Topoly: Python package to analyze topology of polymers. - Pawel Dabrowski-Tumanski; Pawel Rubach; Wanda Niemyska; Bartosz Ambrozy Gren; Joanna I. Sulkowska (Briefings Bioinform., 2021)

AlphaKnot: server to analyze entanglement in structures predicted by AlphaFold methods. - Wanda Niemyska; Pawel Rubach; Bartosz Ambrozy Gren; Mai Lan Nguyen; Wojciech Garstka; Fernando Bruno da Silva; Eric J. Rawdon; Joanna I. Sulkowska (Nucleic Acids Res., 2022)

Knotted artifacts in predicted 3D RNA structures. - Bartosz Ambrozy Gren; Maciej Antczak; Tomasz Zok; Joanna I. Sulkowska; Marta Szachniuk (PLoS Comput. Biol., 2024)