Geometricus represents protein structures as shape-mers derived from moment invariants. - Janani Durairaj; Mehmet Akdel; Dick de Ridder; Aalt D. J. van Dijk (Bioinform., 2020)

Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases. - Janani Durairaj; Elena Melillo; Harro J. Bouwmeester; Jules Beekwilder; Dick de Ridder; Aalt D. J. van Dijk (PLoS Comput. Biol., 2021)

Tunable and Portable Extreme-Scale Drug Discovery Platform at Exascale: the LIGATE Approach. - Gianluca Palermo; Gianmarco Accordi; Davide Gadioli; Emanuele Vitali; Cristina Silvano; Bruno Guindani; Danilo Ardagna; Andrea Rosario Beccari; Domenico Bonanni; Carmine Talarico; Filippo Lunghini; Jan Martinovic; et al. (CF, 2023)

LIGATE - LIgand Generator and portable drug discovery platform AT Exascale. - Gianluca Palermo; Gianmarco Accordi; Davide Gadioli; Yuedong Zhang; Emanuele Vitali; Bruno Guindani; Danilo Ardagna; Cristina Silvano; Andrea Rosario Beccari; Domenico Bonanni; Carmine Talarico; Filippo Lunghini; et al. (CF (Companion), 2024)

Embedding-based alignment: combining protein language models with dynamic programming alignment to detect structural similarities in the twilight-zone. - Lorenzo Pantolini; Gabriel Studer; Joana Pereira; Janani Durairaj; Gerardo Tauriello; Torsten Schwede (Bioinform., 2024)