iSPOT: a web tool to infer the interaction specificity of families of protein modules. - Barbara Brannetti; Manuela Helmer-Citterich (Nucleic Acids Res., 2003)

ELM server: a new resource for investigating short functional sites in modular eukaryotic proteins. - Pål Puntervoll; Rune Linding; Christine Gemünd; Sophie Chabanis-Davidson; Morten Mattingsdal; Scott Cameron; David M. A. Martin; Gabriele Ausiello; Barbara Brannetti; Anna Costantini; Fabrizio Ferrè; Vincenza Maselli; et al. (Nucleic Acids Res., 2003)

Alignment of protein structures in the presence of domain motions. - Roberto Mosca 002; Barbara Brannetti; Thomas R. Schneider (BMC Bioinform., 2008)