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)

SURFACE: a database of protein surface regions for functional annotation. - Fabrizio Ferrè; Gabriele Ausiello; Andreas Zanzoni; Manuela Helmer-Citterich (Nucleic Acids Res., 2004)

Disulfide connectivity prediction using secondary structure information and diresidue frequencies. - Fabrizio Ferrè; Peter Clote (Bioinform., 2005)

Functional annotation by identification of local surface similarities: a novel tool for structural genomics. - Fabrizio Ferrè; Gabriele Ausiello; Andreas Zanzoni; Manuela Helmer-Citterich (BMC Bioinform., 2005)

DiANNA: a web server for disulfide connectivity prediction. - Fabrizio Ferrè; Peter Clote (Nucleic Acids Res., 2005)

DiANNA 1.1: an extension of the DiANNA web server for ternary cysteine classification. - Fabrizio Ferrè; Peter Clote (Nucleic Acids Res., 2006)

BTW: a web server for Boltzmann time warping of gene expression time series. - Fabrizio Ferrè; Peter Clote (Nucleic Acids Res., 2006)

DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities. - Fabrizio Ferrè; Yann Ponty; W. A. Lorenz; Peter Clote (Nucleic Acids Res., 2007)

DBATE: database of alternative transcripts expression. - Valerio Bianchi; Alessio Colantoni; Alberto Calderone; Gabriele Ausiello; Fabrizio Ferrè; Manuela Helmer-Citterich (Database J. Biol. Databases Curation, 2013)

webPDBinder: a server for the identification of ligand binding sites on protein structures. - Valerio Bianchi; Iolanda Mangone; Fabrizio Ferrè; Manuela Helmer-Citterich; Gabriele Ausiello (Nucleic Acids Res., 2013)

Nucleos: a web server for the identification of nucleotide-binding sites in protein structures. - Luca Parca; Fabrizio Ferrè; Gabriele Ausiello; Manuela Helmer-Citterich (Nucleic Acids Res., 2013)

Web-Beagle: a web server for the alignment of RNA secondary structures. - Eugenio Mattei; Marco Pietrosanto; Fabrizio Ferrè; Manuela Helmer-Citterich (Nucleic Acids Res., 2015)

Revealing protein-lncRNA interaction. - Fabrizio Ferrè; Alessio Colantoni; Manuela Helmer-Citterich (Briefings Bioinform., 2016)

BEAM web server: a tool for structural RNA motif discovery. - Marco Pietrosanto; Marta Adinolfi; Riccardo Casula; Gabriele Ausiello; Fabrizio Ferrè; Manuela Helmer-Citterich (Bioinform., 2018)