To content

Publications- Journal Articles

2020

31. Baltruschat, M.; Czodrowski, P. Machine Learning Meets pKa. F1000Research 2020, 9, 113. doi.org/10.12688/f1000research.22090.2.

30. Palei, S.; Buchmuller, B. C.; Wolffgramm, J.; Muñoz-López, Á.; Jung, S.; Czodrowski, P.; Summerer, D. Light-Activatable TET-Dioxygenases Reveal Dynamics of 5-Methylcytosine Oxidation and Transcriptome Reorganization. Journal of the American Chemical Society 2020, 142 (16), 7289–7294. doi.org/10.1021/jacs.0c01193.

2019

29. Vamathevan, J.; Clark, D.; Czodrowski, P.; Dunham, I.; Ferran, E.; Lee, G.; Li, B.; Madabhushi, A.; Shah, P.; Spitzer, M.; et al.
Applications of Machine Learning in Drug Discovery and Development.
Nature reviews / Drug discovery 2019, 2019doi.org/10.1038/s41573-019-0024-5

28. Steinmetz, F. P.; Petersson, C.; Zanelli, U.; Czodrowski, P.
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 2019, 5 (2), 86–91. doi.org/10.1089/aivt.2018.0018

27. Rauh, D.; Smith, S.; Weisner, J.; Landel, I.; Lindemann, M.; Le, T. A.; Hardick, J.; Gontla, R.; Scheinpflug, R.; Czodrowski, P.; et al.
Structural and Chemical Insights into the Covalent-Allosteric Inhibition of the Protein Kinase Akt.
Chemical science 2019, 2019 (10), 3573–3585. doi.org/10.1039/C8SC05212C

2017

26. Schauperl, M.; Czodrowski, P.; Fuchs, J. E.; Huber, R. G.; Waldner, B. J.; Podewitz, M.; Kramer, C.; Liedl, K. R.
Binding Pose Flip Explained via Enthalpic and Entropic Contributions.
Journal of chemical in­for­mation and modeling 2017, 57 (2), 345–354. doi.org/10.1021/acs.jcim.6b00483

2016

25. Mallinger, A.; Schiemann, K.; Rink, C.; Sejberg, J.; Honey, M. A.; Czodrowski, P.; Stubbs, M.; Poeschke, O.; Busch, M.; Schneider, R.; et al.
2,8-Disubstituted-1,6-Naphthyridines and 4,6-Disubstituted-Isoquinolines with Potent, Selective Affinity for CDK8/19.
ACS medicinal chemistry letters / American Chemical Society 2016, 7 (6), 573–578. doi.org/10.1021/acsmedchemlett.6b00022

24. Kokh, D. B.; Czodrowski, P.; Rippmann, F.; Wade, R. C.
Perturbation Approaches for Exploring Protein Binding Site Flexibility to Predict Transient Binding Pockets.
Journal of chemical theory and computation 2016, 12 (8), 4100–4113. doi.org/10.1021/acs.jctc.6b00101

23. Czodrowski, P.; Bolick, W.-G.
OCEAN: Optimized Cross rEActivity estimatioN.
Journal of chemical in­for­mation and modeling 2016, 56 (10), 2013–2023. doi.org/10.1021/acs.jcim.6b00067

22. Mallinger, A.; Schiemann, K.; Rink, C.; Stieber, F.; Calderini, M.; Crumpler, S.; Stubbs, M.; Adeniji-Popoola, O.; Poeschke, O.; Busch, M.; 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 2016, 59 (3), 1078–1101. doi.org/10.1021/acs.jmedchem.5b01685

21. Czodrowski, P.; Mallinger, A.; Wienke, D.; Esdar, C.; Pöschke, O.; Busch, M.; Rohdich, F.; Eccles, S. A.; Ortiz-Ruiz, M.-J.; Schneider, R.; et al.
Structure-Based Optimization of Potent, Selective, and Orally Bioavailable CDK8 Inhibitors Discovered by High-Throughput Screening.
Journal of medicinal chemistry 2016, 59 (20), 9337–9349. doi.org/10.1021/acs.jmedchem.6b00597

20. Schiemann, K.; Mallinger, A.; Wienke, D.; Esdar, C.; Poeschke, O.; Busch, M.; Rohdich, F.; Eccles, S. A.; Schneider, R.; Raynaud, F. I.; et al.
Discovery of Potent and Selective CDK8 Inhibitors from an HSP90 Pharmacophore.
Bioorganic & medicinal chemistry letters 2016, 26 (5), 1443–1451. doi.org/10.1016/j.bmcl.2016.01.062

2015

19. Dale, T.; Clarke, P. A.; Esdar, C.; Waalboer, D.; Adeniji-Popoola, O.; Ortiz-Ruiz, M.-J.; Mallinger, A.; Samant, R. S.; Czodrowski, P.; Musil, D.; et al.
A Selective Chemical Probe for Exploring the Role of CDK8 and CDK19 in Human Disease.
Nature chemical biology 2015, 11 (12), 973–980. doi.org/10.1038/nchembio.1952

18. Czodrowski, P.; Hölzemann, G.; Barnickel, G.; Greiner, H.; Musil, D.
Selection of Fragments for Kinase Inhibitor Design: Decoration Is Key.
Journal of medicinal chemistry 2015, 58 (1), 457–465. doi.org/10.1021/jm501597j

2014

17. Czodrowski, P.
Count on Kappa.
Journal of computer aided molecular design 2014, 28 (11), 1049–1055. doi.org/10.1007/s10822-014-9759-6

16. Samel, S. A.; Czodrowski, P.; Essen, L.-O.
Structure of the Epimerization Domain of Tyrocidine Synthetase A.
Acta crystallographica / D 2014, 70 (5), 1442–1452. doi.org/10.1107/S1399004714004398

15. Betz, U.; Czodrowski, P.; Esdar, C.; Deutsch, C.; Beier, N.; Finsinger, D.; Cezanne, B.; Urbahns, K.; Wucherer-Plietker, M.
Fluctuating Open Teams (FLOT): A New Approach to Boost Team Creativity and In­no­va­ti­on Potential.
Technology transfer and entrepreneurship 2014, 1 (2), 77–81. doi.org/10.2174/2213809901666140401202431#sthash.7mmTE5ZL.dpuf

14. Neeb, M.; Czodrowski, P.; Heine, A.; Barandun, L. J.; Hohn, C.; Diederich, F.; Klebe, G.
Chasing Protons: How Isothermal Titration Calorimetry, Mutagenesis, and pKa Calculations Trace the Locus of Charge in Ligand Binding to a tRNA-Binding Enzyme.
Journal of medicinal chemistry 2014, 57 (13), 5554–5565. doi.org/10.1021/jm500401x

13. Grädler, U.; Czodrowski, P.; Tsaklakidis, C.; Klein, M.; Werkmann, D.; Lindemann, S.; Maskos, K.; Leuthner, B.
Structure-Based Optimization of Non-Peptidic Cathepsin D Inhibitors.
Bioorganic & medicinal chemistry letters 2014, 24 (17), 4141–4150. doi.org/10.1016/j.bmcl.2014.07.054

2013

12. Kokh, D. B.; Richter, S.; Henrich, S.; Czodrowski, P.; Rippmann, F.; Wade, R. C.
TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins.
Journal of chemical in­for­mation and modeling 2013, 53 (5), 1235–1252. doi.org/10.1021/ci4000294

11. Czodrowski, P.
hERG Me out.
Journal of chemical in­for­mation and modeling 2013, 53 (9), 2240–2251. doi.org/10.1021/ci400308z

2012

10. Czodrowski, P.
Who Cares for the Protons?
Bioorganic & medicinal chemistry 2012, 20 (18), 5453–5460. doi.org/10.1016/j.bmc.2012.03.009

2011

9. Czodrowski, P.; Søndergaard, C.; Dohm, S.; Klebe, G.; Nielsen, J.
LigpKa – a Database of pKa Values for Small Molecule Ligands Designed for the Use in Structure-Based pKa Calculations.
Journal of cheminformatics 2011, 3 (Suppl 1), P21. doi.org/10.1186/1758-2946-3-S1-P21

8. Czodrowski, P.
Blind, One-Eyed, or Eagle-Eyed?: pKa Calculations during Blind Predictions with Staphylococcal Nuclease.
Proteins 2011, 79 (12), 3299–3305. doi.org/10.1002/prot.23110

2009

7. Czodrowski, P.; Kriegl, J. M.; Scheuerer, S.; Fox, T.
Computational Approaches to Predict Drug Metabolism.
Expert opinion on drug metabolism & toxicology 2009, 5 (1), 15–27. doi.org/10.1517/17425250802568009

2007

6. Czodrowski, P.; Sotriffer, C. A.; Klebe, G.
Atypical Protonation States in the Active Site of HIV-1 Protease: A Computational Study.
Journal of chemical in­for­mation and modeling 2007, 47 (4), 1590–1598. doi.org/10.1021/ci600522c

5. Steuber, H.; Czodrowski, P.; Sotriffer, C. A.; Klebe, G.
Tracing Changes in Protonation: A Prerequisite to Factorize Thermodynamic Data of Inhibitor Binding to Aldose Reductase.
Journal of molecular biology 2007, 373 (5), 1305–1320. doi.org/10.1016/j.jmb.2007.08.063

4. Czodrowski, P.; Sotriffer, C. A.; Klebe, G.
Protonation Changes upon Ligand Binding to Trypsin and Thrombin: Structural Interpretation Based on pKa Calculations and ITC Experiments.
Journal of molecular biology 2007, 367 (5), 1347–1356. doi.org/10.1016/j.jmb.2007.01.022

3. Dolinsky, T. J.; Czodrowski, P.; Li, H.; Nielsen, J. E.; Jensen, J. H.; Klebe, G.; Baker, N. A.
PDB2PQR: Expanding and Upgrading Automated Preparation of Biomolecular Structures for Molecular Simulations.
Nucleic acids research 2007, 35 (2,1), W522–W525. doi.org/10.1093/nar/gkm276

2006

2. Czodrowski, P.; Dramburg, I.; Sotriffer, C. A.; Klebe, G.
Development, Validation, and Application of Adapted PEOE Charges to Estimate pKa Values of Functional Groups in Protein-Ligand Complexes.
Proteins 2006, 65 (2), 424–437. doi.org/10.1002/prot.21110

1. Wittelsberger, A.; Corich, M.; Thomas, B. E.; Lee, B.-K.; Barazza, A.; Czodrowski, P.; Mierke, D. F.; Chorev, M.; Rosenblatt, M.
The Mid-Region of Parathyroid Hormone (1−34) Serves as a Functional Docking Domain in Receptor Activation†.
Biochemistry 2006, 45 (7), 2027–2034. doi.org/10.1021/bi051833a

Location & approach

The campus of TU Dort­mund University is located close to interstate junction Dort­mund West, where the Sauerlandlinie A 45 (Frankfurt-Dort­mund) crosses the Ruhrschnellweg B 1 / A 40. The best interstate exit to take from A 45 is "Dort­mund-Eichlinghofen" (closer to Campus Süd), and from B 1 / A 40 "Dort­mund-Dorstfeld" (closer to Campus Nord). Signs for the uni­ver­si­ty are located at both exits. Also, there is a new exit before you pass over the B 1-bridge leading into Dort­mund.

To get from Campus Nord to Campus Süd by car, there is the connection via Vogelpothsweg/Baroper Straße. We recommend you leave your car on one of the parking lots at Campus Nord and use the H-Bahn (suspended monorail system), which conveniently connects the two campuses.

TU Dort­mund University has its own train station ("Dort­mund Uni­ver­si­tät"). From there, suburban trains (S-Bahn) leave for Dort­mund main station ("Dort­mund Hauptbahnhof") and Düsseldorf main station via the "Düsseldorf Airport Train Station" (take S-Bahn number 1, which leaves every 20 or 30 minutes). The uni­ver­si­ty is easily reached from Bochum, Essen, Mülheim an der Ruhr and Duisburg.

You can also take the bus or subway train from Dort­mund city to the uni­ver­si­ty: From Dort­mund main station, you can take any train bound for the Station "Stadtgarten", usually lines U41, U45, U 47 and U49. At "Stadtgarten" you switch trains and get on line U42 towards "Hombruch". Look out for the Station "An der Palmweide". From the bus stop just across the road, busses bound for TU Dort­mund University leave every ten minutes (445, 447 and 462). Another option is to take the subway routes U41, U45, U47 and U49 from Dort­mund main station to the stop "Dort­mund Kampstraße". From there, take U43 or U44 to the stop "Dort­mund Wittener Straße". Switch to bus line 447 and get off at "Dort­mund Uni­ver­si­tät S".

The H-Bahn is one of the hallmarks of TU Dort­mund University. There are two stations on Campus Nord. One ("Dort­mund Uni­ver­si­tät S") is directly located at the suburban train stop, which connects the uni­ver­si­ty directly with the city of Dort­mund and the rest of the Ruhr Area. Also from this station, there are connections to the "Technologiepark" and (via Campus Süd) Eichlinghofen. The other station is located at the dining hall at Campus Nord and offers a direct connection to Campus Süd every five minutes.

The AirportExpress is a fast and convenient means of transport from Dort­mund Airport (DTM) to Dort­mund Central Station, taking you there in little more than 20 minutes. From Dort­mund Central Station, you can continue to the uni­ver­si­ty campus by interurban railway (S-Bahn). A larger range of in­ter­na­tio­nal flight connections is offered at Düsseldorf Airport (DUS), which is about 60 kilometres away and can be directly reached by S-Bahn from the uni­ver­si­ty station.

The facilities of TU Dort­mund University are spread over two campuses, the larger Campus North and the smaller Campus South. Additionally, some areas of the uni­ver­si­ty are located in the adjacent "Technologiepark".

Site Map of TU Dort­mund University (Second Page in English).