MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes. - Andreas Braun; Bettina Halwachs; Martina Geier; Katrin Weinhandl; Michael Guggemos; Jan Marienhagen; Anna Joëlle Ruff; Ulrich Schwaneberg; Vincent Rabin; Daniel E. Torres Pazmiño; Gerhard G. Thallinger; Anton Glieder (Database J. Biol. Databases Curation, 2012)

Activity prediction of substrates in NADH-dependent carbonyl reductase by docking requires catalytic constraints and charge parameterization of catalytic zinc environment. - Gaurao V. Dhoke; Christoph Loderer; Mehdi D. Davari; Marion Ansorge-Schumacher; Ulrich Schwaneberg; Marco Bocola (J. Comput. Aided Mol. Des., 2015)

What's My Substrate? Computational Function Assignment of Candida parapsilosis ADH5 by Genome Database Search, Virtual Screening, and QM/MM Calculations. - Gaurao V. Dhoke; Yunus Ensari; Mehdi D. Davari; Anna Joëlle Ruff; Ulrich Schwaneberg; Marco Bocola (J. Chem. Inf. Model., 2016)

Systematically Scrutinizing the Impact of Substitution Sites on Thermostability and Detergent Tolerance for Bacillus subtilis Lipase A. - Christina Nutschel; Alexander Fulton; Olav Zimmermann; Ulrich Schwaneberg; Karl-Erich Jaeger; Holger Gohlke (J. Chem. Inf. Model., 2020)

PyPEF - An Integrated Framework for Data-Driven Protein Engineering. - Niklas E. Siedhoff; Alexander-Maurice Illig; Ulrich Schwaneberg; Mehdi D. Davari (J. Chem. Inf. Model., 2021)

Evolutionary Probability and Stacked Regressions Enable Data-Driven Protein Engineering with Minimized Experimental Effort. - Alexander-Maurice Illig; Niklas E. Siedhoff; Mehdi D. Davari; Ulrich Schwaneberg (J. Chem. Inf. Model., 2024)

CMDmpnn: Combining Comparative Molecular Dynamics and ProteinMPNN to Rapidly Expand Enzyme Substrate Spectrum. - Chuan-qi Sun; Zhi-min Li; Yu Ji; Ulrich Schwaneberg; Zong-lin Li (J. Chem. Inf. Model., 2025)