Strukturbasierte Pharmakophore: Neue Wirkstoffmodelle für die Arzneimittelforschung. - Gerhard Wolber (Ausgezeichnete Informatikdissertationen, 2003)

Comparative Analysis of Protein-Bound Ligand Conformations with Respect to Catalyst's Conformational Space Subsampling Algorithms. - Johannes Kirchmair; Christian Laggner; Gerhard Wolber; Thierry Langer (J. Chem. Inf. Model., 2005)

LigandScout: 3-D Pharmacophores Derived from Protein-Bound Ligands and Their Use as Virtual Screening Filters. - Gerhard Wolber; Thierry Langer (J. Chem. Inf. Model., 2005)

High-throughput structure-based pharmacophore modelling as a basis for successful parallel virtual screening. - Theodora M. Steindl; Daniela Schuster 001; Gerhard Wolber; Christian Laggner; Thierry Langer (J. Comput. Aided Mol. Des., 2006)

Efficient overlay of small organic molecules using 3D pharmacophores. - Gerhard Wolber; Alois A. Dornhofer; Thierry Langer (J. Comput. Aided Mol. Des., 2006)

Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst: A Large-Scale Survey on the Retrieval of Protein-Bound Ligand Conformations. - Johannes Kirchmair; Gerhard Wolber; Christian Laggner; Thierry Langer (J. Chem. Inf. Model., 2006)

Fast and Efficient in Silico 3D Screening: Toward Maximum Computational Efficiency of Pharmacophore-Based and Shape-Based Approaches. - Johannes Kirchmair; Stojanka Ristic; Kathrin Eder; Patrick Markt; Gerhard Wolber; Christian Laggner; Thierry Langer (J. Chem. Inf. Model., 2007)

Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection - What can we learn from earlier mistakes? - Johannes Kirchmair; Patrick Markt; Simona Distinto; Gerhard Wolber; Thierry Langer (J. Comput. Aided Mol. Des., 2008)

Discovery of Novel Cathepsin S Inhibitors by Pharmacophore-Based Virtual High-Throughput Screening. - Patrick Markt; Caroline McGoohan; Brian Walker; Johannes Kirchmair; Clemens Feldmann; Gabriella De Martino; Gudrun M. Spitzer; Simona Distinto; Daniela Schuster 001; Gerhard Wolber; Christian Laggner; Thierry Langer (J. Chem. Inf. Model., 2008)

How To Optimize Shape-Based Virtual Screening: Choosing the Right Query and Including Chemical Information. - Johannes Kirchmair; Simona Distinto; Patrick Markt; Daniela Schuster 001; Gudrun M. Spitzer; Klaus R. Liedl; Gerhard Wolber (J. Chem. Inf. Model., 2009)

Critical Comparison of Virtual Screening Methods against the MUV Data Set. - Pekka Tiikkainen; Patrick Markt; Gerhard Wolber; Johannes Kirchmair; Simona Distinto; Antti Poso; Olli-P. Kallioniemi (J. Chem. Inf. Model., 2009)

Ligand-side tautomer enumeration and scoring for structure-based drug-design. - Thomas Seidel; Gerhard Wolber (J. Cheminformatics, 2010)

3D pharmacophore alignments: does improved geometric accuracy affect virtual screening performance? - Gerhard Wolber; Thomas Seidel; Fabian Bendix (J. Cheminformatics, 2010)

One Concept, Three Implementations of 3D Pharmacophore-Based Virtual Screening: Distinct Coverage of Chemical Search Space. - Gudrun M. Spitzer; Mathias Heiss; Martina Mangold; Patrick Markt; Johannes Kirchmair; Gerhard Wolber; Klaus R. Liedl (J. Chem. Inf. Model., 2010)

Discovery of novel TLR modulators by Molecular Modeling and Virtual Screening. - Manuela S. Murgueitio; Sandra Santos-Sierra; Gerhard Wolber (J. Cheminformatics, 2012)

Identification of Novel Liver X Receptor Activators by Structure-Based Modeling. - Susanne von Grafenstein; Judit Mihaly-Bison; Gerhard Wolber; Valery N. Bochkov; Klaus R. Liedl; Daniela Schuster 001 (J. Chem. Inf. Model., 2012)

Molecular dynamics simulation and linear interaction energy study of d-Glu-based inhibitors of the MurD ligase. - Andrej Perdih; Gerhard Wolber; Tomaz Solmajer (J. Comput. Aided Mol. Des., 2013)

Discovery of novel α-amylase inhibitors using structure-based drug design. - Jamil Al-Asri; Gerhard Wolber (J. Cheminformatics, 2014)

Dualsteric modulators of the M2 muscarinic acetylcholine receptor. - Marcel Bermudez; Gerhard Wolber (J. Cheminformatics, 2014)

Balancing selectivity vs stability using molecular dynamics and umbrella sampling. - Jérémie Mortier; Elisabeth K. Nyakatura; Markus Miettinen; Carsten Baldauf; Gerhard Wolber; Beate Koksch (J. Cheminformatics, 2014)

Combining pharmacophore- and MD-based modelling for phase II metabolism prediction. - Christin Rakers; Gerhard Wolber (J. Cheminformatics, 2014)

Using structure- and Ligand-based pharmacophores as filters to discriminate Human Aryl Sulfotransferase 1A1 (SUL1A1) binders into substrates and inhibitors. - Salwa M. Soliman; Gerhard Wolber (J. Cheminformatics, 2014)

Inhibitor Design Strategy Based on an Enzyme Structural Flexibility: A Case of Bacterial MurD Ligase. - Andrej Perdih; Martina Hrast; Hélène Barreteau; Stanislav Gobec; Gerhard Wolber; Tomaz Solmajer (J. Chem. Inf. Model., 2014)

Furan-based benzene mono- and dicarboxylic acid derivatives as multiple inhibitors of the bacterial Mur ligases (MurC-MurF): experimental and computational characterization. - Andrej Perdih; Martina Hrast; Kaja Pureber; Hélène Barreteau; Simona Golic Grdadolnik; Darko Kocjan; Stanislav Gobec; Tomaz Solmajer; Gerhard Wolber (J. Comput. Aided Mol. Des., 2015)

Coiled-Coils in Phage Display Screening: Insight into Exceptional Selectivity Provided by Molecular Dynamics. - Jérémie Mortier; Elisabeth K. Nyakatura; Oliver Reimann; Susanne Huhmann; Jan O. Daldrop; Carsten Baldauf; Gerhard Wolber; Markus Miettinen; Beate Koksch (J. Chem. Inf. Model., 2015)

PyRod: Tracing Water Molecules in Molecular Dynamics Simulations. - David Schaller 002; Szymon Pach; Gerhard Wolber (J. Chem. Inf. Model., 2019)

CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein. - Fengling Li; Suzanne Ackloo; Cheryl H. Arrowsmith; Fuqiang Ban; Christopher J. Barden; Hartmut Beck; Jan Beránek; Francois Berenger; Albina Bolotokova; Guillaume Bret; Marko Breznik; Emanuele Carosati; et al. (J. Chem. Inf. Model., 2024)

CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13. - Oleksandra Herasymenko; Madhushika Silva; Abd Al-Aziz A. Abu-Saleh; Ayaz Ahmad; Jesus Alvarado-Huayhuaz; Oscar Emilio Arrúa Arce; Roly J. Armstrong; Cheryl H. Arrowsmith; Kelly E. Bachta; Hartmut Beck; Dénes Berta; Mateusz K. Bieniek; et al. (J. Chem. Inf. Model., 2025)

Integrated Virtual Screening Approach Identifies New CYP19A1 Inhibitors. - Sijie Liu; Jie Wu; Ya Chen 002; Clemens Alexander Wolf; Matthias Bureik; Johannes Kirchmair; Mario Andrea Marchisio; Gerhard Wolber (J. Chem. Inf. Model., 2025)

OpenMMDL - Simplifying the Complex: Building, Simulating, and Analyzing Protein-Ligand Systems in OpenMM. - Valerij Talagayev; Yu Chen; Niklas Piet Doering; Leon Obendorf; Katrin Denzinger; Kristina Puls; Kevin Lam; Sijie Liu; Clemens Alexander Wolf; Theresa Noonan; Marko Breznik; Petra Knaus; et al. (J. Chem. Inf. Model., 2025)

Agonists and Antagonists Show Different Unbinding Paths from the TLR8 Receptor. - Valerij Talagayev; Gerhard Wolber; Ariane Nunes-Alves (J. Chem. Inf. Model., 2025)