Feasibility of Active Machine Learning for Multiclass Compound Classification. - Tobias Lang 001; Florian Flachsenberg; Ulrike von Luxburg; Matthias Rarey (J. Chem. Inf. Model., 2016)

RingDecomposerLib: An Open-Source Implementation of Unique Ring Families and Other Cycle Bases. - Florian Flachsenberg; Niek Andresen; Matthias Rarey (J. Chem. Inf. Model., 2017)

High-Quality Dataset of Protein-Bound Ligand Conformations and Its Application to Benchmarking Conformer Ensemble Generators. - Nils-Ole Friedrich; Agnes Meyder; Christina de Bruyn Kops; Kai Sommer; Florian Flachsenberg; Matthias Rarey; Johannes Kirchmair (J. Chem. Inf. Model., 2017)

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)

Benchmarking Commercial Conformer Ensemble Generators. - Nils-Ole Friedrich; Christina de Bruyn Kops; Florian Flachsenberg; Kai Sommer; Matthias Rarey; Johannes Kirchmair (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)

StructureProfiler: an all-in-one tool for 3D protein structure profiling. - Agnes Meyder; Stefanie Kampen; Jochen Sieg; Rainer Fährrolfes; Nils-Ole Friedrich; Florian Flachsenberg; Matthias Rarey (Bioinform., 2019)

Conformator: A Novel Method for the Generation of Conformer Ensembles. - Nils-Ole Friedrich; Florian Flachsenberg; Agnes Meyder; Kai Sommer; Johannes Kirchmair; Matthias Rarey (J. Chem. Inf. Model., 2019)

In Need of Bias Control: Evaluating Chemical Data for Machine Learning in Structure-Based Virtual Screening. - Jochen Sieg; Florian Flachsenberg; Matthias Rarey (J. Chem. Inf. Model., 2019)

A Consistent Scheme for Gradient-Based Optimization of Protein-Ligand Poses. - Florian Flachsenberg; Agnes Meyder; Kai Sommer; Patrick Penner; Matthias Rarey (J. Chem. Inf. Model., 2020)

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)

LSLOpt: An open-source implementation of the step-length controlled LSL-BFGS algorithm. - Florian Flachsenberg; Matthias Rarey (J. Comput. Chem., 2021)

FastGrow: on-the-fly growing and its application to DYRK1A. - Patrick Penner; Virginie Y. Martiny; Louis Bellmann; Florian Flachsenberg; Marcus Gastreich; Isabelle Theret; Christophe Meyer; Matthias Rarey (J. Comput. Aided Mol. Des., 2022)

ProteinsPlus: a comprehensive collection of web-based molecular modeling tools. - Katrin Schöning-Stierand; Konrad Diedrich; Christiane Ehrt; Florian Flachsenberg; Joel Graef; Jochen Sieg; Patrick Penner; Martin Poppinga; Annett Ungethüm; Matthias Rarey (Nucleic Acids Res., 2022)

Redocking the PDB. - Florian Flachsenberg; Christiane Ehrt; Torben Gutermuth; Matthias Rarey (J. Chem. Inf. Model., 2024)

SpaceGrow: efficient shape-based virtual screening of billion-sized combinatorial fragment spaces. - Sophia M. N. Hönig; Florian Flachsenberg; Christiane Ehrt; Alexander Neumann; Robert Schmidt 002; Christian Lemmen; Matthias Rarey (J. Comput. Aided Mol. Des., 2024)