DEKOIS: Demanding Evaluation Kits for Objective in Silico Screening - A Versatile Tool for Benchmarking Docking Programs and Scoring Functions. - Simon M. Vogel; Matthias R. Bauer; Frank M. Boeckler (J. Chem. Inf. Model., 2011)

Inferring multi-target QSAR models with taxonomy-based multi-task learning. - Lars Rosenbaum; Alexander Dörr; Matthias R. Bauer; Frank M. Boeckler; Andreas Zell (J. Cheminformatics, 2013)

Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0 - A Public Library of Challenging Docking Benchmark Sets. - Matthias R. Bauer; Tamer M. Ibrahim; Simon M. Vogel; Frank M. Boeckler (J. Chem. Inf. Model., 2013)

Use of DEKOIS 2.0 to gain insights for virtual screening. - Frank M. Boeckler; Matthias R. Bauer; Tamer M. Ibrahim; Simon M. Vogel (J. Cheminformatics, 2014)

Probing the impact of protein and ligand preparation procedures on chemotype enrichment in structure-based virtual screening using DEKOIS 2.0 benchmark sets. - Tamer M. Ibrahim; Matthias R. Bauer; Frank M. Boeckler (J. Cheminformatics, 2014)

Machine Learning Estimates of Natural Product Conformational Energies. - Matthias Rupp; Matthias R. Bauer; Rainer Wilcken; Andreas Lange; Michael Reutlinger; Frank M. Boeckler; Gisbert Schneider (PLoS Comput. Biol., 2014)

Applying DEKOIS 2.0 in structure-based virtual screening to probe the impact of preparation procedures and score normalization. - Tamer M. Ibrahim; Matthias R. Bauer; Frank M. Boeckler (J. Cheminformatics, 2015)

pROC-Chemotype Plots Enhance the Interpretability of Benchmarking Results in Structure-Based Virtual Screening. - Tamer M. Ibrahim; Matthias R. Bauer; Alexander Dörr; Erdem Veyisoglu; Frank M. Boeckler (J. Chem. Inf. Model., 2015)

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)

Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules. - J. Harry Moore; Matthias R. Bauer; Jeff Guo; Atanas Patronov; Ola Engkvist; Christian Margreitter (Bioinform., 2022)