GradPose: a very fast and memory-efficient gradient descent-based tool for superimposing millions of protein structures from computational simulations. - Daniel-T. Rademaker; Kevin J. van Geemen; Li C. Xue (Bioinform., 2023)

DeepRank2: Mining 3D Protein Structures with Geometric Deep Learning. - Giulia Crocioni; Dani L. Bodor; Coos Baakman; Farzaneh M. Parizi; Daniel-T. Rademaker; Gayatri Ramakrishnan; Sven van der Burg; Dario F. Marzella; João M. C. Teixeira; Li C. Xue (J. Open Source Softw., 2024)