Evidence of Water Molecules - A Statistical Evaluation of Water Molecules Based on Electron Density. - Eva Nittinger; Nadine Schneider; Gudrun Lange; Matthias Rarey (J. Chem. Inf. Model., 2015)

mRAISE: an alternative algorithmic approach to ligand-based virtual screening. - Mathias M. von Behren; Stefan Bietz; Eva Nittinger; Matthias Rarey (J. Comput. Aided Mol. Des., 2016)

ProteinsPlus: a web portal for structure analysis of macromolecules. - Rainer Fährrolfes; Stefan Bietz; Florian Flachsenberg; Agnes Meyder; Eva Nittinger; Thomas Otto; Andrea Volkamer; Matthias Rarey (Nucleic Acids Res., 2017)

NAOMInova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures. - Therese Inhester; Eva Nittinger; Kai Sommer; Pascal Schmidt; Stefan Bietz; Matthias Rarey (J. Chem. Inf. Model., 2017)

Estimating Electron Density Support for Individual Atoms and Molecular Fragments in X-ray Structures. - Agnes Meyder; Eva Nittinger; Gudrun Lange; Robert Klein; Matthias Rarey (J. Chem. Inf. Model., 2017)

Placement of Water Molecules in Protein Structures: From Large-Scale Evaluations to Single-Case Examples. - Eva Nittinger; Florian Flachsenberg; Stefan Bietz; Gudrun Lange; Robert Klein; Matthias Rarey (J. Chem. Inf. Model., 2018)

Water Molecules Within the HYDE Scoring Function : Placement, Optimization, and Energetic Contributions (Platzierung, Optimierung und Energetische Bewertung von Wassermolekülen auf Basis der HYDE Bewertungsfunktion) - Eva Nittinger (2018)

Water molecules in protein-ligand interfaces. Evaluation of software tools and SAR comparison. - Eva Nittinger; Paul Gibbons; Charles Eigenbrot; Doug R. Davies; Brigitte Maurer; Christine L. Yu; James R. Kiefer; Andreas Kuglstatter; Jeremy Murray; Daniel F. Ortwine; Yong Tang; Vickie Tsui (J. Comput. Aided Mol. Des., 2019)

ProteinsPlus: interactive analysis of protein-ligand binding interfaces. - Katrin Schöning-Stierand; Konrad Diedrich; Rainer Fährrolfes; Florian Flachsenberg; Agnes Meyder; Eva Nittinger; Ruben Steinegger; Matthias Rarey (Nucleic Acids Res., 2020)

Nonadditivity in public and inhouse data: implications for drug design. - Dea Gogishvili; Eva Nittinger; Christian Margreitter; Christian Tyrchan (J. Cheminformatics, 2021)

DockStream: a docking wrapper to enhance de novo molecular design. - Jeff Guo; Jon Paul Janet; Matthias R. Bauer; Eva Nittinger; Kathryn A. Giblin; Kostas Papadopoulos; Alexey Voronov; Atanas Patronov; Ola Engkvist; Christian Margreitter (J. Cheminformatics, 2021)

Molecular optimization by capturing chemist's intuition using deep neural networks. - Jiazhen He; Huifang You; Emil Sandström; Eva Nittinger; Esben Jannik Bjerrum; Christian Tyrchan; Werngard Czechtizky; Ola Engkvist (J. Cheminformatics, 2021)

Transformer-based molecular optimization beyond matched molecular pairs. - Jiazhen He; Eva Nittinger; Christian Tyrchan; Werngard Czechtizky; Atanas Patronov; Esben Jannik Bjerrum; Ola Engkvist (J. Cheminformatics, 2022)

Improving reproducibility and reusability in the Journal of Cheminformatics. - Charles Tapley Hoyt; Barbara Zdrazil; Rajarshi Guha; Nina Jeliazkova; Karina Martínez-Mayorga; Eva Nittinger (J. Cheminformatics, 2023)

Biomedical data analyses facilitated by open cheminformatics workflows. - Eva Nittinger; Alex Clark; Anna Gaulton; Barbara Zdrazil (J. Cheminformatics, 2023)

Similarity-based pairing improves efficiency of siamese neural networks for regression tasks and uncertainty quantification. - Yumeng Zhang; Janosch Menke; Jiazhen He; Eva Nittinger; Christian Tyrchan; Oliver Koch; Hongtao Zhao (J. Cheminformatics, 2023)

Towards Interpretable Models of Chemist Preferences for Human-in-the-Loop Assisted Drug Discovery. - Yasmine Nahal; Markus Heinonen; Mikhail Kabeshov; Jon Paul Janet; Eva Nittinger; Ola Engkvist; Samuel Kaski (AIDD@ICANN, 2024)

Challenge for Deep Learning: Protein Structure Prediction of Ligand-Induced Conformational Changes at Allosteric and Orthosteric Sites. - Gustav Olanders; Giulia Testa; Alessandro Tibo; Eva Nittinger; Christian Tyrchan (J. Chem. Inf. Model., 2024)

Evaluation of reinforcement learning in transformer-based molecular design. - Jiazhen He; Alessandro Tibo; Jon Paul Janet; Eva Nittinger; Christian Tyrchan; Werngard Czechtizky; Ola Engkvist (J. Cheminformatics, 2024)

Human-in-the-loop active learning for goal-oriented molecule generation. - Yasmine Nahal; Janosch Menke; Julien Martinelli; Markus Heinonen; Mikhail Kabeshov; Jon Paul Janet; Eva Nittinger; Ola Engkvist; Samuel Kaski (J. Cheminformatics, 2024)

The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks. - Christian Kramer; John D. Chodera; Kelly L. Damm-Ganamet; Michael K. Gilson; Judith Guenther; Uta F. Lessel; Richard A. Lewis; David L. Mobley; Eva Nittinger; Adam Pecina; Matthieu Schapira; W. Patrick Walters (J. Chem. Inf. Model., 2025)

AI-Augmented R-Group Exploration in Medicinal Chemistry. - Hongtao Zhao; Karolina Kwapien; Eva Nittinger; Christian Tyrchan; Magnus Nilsson; Susanne Berglund; Werngard Czechtizky (J. Chem. Inf. Model., 2025)