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)

Query3d: a new method for high-throughput analysis of functional residues in protein structures. - Gabriele Ausiello; Allegra Via; Manuela Helmer-Citterich (BMC Bioinform., 2005)

A neural strategy for the inference of SH3 domain-peptide interaction specificity. - Enrico Ferraro; Allegra Via; Gabriele Ausiello; Manuela Helmer-Citterich (BMC 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)

pdbFun: mass selection and fast comparison of annotated PDB residues. - Gabriele Ausiello; Andreas Zanzoni; Daniele Peluso; Allegra Via; Manuela Helmer-Citterich (Nucleic Acids Res., 2005)

A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity. - Enrico Ferraro; Allegra Via; Gabriele Ausiello; Manuela Helmer-Citterich (Bioinform., 2006)

Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites. - Gabriele Ausiello; Daniele Peluso; Allegra Via; Manuela Helmer-Citterich (BMC Bioinform., 2007)

False occurrences of functional motifs in protein sequences highlight evolutionary constraints. - Allegra Via; Pier Federico Gherardini; Enrico Ferraro; Gabriele Ausiello; Gianpaolo Scalia Tomba; Manuela Helmer-Citterich (BMC Bioinform., 2007)

SH3-Hunter: discovery of SH3 domain interaction sites in proteins. - Enrico Ferraro; Daniele Peluso; Allegra Via; Gabriele Ausiello; Manuela Helmer-Citterich (Nucleic Acids Res., 2007)

3dLOGO: a web server for the identification, analysis and use of conserved protein substructures. - Allegra Via; Daniele Peluso; Pier Federico Gherardini; Emanuele de Rinaldis; Teresa Colombo; Gabriele Ausiello; Manuela Helmer-Citterich (Nucleic Acids Res., 2007)

Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. - Andreas Zanzoni; Gabriele Ausiello; Allegra Via; Pier Federico Gherardini; Manuela Helmer-Citterich (Nucleic Acids Res., 2007)

FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. - Gabriele Ausiello; Pier Federico Gherardini; Paolo Marcatili; Anna Tramontano; Allegra Via; Manuela Helmer-Citterich (BMC Bioinform., 2008)

Structural motifs recurring in different folds recognize the same ligand fragments. - Gabriele Ausiello; Pier Federico Gherardini; Elena Gatti; Ottaviano Incani; Manuela Helmer-Citterich (BMC Bioinform., 2009)

Phosfinder: a web server for the identification of phosphate-binding sites on protein structures. - Luca Parca; Iolanda Mangone; Pier Federico Gherardini; Gabriele Ausiello; Manuela Helmer-Citterich (Nucleic Acids Res., 2011)

Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities. - Valerio Bianchi; Pier Federico Gherardini; Manuela Helmer-Citterich; Gabriele Ausiello (BMC Bioinform., 2012)

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)

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)

Kinome-wide identification of phosphorylation networks in eukaryotic proteomes. - Luca Parca; Bruno Ariano; Andrea Cabibbo; Marco Paoletti; Annalaura Tamburrini; Antonio Palmeri; Gabriele Ausiello; Manuela Helmer-Citterich (Bioinform., 2019)

Revisiting the "satisfaction of spatial restraints" approach of MODELLER for protein homology modeling. - Giacomo Janson; Alessandro Grottesi; Marco Pietrosanto; Gabriele Ausiello; Giulia Guarguaglini; Alessandro Paiardini (PLoS Comput. Biol., 2019)

BRIO: a web server for RNA sequence and structure motif scan. - Andrea Guarracino; Gerardo Pepe; Francesco Ballesio; Marta Adinolfi; Marco Pietrosanto; Elisa Sangiovanni; Ilio Vitale; Gabriele Ausiello; Manuela Helmer-Citterich (Nucleic Acids Res., 2021)