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)

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)

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)

GateFinder: projection-based gating strategy optimization for flow and mass cytometry. - Nima Aghaeepour; Erin F. Simonds; David J. H. F. Knapp; Robert V. Bruggner; Karen Sachs; Anthony Culos; Pier Federico Gherardini; Nikolay Samusik; Gabriela K. Fragiadakis; Sean Bendall; Brice Gaudilliere; Martin S. Angst; et al. (Bioinform., 2018)