Similarity based SAR (SIBAR) as tool for early ADME profiling. - Christian Th. Klein; Dominik Kaiser; Stephan Kopp; Peter Chiba; Gerhard F. Ecker (J. Comput. Aided Mol. Des., 2002)

MCASE study of the multidrug resistance reversal activity of propafenone analogs. - Gilles Klopman; Hao Zhu 012; Gerhard F. Ecker; Peter Chiba (J. Comput. Aided Mol. Des., 2003)

Topological Distance Based 3D Descriptors for Use in QSAR and Diversity Analysis. - Christian Th. Klein; Dominik Kaiser; Gerhard F. Ecker (J. Chem. Inf. Model., 2004)

Insights into Phenylalanine Derivatives Recognition of VLA-4 Integrin: From a Pharmacophoric Study to 3D-QSAR and Molecular Docking Analyses. - Antonio Macchiarulo; Gabriele Costantino; Mirco Meniconi; Karin Pleban; Gerhard F. Ecker; Daniele Bellocchi; Roberto Pellicciari (J. Chem. Inf. Model., 2004)

Similarity-based descriptors (SIBAR) - A tool for safe exchange of chemical information? - Dominik Kaiser; Barbara Zdrazil; Gerhard F. Ecker (J. Comput. Aided Mol. Des., 2005)

On the Relationship Between Feature Selection and Classification Accuracy. - Andreas Janecek; Wilfried N. Gansterer; Michael Demel; Gerhard F. Ecker (FSDM, 2008)

Exhaustive Sampling of Docking Poses Reveals Binding Hypotheses for Propafenone Type Inhibitors of P-Glycoprotein. - Freya Klepsch; Peter Chiba; Gerhard F. Ecker (PLoS Comput. Biol., 2011)

A computational model for predicting the transport of compounds by ABCC2. - Marta Pinto; Gerhard F. Ecker (J. Cheminformatics, 2012)

Insights into binding events of GABA- and Tiagabine- analogues in the Gamma-Aminobutyric Acid Transporter 1 by means of Molecular Modelling. - Barbara Zdrazil; Andreas Jurik; Regina Reicherstorfer; Thomas Stockner; Harald H. Sitte; Gerhard F. Ecker (J. Cheminformatics, 2012)

2D- and 3D-QSAR studies of a series of benzopyranes and benzopyrano[3, 4b][1, 4]-oxazines as inhibitors of the multidrug transporter P-glycoprotein. - Ishrat Jabeen; Penpun Wetwitayaklung; Peter Chiba; Manuel Pastor; Gerhard F. Ecker (J. Comput. Aided Mol. Des., 2013)

Pairwise structural comparison of tiagabine analogs gives new insights into their protein binding modes. - Barbara Zdrazil; Andreas Jurik; Harald H. Sitte; Gerhard F. Ecker (J. Cheminformatics, 2013)

Mutational Analysis of the High-Affinity Zinc Binding Site Validates a Refined Human Dopamine Transporter Homology Model. - Thomas Stockner; Therese R. Montgomery; Oliver Kudlacek; Rene Weissensteiner; Gerhard F. Ecker; Michael Freissmuth; Harald H. Sitte (PLoS Comput. Biol., 2013)

Applicability Domain Analysis (ADAN): A Robust Method for Assessing the Reliability of Drug Property Predictions. - Pau Carrió; Marta Pinto; Gerhard F. Ecker; Ferran Sanz; Manuel Pastor (J. Chem. Inf. Model., 2014)

Ligand and Structure-Based Classification Models for Prediction of P-Glycoprotein Inhibitors. - Freya Klepsch; Poongavanam Vasanthanathan; Gerhard F. Ecker (J. Chem. Inf. Model., 2014)

Refinement of the Central Steps of Substrate Transport by the Aspartate Transporter GltPh: Elucidating the Role of the Na2 Sodium Binding Site. - Santhosh Kannan Venkatesan; Kusumika Saha; Azmat Sohail; Walter Sandtner; Michael Freissmuth; Gerhard F. Ecker; Harald H. Sitte; Thomas Stockner (PLoS Comput. Biol., 2015)

Selectivity profiling of BCRP versus P-gp inhibition: from automated collection of polypharmacology data to multi-label learning. - Floriane Montanari; Barbara Zdrazil; Daniela Digles; Gerhard F. Ecker (J. Cheminformatics, 2016)

Empowering pharmacoinformatics by linked life science data. - Daria Goldmann; Barbara Zdrazil; Daniela Digles; Gerhard F. Ecker (J. Comput. Aided Mol. Des., 2017)

Structure based classification for bile salt export pump (BSEP) inhibitors using comparative structural modeling of human BSEP. - Sankalp Jain; Melanie Grandits; Lars Richter; Gerhard F. Ecker (J. Comput. Aided Mol. Des., 2017)

Predicting Drug-Induced Cholestasis with the Help of Hepatic Transporters - An in Silico Modeling Approach. - Eleni Kotsampasakou; Gerhard F. Ecker (J. Chem. Inf. Model., 2017)

Comparing the performance of meta-classifiers - a case study on selected imbalanced data sets relevant for prediction of liver toxicity. - Sankalp Jain; Eleni Kotsampasakou; Gerhard F. Ecker (J. Comput. Aided Mol. Des., 2018)

SAR-Guided Scoring Function and Mutational Validation Reveal the Binding Mode of CGS-8216 at the α1+/γ2- Benzodiazepine Site. - David C. B. Siebert; Marcus Wieder; Lydia Schlener; Petra Scholze; Stefan Boresch; Thierry Langer; Michael Schnürch; Marko D. Mihovilovic; Lars Richter; Margot Ernst; Gerhard F. Ecker (J. Chem. Inf. Model., 2018)

Conformational Oversampling as Data Augmentation for Molecules. - Jennifer Hemmerich; Ece Asilar; Gerhard F. Ecker (ICANN (Workshop), 2019)

Predicting Residence Time and Drug Unbinding Pathway through Scaled Molecular Dynamics. - Doris A. Schuetz; Mattia Bernetti; Martina Bertazzo; Djordje Musil; Hans-Michael Eggenweiler; Maurizio Recanatini; Matteo Masetti; Gerhard F. Ecker; Andrea Cavalli (J. Chem. Inf. Model., 2019)

COVER: conformational oversampling as data augmentation for molecules. - Jennifer Hemmerich; Ece Asilar; Gerhard F. Ecker (J. Cheminformatics, 2020)

Image Based Liver Toxicity Prediction. - Ece Asilar; Jennifer Hemmerich; Gerhard F. Ecker (J. Chem. Inf. Model., 2020)

KNIME workflow for retrieving causal drug and protein interactions, building networks, and performing topological enrichment analysis demonstrated by a DILI case study. - Barbara Füzi; Rahuman S. Malik-Sheriff; Emma J. Manners; Henning Hermjakob; Gerhard F. Ecker (J. Cheminformatics, 2022)

Off-targetP ML: an open source machine learning framework for off-target panel safety assessment of small molecules. - Doha Naga; Wolfgang Muster; Eunice Musvasva; Gerhard F. Ecker (J. Cheminformatics, 2022)

Using Jupyter Notebooks for re-training machine learning models. - Aljosa Smajic; Melanie Grandits; Gerhard F. Ecker (J. Cheminformatics, 2022)

Exploring diverse approaches for predicting interferon-gamma release: utilizing MHC class II and peptide sequences. - Abir Omran; Alexander Amberg; Gerhard F. Ecker (Briefings Bioinform., 2025)

Refining Drug-Induced Cholestasis Prediction: An Explainable Consensus Model Integrating Chemical and Biological Fingerprints. - Palle S. Helmke; Gerhard F. Ecker (J. Chem. Inf. Model., 2025)