Hooke: an open software platform for force spectroscopy. - Massimo Sandal; Fabrizio Benedetti; Marco Brucale; Alberto Gomez-Casado; Bruno Samorì (Bioinform., 2009)

Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids. - Julien Dorier; Dimos Goundaroulis; Fabrizio Benedetti; Andrzej Stasiak (Bioinform., 2018)