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)

A structural study for the optimisation of functional motifs encoded in protein sequences. - Allegra Via; Manuela Helmer-Citterich (BMC Bioinform., 2004)

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

Seq2Struct: a resource for establishing sequence-structure links. - Allegra Via; Andreas Zanzoni; Manuela Helmer-Citterich (Bioinform., 2005)

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)

Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society. - Manuela Helmer-Citterich; Rita Casadio; Alessandro Guffanti; Giancarlo Mauri; Luciano Milanesi; Graziano Pesole; Giorgio Valle; Cecilia Saccone (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)

Bioinformatics in Italy: BITS2006, the third annual meeting of the Italian Society of Bioinformatics. - Rita Casadio; Manuela Helmer-Citterich; Graziano Pesole (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)

Bioinformatics in Italy: BITS2007, the fourth annual meeting of the Italian Society of Bioinformatics. - Graziano Pesole; 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)

A structure filter for the Eukaryotic Linear Motif Resource. - Allegra Via; Cathryn M. Gould; Christine Gemünd; Toby J. Gibson; Manuela Helmer-Citterich (BMC Bioinform., 2009)

ELM: the status of the 2010 eukaryotic linear motif resource. - Cathryn M. Gould; Francesca Diella; Allegra Via; Pål Puntervoll; Christine Gemünd; Sophie Chabanis-Davidson; Sushama Michael; Ahmed Sayadi; Jan Christian Bryne; Claudia Chica; Markus Seiler; Norman E. Davey; et al. (Nucleic Acids Res., 2010)

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)

Phospho3D 2.0: an enhanced database of three-dimensional structures of phosphorylation sites. - Andreas Zanzoni; Daniel Carbajo; Francesca Diella; Pier Federico Gherardini; Anna Tramontano; Manuela Helmer-Citterich; Allegra Via (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)

Modeling gene regulatory network motifs using statecharts. - Fabio Fioravanti; Manuela Helmer-Citterich; Enrico Nardelli (BMC Bioinform., 2012)

Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics. - Paolo Romano 001; Manuela Helmer-Citterich (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)

Bioinformatics in Italy: BITS 2012, the ninth annual meeting of the Italian Society of Bioinformatics. - Carmela Gissi; Paolo Romano 001; Alfredo Ferro; Rosalba Giugno; Alfredo Pulvirenti; Angelo M. Facchiano; Manuela Helmer-Citterich (BMC Bioinform., 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)

Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics. - Angelo M. Facchiano; Claudia Angelini; Roberta Bosotti; Alessandro Guffanti; Anna Marabotti; Roberto Marangoni; Stefano Pascarella; Paolo Romano 001; Andreas Zanzoni; Manuela Helmer-Citterich (BMC Bioinform., 2015)

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)

Tools and data services registry: a community effort to document bioinformatics resources. - Jon C. Ison; Kristoffer Rapacki; Hervé Ménager; Matús Kalas; Emil Rydza; Piotr Chmura; Christian Anthon; Niall Beard; Karel Berka; Dan M. Bolser; Tim Booth; Anthony Bretaudeau; et al. (Nucleic Acids Res., 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)

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)

PDBe-KB: a community-driven resource for structural and functional annotations. - Mihaly Varadi; John M. Berrisford; Mandar S. Deshpande; Sreenath Nair; Aleksandras Gutmanas; David R. Armstrong; Lukás Pravda; Bissan Al-Lazikani; Stephen Anyango; Geoffrey J. Barton; Karel Berka; Tom L. Blundell; et al. (Nucleic Acids Res., 2020)

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)

PDBe-KB: collaboratively defining the biological context of structural data. - Mihaly Varadi; Stephen Anyango; David R. Armstrong; John M. Berrisford; Preeti Choudhary; Mandar S. Deshpande; Nurul Nadzirin; Sreenath Nair; Lukás Pravda; Ahsan Tanweer; Bissan Al-Lazikani; Claudia Andreini; et al. (Nucleic Acids Res., 2022)