Partner 7

Short name: UR2

Principal Investigator: Prof. Manuela Helmer-Citterich, University of Rome Tor Vergata

Host Institution

The University of Rome Tor Vergata is a public institution whose main fields of activities are research and higher education. The Centre for Molecular Bioinformatics, hosted in the Dept of Biology, is a research and teaching centre with excellent relationships with experimental groups. The group expertise is primarily focused on protein structure analysis for functional annotation: inference of protein interaction specificity specially focused on ePK and ATP binding sites. The group develops methods and build databases, one of which is dedicated to protein kinases 3D structures (Phospho3D, Zanzoni et al., 2007). Gabriele Ausiello (post-doc, biologist) will contribute to the project.

Prof. Manuela Helmer-Citterich

is a physicist who was trained as experimental molecular biologist in the laboratory of Prof. G. Macino, at the University of Rome La Sapienza. She became research assistant in 1984 in the molecular genetics group with Prof. E. Calef. She worked as a post doc at EMBL Heidelberg for two years with Prof. G. Cesareni. After more than 12 years as wet-bench biologist, she went to work with Anna Tramontano at IRBM and began working exclusively in bioinformatics. She currently is professor of Molecular Biology at the Dept. of Biology in the University of Rome Tor Vergata and Director of the Centre for Molecular Bioinformatics. Her laboratory is equipped with 3 IBM servers, one graphic workstation and a number of laptops.

Selected Publications:

1. Zanzoni, A., Ausiello, G., Via, A., Gherardini, P.F., Helmer-Citterich, M. (2007). Phospho3D: a database of three-dimensional structures of protein phosphorylation sites. Nucl. Acids Res., 35:D229-D231.

2. Ferraro, E., Via, A., Ausiello, G., Helmer-Citterich, M. (2006) A novel structure-based encoding for machine-learning applied to the inference of SH3 domain specificity. Bioinformatics, 22:2333-2339.

3. Ausiello, G., Via, A., Helmer-Citterich, M. (2005). Query3d: a new method for high-throughput analysis of functional residues in protein structures. BMC Bioinformatics, 6(Suppl 4):S5.
4. Ferrè, F., Ausiello, G., Zanzoni, A., Helmer-Citterich, M. (2005). Functional annotation by identification of local surface similarities: a novel tool for structural genomics. BMC Bioinformatics, 6:19.
5. Via, A., Ferre', F., Brannetti, B., Valencia, A. and Helmer Citterich, M. (2000). 3D view of the surface motif associated to the Ploop structure: cis and trans cases of convergent evolution. J.Mol.Biol., 303, 455-465.