Protein Structure Prediction with Stochastic Optimization Methods: Folding and Misfolding the Villin Headpiece. - Thomas Herges; Alexander Schug; Wolfgang Wenzel (ICCSA (3), 2004)

Massively Parallel All Atom Protein Folding in a Single Day. - Abhinav Verma; Srinivasa M. Gopal; Alexander Schug; Jung S. Oh; Konstantin V. Klenin; Kyu H. Lee; Wolfgang Wenzel (PARCO, 2007)

eSBMTools 1.0: enhanced native structure-based modeling tools. - Benjamin Lutz; Claude Sinner; Geertje Heuermann; Abhinav Verma; Alexander Schug (Bioinform., 2013)

Integration of eSBMTools into the MoSGrid Portal Using the gUSE Technology. - Stefan Bozic; Jens Krüger 002; Claude Sinner; Benjamin Lutz; Alexander Schug; Ivan Kondov (IWSG, 2014)

Native structure-based modeling and simulation of biomolecular systems per mouse click. - Benjamin Lutz; Claude Sinner; Stefan Bozic; Ivan Kondov; Alexander Schug (BMC Bioinform., 2014)

Maxent-Stress Optimization of 3D Biomolecular Models. - Michael Wegner; Oskar Taubert; Alexander Schug; Henning Meyerhenke (ESA, 2017)

diSTruct v1.0: generating biomolecular structures from distance constraints. - Oskar Taubert; Ines Reinartz; Henning Meyerhenke; Alexander Schug (Bioinform., 2019)

Optimization of the dielectric layer for electrowetting on dielectric. - Semih Turk; Alexander Schug; Reinhard Viga; Andreas Jupe; Holger Vogt (Integr., 2019)

Rapid interpretation of small-angle X-ray scattering data. - Marie Weiel; Ines Reinartz; Alexander Schug (PLoS Comput. Biol., 2019)

Loss Scheduling for Class-Imbalanced Image Segmentation Problems. - Oskar Taubert; Markus Götz; Alexander Schug; Achim Streit (ICMLA, 2020)

pydca v1.0: a comprehensive software for direct coupling analysis of RNA and protein sequences. - Mehari B. Zerihun; Fabrizio Pucci; Emanuel K. Peter; Alexander Schug (Bioinform., 2020)

Cells in Silico - introducing a high-performance framework for large-scale tissue modeling. - Marco Berghoff; Jakob Rosenbauer; Felix Hoffmann; Alexander Schug (BMC Bioinform., 2020)

Modeling of Wnt-mediated tissue patterning in vertebrate embryogenesis. - Jakob Rosenbauer; Chengting Zhang; Benjamin Mattes; Ines Reinartz; Kyle Wedgwood; Simone Schindler; Claude Sinner; Steffen Scholpp; Alexander Schug (PLoS Comput. Biol., 2020)

JUWELS Booster - A Supercomputer for Large-Scale AI Research. - Stefan Kesselheim; Andreas Herten; Kai Krajsek; Jan Ebert; Jenia Jitsev; Mehdi Cherti; Michael Langguth; Bing Gong; Scarlet Stadtler; Amirpasha Mozaffari; Gabriele Cavallaro; Rocco Sedona; et al. (ISC Workshops, 2021)

pyrexMD: Workflow-Orientated Python Package for Replica Exchange Molecular Dynamics. - Arthur Voronin; Alexander Schug (J. Open Source Softw., 2021)

Dynamic particle swarm optimization of biomolecular simulation parameters with flexible objective functions. - Marie Weiel; Markus Götz; André Klein; Daniel Coquelin; Ralf Floca; Alexander Schug (Nat. Mach. Intell., 2021)

Structural Analysis of a Genetically Encoded FRET Biosensor by SAXS and MD Simulations. - Ines Reinartz; Mona Sarter; Julia Otten; Henning Höfig; Martina Pohl; Alexander Schug; Andreas M. Stadler; Jörg Fitter (Sensors, 2021)

Massively Parallel Genetic Optimization Through Asynchronous Propagation of Populations. - Oskar Taubert; Marie Weiel; Daniel Coquelin; Anis Farshian; Charlotte Debus; Alexander Schug; Achim Streit; Markus Götz (ISC, 2023)

Development of a scoring function for comparing simulated and experimental tumor spheroids. - Julian Herold; Eric Behle; Jakob Rosenbauer; Jacopo Ferruzzi; Alexander Schug (PLoS Comput. Biol., 2023)

pycofitness - Evaluating the fitness landscape of RNA and protein sequences. - Fabrizio Pucci; Mehari B. Zerihun; Marianne Rooman; Alexander Schug (Bioinform., 2024)

Large-Scale Modeling of the Extracellular Matrix on Hybrid Supercomputers Using Highly Parallel Stencil Computations. - Julian Herold; Paul Brinkmeier; Markus Götz; Alexander Schug; Achim Streit (ISC, 2025)