Atypical Protonation States in the Active Site of HIV-1 Protease: A Computational Study. - Paul Czodrowski; Christoph A. Sotriffer; Gerhard Klebe (J. Chem. Inf. Model., 2007)

PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. - Todd J. Dolinsky; Paul Czodrowski; Hui Li; Jens Erik Nielsen; Jan H. Jensen; Gerhard Klebe; Nathan A. Baker (Nucleic Acids Res., 2007)

LigpKa - a database of pKa values for small molecule ligands designed for the use in structure-based pKa calculations. - Paul Czodrowski; Chresten R. Søndergaard; Sebastian Dohm; Gerhard Klebe; Jens Erik Nielsen (J. Cheminformatics, 2011)

hERG Me Out. - Paul Czodrowski (J. Chem. Inf. Model., 2013)

TRAPP: A Tool for Analysis of Transient Binding Pockets in Proteins. - Daria B. Kokh; Stefan Richter 002; Stefan Henrich; Paul Czodrowski; Friedrich Rippmann; Rebecca C. Wade (J. Chem. Inf. Model., 2013)

Count on kappa. - Paul Czodrowski (J. Comput. Aided Mol. Des., 2014)

OCEAN: Optimized Cross rEActivity estimatioN. - Paul Czodrowski; Wolf-Guido Bolick (J. Chem. Inf. Model., 2016)

Binding Pose Flip Explained via Enthalpic and Entropic Contributions. - Michael Schauperl; Paul Czodrowski; Julian E. Fuchs; Roland G. Huber; Birgit J. Waldner; Maren Podewitz; Christian Kramer; Klaus R. Liedl (J. Chem. Inf. Model., 2017)

Machine learning meets pKa. - Marcel Baltruschat; Paul Czodrowski (F1000Research, 2020)

Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects. - Christina E. M. Schindler; Hannah M. Baumann; Andreas Blum; Dietrich Böse; Hans-Peter Buchstaller; Lars Burgdorf; Daniel Cappel; Eugene Chekler; Paul Czodrowski; Dieter Dorsch; Merveille K. I. Eguida; Bruce Follows; et al. (J. Chem. Inf. Model., 2020)

Pseudonatural Products Occur Frequently in Biologically Relevant Compounds. - José-Manuel Gally; Axel Pahl; Paul Czodrowski; Herbert Waldmann (J. Chem. Inf. Model., 2021)

VSFlow: an open-source ligand-based virtual screening tool. - Sascha Jung; Helge Vatheuer; Paul Czodrowski (J. Cheminformatics, 2023)