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)

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)

Peptide-based drug discovery through artificial intelligence: towards an autonomous design of therapeutic peptides. - Montserrat Goles; Anamaria Sanchez-Daza; Gabriel Cabas-Mora; Lindybeth Sarmiento-Varón; Julieta Sepúlveda-Yañez; Hoda Anvari-Kazemabad; Mehdi D. Davari; Roberto Uribe Paredes; Alvaro Olivera-Nappa; Marcelo A. Navarrete; David Medina-Ortiz (Briefings Bioinform., 2024)

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)

Peptipedia v2.0: a peptide sequence database and user-friendly web platform. A major update. - Gabriel Cabas-Mora; Anamaria Sanchez-Daza; Nicole Soto-García; Valentina Garrido; Diego Álvarez-Saravia; Marcelo A. Navarrete; Lindybeth Sarmiento-Varón; Julieta Sepúlveda-Yañez; Mehdi D. Davari; Frédéric Cadet; Alvaro Olivera-Nappa; Roberto Uribe Paredes; et al. (Database J. Biol. Databases Curation, 2024)

FlavorMiner: a machine learning platform for extracting molecular flavor profiles from structural data. - Fabio Herrera-Rocha; Miguel Fernández-Niño; Jorge Duitama; Mónica P. Cala; María José Chica; Ludger A. Wessjohann; Mehdi D. Davari; Andrés Fernando González Barrios (J. Cheminformatics, 2024)

From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering. - Wen-ran Li; Xavier F. Cadet; David Medina-Ortiz; Mehdi D. Davari; Ramanathan Sowdhamini; Cedric Damour; Yu Li; Alain Miranville; Frédéric Cadet (CoRR, 2025)

Semi-supervised prediction of protein fitness for data-driven protein engineering. - Alicia Olivares-Gil; José Antonio Barbero-Aparicio; Juan José Rodríguez; José-Francisco Díez-Pastor; César García-Osorio; Mehdi D. Davari (J. Cheminformatics, 2025)