Manuela Helmer-Citterich
e-mail: citterich AT uniroma2.it
website: bioinformatica.uniroma2.it/~manuela/
affiliation: Università di Roma Tor Vergata
research area(s): Computational Biology, Molecular Biology
Course:
Cell and Molecular Biology
University/Istitution: Università di Roma Tor Vergata
University/Istitution: Università di Roma Tor Vergata
Education and Training
1981: Degree in Physics
1981-1984: fellow with Giuseppe Macino, working on gene arrangement and transcription regulation in Neurospora crassa mitochondria (molecular biology)
1986-1988:EMBL post-doc with Gianni Cesareni, working on RNA-protein interaction in the ColE1 system (molecular biology)
1991-1993: guest scientist at IRBM with Anna Tramontano, developing a docking program, i.e. a software for the reconstruction of protein complexes starting from the 3d coordinates of their separated components (structural bioinformatics)
Scientific Profile:2005-nowadays: Full Professor in Bioinformatics
1981: Degree in Physics
1981-1984: fellow with Giuseppe Macino, working on gene arrangement and transcription regulation in Neurospora crassa mitochondria (molecular biology)
1986-1988:EMBL post-doc with Gianni Cesareni, working on RNA-protein interaction in the ColE1 system (molecular biology)
1991-1993: guest scientist at IRBM with Anna Tramontano, developing a docking program, i.e. a software for the reconstruction of protein complexes starting from the 3d coordinates of their separated components (structural bioinformatics)
Scientific Profile:2005-nowadays: Full Professor in Bioinformatics
Development of computational methods for the analysis of protein structure and the inference of protein interaction and interaction specificity
Minguez P, Parca L, Diella F, Mende DR, Kumar R, Helmer-Citterich M, Gavin AC, van Noort V, Bork P (2012). Deciphering a global network of functionally associated post-translational modifications. Mol. Syst. Biol, 8:599.
Fioravanti F, Helmer-Citterich M, Nardelli E. (2012). Modeling Gene Regulatory Network Motifs using Statecharts. BMC Bioinformatics, 13(Suppl 4):S20.
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.
Tsigankov P, Gherardini PF, Helmer-Citterich M, Zilberstein D. What have proteomics taught us about Leishmania development inside its host? Parasitology, 28:1-12.
Palmeri A, Gherardini PF, Tsigankov P, Ausiello G, Spaeth 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.
Schmidt-Arras,D., Leclercq, O., Gherardini, P.F., Helmer-Citterich, M., Faigle, W., Loew, D., Spaeth, G. (2011). Adaptation of a 2D in-gel kinase assay to trace phosphotransferase activities in the human pathogen Leishmania donovani. J Proteomics, Mar 26. [Epub ahead of print].
Via, A., Diella, F., Gibson, TJ., Helmer-Citterich, M. (2011). From sequence to structural analysis in protein phosphorylation motifs. Frontiers in Bioscience, 16: 1261-1275.
Zanzoni A, Carbajo D, Diella F, Gherardini PF, Tramontano A, Helmer-Citterich M, Via A (2011). Phospho3D 2.0: An enhanced database of three-dimensional structures of phosphorylation sites. Nucl. Acids Res., 39 (Database issue): D268-71.
Parca L, Gherardini PF, Helmer-Citterich M, Ausiello G (2010). Phosphate binding-sites identification in protein structures. Nucl. Acids Res., 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.
Hem, S, Gherardini, PF, Fortea, JO, Hourdel, V, Morales, MA, Watanabe, R, Pescher, P, Kuzyk, MA, Smith, D, Borchers, CH, Zilberstein, D, Helmer-Citterich, M, Namane, A, Spaeth GF (2010). Identification of Leishmania-specific protein phosphorylation sites by LC-MS/MS and comparative genomics analyses. Proteomics, 21: 3868-6883.
Yau WL, Blisnick T, Taly JF, Helmer-Citterich M, Schiene-Fischer C, Leclercq O, Li J, Schmidt-Arras D, Morales MA, Notredame C, Romo D, Bastin P, Spaeth GF (2010). Cyclosporin A treatment of Leishmania donovani reveals stage-specific functions of cyclophilins in parasite differentiation, proliferation, and viability. PLoS Negl Trop Dis., 4(6):e729.
Gherardini, PF, Ausiello, G, Russell, RB, Helmer-Citterich, M (2010). Modular architecture of nucleotide binding pockets. Nucl. Acids Res., 38: 3809-3816.
Gould C, Diella F, Via A, Puntervoll P, Gemuend, C., Michael S, Sayadi A, Bryne JC, Chica C, Davey N, Haslam N, Budd A, Hughes T, Pas J, Rychlewski L, Trave' G, Aasland R, Helmer-Citterich M, Linding R, Gibson TJ (2010) ELM: The status of the 2010 Eukaryotic Linear Motif Resource. Nucl. Acids Res., 38(Database issue):D167-180.
Via A, Gould CM, Gemuend C, Gibson TJ, Helmer-Citterich M (2009) A structure filter for the Eukaryotic Linear Motif Resource. BMC Bioinformatics, 10(1):351.
Ausiello G, Gherardini PF, Gatti E, Incani, O., Helmer-Citterich, M. (2009). Structural motifs recurring in different folds recognize the same ligand fragments. BMC Bioinformatics, 10:182.
Gherardini PF, Helmer-Citterich M. (2008). Structure-based function prediction: approaches and applications. Brief Funct Genomic Proteomic, 7:291-302.
Ausiello G, Gherardini PF, 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.
Fioravanti F, Helmer-Citterich M, Nardelli E. (2012). Modeling Gene Regulatory Network Motifs using Statecharts. BMC Bioinformatics, 13(Suppl 4):S20.
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.
Tsigankov P, Gherardini PF, Helmer-Citterich M, Zilberstein D. What have proteomics taught us about Leishmania development inside its host? Parasitology, 28:1-12.
Palmeri A, Gherardini PF, Tsigankov P, Ausiello G, Spaeth 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.
Schmidt-Arras,D., Leclercq, O., Gherardini, P.F., Helmer-Citterich, M., Faigle, W., Loew, D., Spaeth, G. (2011). Adaptation of a 2D in-gel kinase assay to trace phosphotransferase activities in the human pathogen Leishmania donovani. J Proteomics, Mar 26. [Epub ahead of print].
Via, A., Diella, F., Gibson, TJ., Helmer-Citterich, M. (2011). From sequence to structural analysis in protein phosphorylation motifs. Frontiers in Bioscience, 16: 1261-1275.
Zanzoni A, Carbajo D, Diella F, Gherardini PF, Tramontano A, Helmer-Citterich M, Via A (2011). Phospho3D 2.0: An enhanced database of three-dimensional structures of phosphorylation sites. Nucl. Acids Res., 39 (Database issue): D268-71.
Parca L, Gherardini PF, Helmer-Citterich M, Ausiello G (2010). Phosphate binding-sites identification in protein structures. Nucl. Acids Res., 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.
Hem, S, Gherardini, PF, Fortea, JO, Hourdel, V, Morales, MA, Watanabe, R, Pescher, P, Kuzyk, MA, Smith, D, Borchers, CH, Zilberstein, D, Helmer-Citterich, M, Namane, A, Spaeth GF (2010). Identification of Leishmania-specific protein phosphorylation sites by LC-MS/MS and comparative genomics analyses. Proteomics, 21: 3868-6883.
Yau WL, Blisnick T, Taly JF, Helmer-Citterich M, Schiene-Fischer C, Leclercq O, Li J, Schmidt-Arras D, Morales MA, Notredame C, Romo D, Bastin P, Spaeth GF (2010). Cyclosporin A treatment of Leishmania donovani reveals stage-specific functions of cyclophilins in parasite differentiation, proliferation, and viability. PLoS Negl Trop Dis., 4(6):e729.
Gherardini, PF, Ausiello, G, Russell, RB, Helmer-Citterich, M (2010). Modular architecture of nucleotide binding pockets. Nucl. Acids Res., 38: 3809-3816.
Gould C, Diella F, Via A, Puntervoll P, Gemuend, C., Michael S, Sayadi A, Bryne JC, Chica C, Davey N, Haslam N, Budd A, Hughes T, Pas J, Rychlewski L, Trave' G, Aasland R, Helmer-Citterich M, Linding R, Gibson TJ (2010) ELM: The status of the 2010 Eukaryotic Linear Motif Resource. Nucl. Acids Res., 38(Database issue):D167-180.
Via A, Gould CM, Gemuend C, Gibson TJ, Helmer-Citterich M (2009) A structure filter for the Eukaryotic Linear Motif Resource. BMC Bioinformatics, 10(1):351.
Ausiello G, Gherardini PF, Gatti E, Incani, O., Helmer-Citterich, M. (2009). Structural motifs recurring in different folds recognize the same ligand fragments. BMC Bioinformatics, 10:182.
Gherardini PF, Helmer-Citterich M. (2008). Structure-based function prediction: approaches and applications. Brief Funct Genomic Proteomic, 7:291-302.
Ausiello G, Gherardini PF, 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.
Project Title:
High-throughput identification of natural binders and specific inhibitors for protein kinases and phosphatases
Aim of the project is the development of a method for the inference of interactions between selected proteins, i.e. kinases (PTKs) and phosphatases (PTPs), and compounds of potential therapeutic impact in cancer. Our method is designed for the identification of natural binders of PTKs and PTPs of known structure and as a help in drug design. More specifically, we want to exploit the enormous amount of structural information available in the database of known structures in order to improve our ability in inferring a potential interaction between a given protein and small potentially interacting ligand molecules. In the project we describe a computational and an experimental validation to be performed on the complete ensemble of human protein tyrosine phosphatases of known structure. The work will also include the development of the databases and web servers needed to make this new methodology and all the obtained data publicly available.