Funding
2008 – FIRB Futuro in ricerca
Professional Memberships
2004-present BITS (Bioinformatics ITalian Society)
Research field
Identification of phosphate binding sites in protein structures. Prediction of ligand binding sites in protein structures. Classification and identification of protein structural motifs.
Publications
Pietrosanto M, Adinolfi M, Casula R, Ausiello G, Ferrè F, Helmer-Citterich M. Bioinformatics. 2017 Oct 31. BEAM web server: A tool for structural RNA motif discovery.
Palmeri A, Ausiello G, Ferre F, Helmer-Citterich M, Gherardini PF. Mol Cell Proteomics. 2014 May 15. A proteome-wide Domain-centric Perspective on Protein Phosphorylation.
Mattei E, Ausiello G, Ferrè F, Helmer-Citterich M. Nucleic Acids Res. 2014 Jun;42(10):6146-57. A novel approach to represent and compare RNA secondary structures.
Colantoni A, Bianchi V, Gherardini PF, Tomba GS, Ausiello G, Helmer-Citterich M, Ferrè F. BMC Genomics. 2013 Jun 7;14:379. Alternative splicing tends to avoid partial removals of protein-protein interaction sites
Bianchi V, Mangone I, Ferrè F, Helmer-Citterich M, Ausiello G. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W308-13. webPDBinder: a server for the identification of ligand binding sites on protein structures.
Parca L, Ferré F, Ausiello G, Helmer-Citterich M. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W281-5. Nucleos: a web server for the identification of nucleotide-binding sites in protein structures.
Parca L, Gherardini PF, Truglio M, Mangone I, Ferre’ F, Helmer-Citterich M, Ausiello G. (2012). Identification of nucleotide-binding sites in protein structures: a novel approach based on nucleotide modularity. PLoS One, 7(11):e50240.
Bianchi V, Gherardini PF, Helmer-Citterich M, Ausiello G. (2012). Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities. BMC Bioinformatics, 13(Suppl 4):S17.
Palmeri A, Gherardini PF, Tsigankov P, Ausiello G, Späth GF, Zilberstein D, Helmer-Citterich M. (2011) PhosTryp: a phosphorylation sites predictor specific for parasitic protozoa of the family trypanosomatidae. BMC Genomics, 12:614.
Parca L, Mangone I, Gherardini PF, Ausiello G, Helmer-Citterich M (2011). Phosfinder: a web server for the identification of phosphate binding sites on protein structures. Nucl. Acids Res. 39(Web Server issue):W278-282. May 26.
Parca L, Gherardini PF, Helmer-Citterich M, Ausiello G (2010). Phosphate binding-sites identification in protein structures. Nucl. Acids Res., 39(4):1231-1242.
Gherardini, PF, Ausiello, A, Helmer-Citterich, M. (2010). Superpose3D: a local structural comparison program that allows for user-defined structure representations. PLoS One, 5(8): e11988.
Gherardini, PF, Ausiello, G, Russell, RB, Helmer-Citterich, M (2010). Modular architecture of nucleotide binding pockets. Nucl. Acids Res., 38: 3809-3816.
Ausiello, G., Gherardini, P.F., Gatti, E., Incani, O., Helmer-Citterich, M. (2009). Structural motifs recurring in different folds recognize the same ligand fragments. BMC Bioinformatics, 10:182.
Ausiello, G., Gherardini, P.F., Marcatili, P., Tramontano, A., Via, A., Helmer-Citterich, M. (2008). FunClust: A web server for the identification of structural motifs in a set of non-homologous protein structures. BMC Bioinformatics, 9,(Suppl. 2): S1.
