 2249–2267
  5. Christoph Steinbeck, Nicole Jung, Felix Bach, Steffen Neumann, Sonja Herres‐Pawlis, Johannes C. Liermann, Oliver Koepler, Christoph Bannwarth, Theo Bender, Thomas Wilhelm Bocklitz et al.. Proposal NFDI4Chem 2025-2030 In the National Research Data Infrastructure (NFDI) — Our Vision: All Chemists Publish FAIR Data Research Ideas and Outcomes, 11
  6. Helge Vatheuer, Jonas Paulus, Lisa Johannknecht, Gerald Keller, Rebecca Maria Ziora, Lukas S. Stelzl, Paul Czodrowski. Proton First: Rationalizing a Proton Transfer in a Protein‐Fragment Complex ChemMedChem, 20(20), e202500244
  7. Helge Vatheuer, Oscar Palomino‐Hernández, Janis Müller, Phillip Galonska, Serghei Glinca, Paul Czodrowski. Protonation effects in protein-ligand complexes : a case study of Endothiapepsin and Pepstatin A with omputational and experimental methods Gutenberg Open Science
  8. Helge Vatheuer, Oscar Palomino‐Hernández, Janis Müller, Phillip Galonska, Serghei Glinca, Paul Czodrowski. Protonation Effects in Protein‐Ligand Complexes – A Case Study of Endothiapepsin and Pepstatin A with Computational and Experimental Methods ChemMedChem, 20(8), e202400953
  9. Nicolas Tielker, Michel Lim, Patrick Kibies, Juliana Gretz, Björn Hein‐Janke, Christian Chodun, Ricardo A. Mata, Paul Czodrowski, Stefan Michael Kast. The euroSAMPL1 p K a blind prediction and reproducible research data management challenge Physical Chemistry Chemical Physics, 27(36), 18855–18869

2024

  1. Son V. Ha, Lucas Leuschner, Paul Czodrowski. FSL-CP: a benchmark for small molecule activity few-shot prediction using cell microscopy images Digital Discovery, 3(4), 719–727
  2. Aishvarya Tandon, Anna Santura, Herbert Waldmann, Axel Pahl, Paul Czodrowski. Identification of lysosomotropism using explainable machine learning and morphological profiling cell painting data RSC Medicinal Chemistry, 15(8), 2677–2691
  3. Julien Hazemann, Thierry Kimmerlin, Roland Lange, A. Mac Sweeney, Geoffroy Bourquin, Daniel Ritz, Paul Czodrowski. Identification of SARS-CoV-2 Mpro inhibitors through deep reinforcement learning for de novo drug design and computational chemistry approaches RSC Medicinal Chemistry, 15(6), 2146–2159
  4. Son V. Ha, Steffen Jaensch, Lorena G. A. Freitas, Dorota Herman, Paul Czodrowski, Hugo Ceulemans. Low concentration cell painting images enable the identification of highly potent compounds Scientific Reports, 14(1), 24403

2023

  1. Susanne Grünewald, Lillian Rose Klug, Thomas Mühlenberg, Jonas Lategahn, Johanna Falkenhorst, Ajia Town, Christiane Ehrt, Eva Wardelmann, Wolfgang Hartmann, Hans‐Ulrich Schildhaus et al.. Data from Resistance to Avapritinib in PDGFRA-Driven GIST Is Caused by Secondary Mutations in the PDGFRA Kinase Domain
  2. Mike Bührmann, Shivakrishna Kallepu, Jonas D. Warmuth, Jan N. Wiese, Christiane Ehrt, Helge Vatheuer, Wolf Hiller, Carina Seitz, Laura M. Levy, Paul Czodrowski et al.. F ragtory : Pharmacophore-Focused Design, Synthesis, and Evaluation of an sp3-Enriched Fragment Library Journal of Medicinal Chemistry, 66(9), 6297–6314
  3. Lisa Goebel, Tonia Kirschner, Sandra Koska, Amrita Rai, Petra Janning, Stefano Maffini, Helge Vatheuer, Paul Czodrowski, Roger Sidney Goody, Matthias Philipp Müller et al.. Targeting oncogenic KRasG13C with nucleotide-based covalent inhibitors eLife, 12
  4. Sascha Jung, Helge Vatheuer, Paul Czodrowski. VSFlow: an open-source ligand-based virtual screening tool Journal of Cheminformatics, 15(1), 40

2021

  1. Jürgen Kolos, Sebastian J. Pomplun, Sascha Jung, Benedikt Rieß, Patrick L. Purder, Andreas M. Voll, Stephanie Merz, Monika T. Gnatzy, Thomas M. Geiger, Ingrid Quist-Løkken et al.. Picomolar FKBP inhibitors enabled by a single water-displacing methyl group in bicyclic [4.3.1] aza-amides Chemical Science, 12(44), 14758–14765
  2. José‐Manuel Gally, Axel Pahl, Paul Czodrowski, Herbert Waldmann. Pseudonatural Products Occur Frequently in Biologically Relevant Compounds Journal of Chemical Information and Modeling, 61(11), 5458–5468

2020

  1. Homma M. Khosroyani, Lillian Rose Klug, Ajia Town, Jonas Lategahn, Johanna Falkenhorst, Susanne Grünewald, Thomas Mühlenberg, Christiane Ehrt, E. Wardelmann, Wolfgang Hartmann et al.. Abstract 3005: Comprehensive profile of platelet derived growth factor receptor alpha (PDGFRA) mutations in gastrointestinal stromal tumors Cancer Research, 80(16_Supplement), 3005
  2. Christina Schindler, Hannah Magdalena Baumann, Andreas Blum, Dietrich Böse, Hans‐Peter Buchstaller, Lars T. Burgdorf, Daniel Cappel, Eugene L. Piatnitski Chekler, Paul Czodrowski, Dieter Dorsch et al.. Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects Journal of Chemical Information and Modeling, 60(11), 5457–5474
  3. Shubhendu Palei, Benjamin C. Buchmuller, Jan Wolffgramm, Álvaro Muñoz‐López, Sascha Jung, Paul Czodrowski, Daniel Summerer. Light-Activatable TET-Dioxygenases Reveal Dynamics of 5-Methylcytosine Oxidation and Transcriptome Reorganization Journal of the American Chemical Society, 142(16), 7289–7294
  4. Marcel Baltruschat, Paul Czodrowski. Machine learning meets pKa F1000Research, 9, 113
  5. Christoph Steinbeck, Oliver Koepler, Felix Bach, Sonja Herres‐Pawlis, Nicole Jung, Johannes C. Liermann, Steffen Neumann, Matthias Razum, Carsten Baldauf, Frank Biedermann et al.. NFDI4Chem – Towards a National Research Data Infrastructure for Chemistry in Germany Research Ideas and Outcomes, 6
  6. Susanne Grünewald, Lillian Rose Klug, Thomas Mühlenberg, Jonas Lategahn, Johanna Falkenhorst, Ajia Town, Christiane Ehrt, Eva Wardelmann, Wolfgang Hartmann, Hans‐Ulrich Schildhaus et al.. Resistance to Avapritinib in PDGFRA-Driven GIST Is Caused by Secondary Mutations in the PDGFRA Kinase Domain Cancer Discovery, 11(1), 108–125

2019

  1. Jessica J. Vamathevan, Dominic A. Clark, Paul Czodrowski, Ian Dunham, Edgardo A. Ferrán, George Lee, Bin Li, Anant Madabhushi, Parantu K. Shah, Michaela Spitzer et al.. Applications of machine learning in drug discovery and development Nature Reviews Drug Discovery, 18(6), 463–477
  2. Niklas Uhlenbrock, Steven P. Smith, Jörn Weisner, Ina Landel, Marius Lindemann, Thien Anh Le, Julia Hardick, Rajesh Gontla, Rebekka Scheinpflug, Paul Czodrowski et al.. Structural and chemical insights into the covalent-allosteric inhibition of the protein kinase Akt Chemical Science, 10(12), 3573–3585

2018

  1. Fabian Pitter Steinmetz, Carl Petersson, Ugo Zanelli, Paul Czodrowski. Building In Silico Models to Trigger Retesting: A Strategy on How to Use Predictive Models to Identify Potentially Incorrect In Vitro Intrinsic Clearance Results Applied In Vitro Toxicology, 5(2), 86–91

2017

  1. Michael Schauperl, Paul Czodrowski, Julian E. Fuchs, Roland G. Huber, Birgit J. Waldner, Maren Podewitz, Christian Krämer, Klaus Roman Liedl. Binding Pose Flip Explained via Enthalpic and Entropic Contributions Journal of Chemical Information and Modeling, 57(2), 345–354

2016

  1. Aurélie Mallinger, Kai Schiemann, Christian Rink, Jimmy J. P. Sejberg, Mark A. Honey, Paul Czodrowski, Mark Stubbs, Oliver Poeschke, Michael Busch, Richard Schneider et al.. 2,8-Disubstituted-1,6-Naphthyridines and 4,6-Disubstituted-Isoquinolines with Potent, Selective Affinity for CDK8/19 ACS Medicinal Chemistry Letters, 7(6), 573–578
  2. Paul Andrew Clarke, Christina Esdar, Aurélie Mallinger, Kai Schiemann, Dennis Waalboer, Simon Crumpler, Christian Rink, Frank Stieber, Michel Calderini, Olajumoke Adeniji-Popoola et al.. Abstract 3025: Discovery of preclinical development candidate inhibitors of the mediator complex-associated kinases CDK8 and CDK19 and evaluation of their therapeutic potential Cancer Research, 76(14_Supplement), 3025
  3. Kai Schiemann, Aurélie Mallinger, Dirk Wienke, Christina Esdar, Oliver Poeschke, Michael Busch, Felix Rohdich, Suzanne A. Eccles, Richard Schneider, Florence I. Raynaud et al.. Discovery of potent and selective CDK8 inhibitors from an HSP90 pharmacophore Bioorganic & Medicinal Chemistry Letters, 26(5), 1443–1451
  4. Aurélie Mallinger, Kai Schiemann, Christian Rink, Frank Stieber, Michel Calderini, Simon Crumpler, Mark Stubbs, Olajumoke Adeniji-Popoola, Oliver Poeschke, Michael Busch et al.. Discovery of Potent, Selective, and Orally Bioavailable Small-Molecule Modulators of the Mediator Complex-Associated Kinases CDK8 and CDK19 Journal of Medicinal Chemistry, 59(3), 1078–1101
  5. Paul Czodrowski, Wolf-Guido Bolick. OCEAN: Optimized Cross rEActivity estimatioN Journal of Chemical Information and Modeling, 56(10), 2013–2023
  6. Daria B. Kokh, Paul Czodrowski, Friedrich Rippmann, Rebecca C. Wade. Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets Journal of Chemical Theory and Computation, 12(8), 4100–4113
  7. Paul Czodrowski, Aurélie Mallinger, Dirk Wienke, Christina Esdar, Oliver Poeschke, Michael Busch, Felix Rohdich, Suzanne A. Eccles, Maria-Jesus Ortiz-Ruiz, Richard Schneider et al.. Structure-Based Optimization of Potent, Selective, and Orally Bioavailable CDK8 Inhibitors Discovered by High-Throughput Screening Journal of Medicinal Chemistry, 59(20), 9337–9349

2015

  1. Trevor C. Dale, Paul Andrew Clarke, Christina Esdar, Dennis Waalboer, Olajumoke Adeniji-Popoola, Maria-Jesus Ortiz-Ruiz, Aurélie Mallinger, Rahul S. Samant, Paul Czodrowski, Djordje Müsil et al.. A selective chemical probe for exploring the role of CDK8 and CDK19 in human disease Nature Chemical Biology, 11(12), 973–980

2014

  1. M. Neeb, Paul Czodrowski, A. Heine, Luzi Jakob Barandun, Christoph Hohn, François Diederich, Gerhard Klebe. Chasing Protons: How Isothermal Titration Calorimetry, Mutagenesis, and pKaCalculations Trace the Locus of Charge in Ligand Binding to a tRNA-Binding Enzyme Journal of Medicinal Chemistry, 57(13), 5554–5565
  2. Paul Czodrowski. Count on kappa Journal of Computer-Aided Molecular Design, 28(11), 1049–1055
  3. Ulrich A. K. Betz, Paul Czodrowski, Christina Esdar, Carl Deutsch, Norbert Beier, Dirk Finsinger, Bertram Cezanne, Klaus Urbahns, Margarita Wucherer-Plietker. Fluctuating Open Teams (FLOT) – A New Approach to Boost Team Creativity and Innovation Potential Technology Transfer and Entrepreneurship, 1(2), 77–81
  4. Paul Czodrowski, Günter Hölzemann, Gerhard Barnickel, Hartmut E. Greiner, Djordje Müsil. Selection of Fragments for Kinase Inhibitor Design: Decoration Is Key Journal of Medicinal Chemistry, 58(1), 457–465
  5. Stefan A. Samel, Paul Czodrowski, Lars‐Oliver Essen. Structure of the epimerization domain of tyrocidine synthetase A Acta Crystallographica Section D Biological Crystallography, 70(5), 1442–1452
  6. Ulrich Grädler, Paul Czodrowski, Christos Tsaklakidis, Markus Klein, Daniela Werkmann, S. Lindemann, K. Maskos, Birgitta Leuthner. Structure-based optimization of non-peptidic Cathepsin D inhibitors Bioorganic & Medicinal Chemistry Letters, 24(17), 4141–4150

2013

  1. Paul Czodrowski. hERG Me Out Journal of Chemical Information and Modeling, 53(9), 2240–2251
  2. Daria B. Kokh, Stefan Richter, Stefan Henrich, Paul Czodrowski, Friedrich Rippmann, Rebecca C. Wade. TRAPP: A Tool for Analysis ofTransient BindingPockets inProteins Journal of Chemical Information and Modeling, 53(5), 1235–1252

2012

  1. Paul Czodrowski. Who cares for the protons? Bioorganic & Medicinal Chemistry, 20(18), 5453–5460

2011

  1. Paul Czodrowski. Blind, one‐eyed, or eagle‐eyed? pKa calculations during blind predictions with staphylococcal nuclease Proteins Structure Function and Bioinformatics, 79(12), 3299–3305
  2. Paul Czodrowski, Chresten R. Søndergaard, Sebastian Dohm, Gerhard Klebe, Jens Erik Nielsen. LigpKa – a database of pKa values for small molecule ligands designed for the use in structure-based pKa calculations Journal of Cheminformatics, 3(S1)

2009

  1. Paul Czodrowski, Jan M. Kriegl, Stefan Scheuerer, Thomas Fox. Computational approaches to predict drug metabolism Expert Opinion on Drug Metabolism & Toxicology, 5(1), 15–27

2007

  1. Paul Czodrowski, Christoph Sotriffer, Gerhard Klebe. Atypical Protonation States in the Active Site of HIV-1 Protease: A Computational Study Journal of Chemical Information and Modeling, 47(4), 1590–1598
  2. Todd J. Dolinsky, Paul Czodrowski, Hui Li, Jens Erik Nielsen, Jan Halborg Jensen, Gerhard Klebe, Nathan Baker. PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations Nucleic Acids Research, 35(Web Server), W522–W525
  3. Paul Czodrowski, Christoph Sotriffer, Gerhard Klebe. Protonation Changes upon Ligand Binding to Trypsin and Thrombin: Structural Interpretation Based on pKa Calculations and ITC Experiments Journal of Molecular Biology, 367(5), 1347–1356
  4. H. Steuber, Paul Czodrowski, Christoph Sotriffer, Gerhard Klebe. Tracing Changes in Protonation: A Prerequisite to Factorize Thermodynamic Data of Inhibitor Binding to Aldose Reductase Journal of Molecular Biology, 373(5), 1305–1320

2006

  1. Paul Czodrowski, Ingo Dramburg, Christoph Sotriffer, Gerhard Klebe. Development, validation, and application of adapted PEOE charges to estimate pKa values of functional groups in protein–ligand complexes Proteins Structure Function and Bioinformatics, 65(2), 424–437
  2. Paul Czodrowski. Prediction of protonation states in ligand-protein complexes upon ligand binding Publikationsserver (Universitat Marburg)
  3. Angela Wittelsberger, Martina Corich, Beena E. Thomas, Byung-Kwon Lee, Alessandra Barazza, Paul Czodrowski, Dale F. Mierke, Michael Chorev, Michael Rosenblatt. The Mid-Region of Parathyroid Hormone (1−34) Serves as a Functional Docking Domain in Receptor Activation Biochemistry, 45(7), 2027–2034

Last updated: 21 October 2026