Research Groups
Protein Structure and Bioinformatics
Research Interests and Description
Research Interests
Bioinformatics and systems biology of genomes and proteomes, models of communication and cooperation in biology, NOTCH signaling, network models, protein chemistry.
Description of Research
The Group is interested in the principles of communicaton and cooperation in biology that we study with the tools of bioinformatics, structural biology and protein chemistry. Both the structural organization and the molecular interactions of proteins can be described as specific and robust networks. A better knowledge of the macromolecular stability and specificity is important for practical purposes such as understanding the cellular mechanisms or the design of better pharmacons. The lab uses the approaches of bioinformatics, peptide chemistry, NMR, mass spectrometry and recombinant DNA technologies. It studies the proteins of the Notch signalling network and its involvement in genetic diseases. In particular, it looks at the formation of disulfide bonds in proteins; evolution of network stability and systems biology; prediction of protein structure and function using machine learning approaches, and aspects of protein chemistry including synthesis of modified peptides and pharmaceutical applications.
Our current bioinformatics topics include the development of computational tools for manycore computer architectures, novel search techniques for proteomics and computational modelling of bacterial communications. More
Recent Publications
Netotea, S., Bertani, I., Steindler, L., Kerényi, A., Venturi, V., Pongor, S. 2009. A simple model for the early events of quorum sensing in Pseudomonas aeruginosa: modeling bacterial swarming as the movement of an "activation zone". Biology Direct 4, 6
Kuzniar, A., van Ham, R.C.H.J., Pongor, S., Leunissen, J.A.M. 2008. The Quest for Orthologs: Finding Gene Correspondences across Genomes, Trends Genet. 24, 539-551
De Biasio, A., Guarnaccia, C., Popovic, M., Uversky, V.N., Pintar, A., Pongor, S. 2008. Prevalence of Intrinsic Disorder in the Intracellular Region of Human Single-Pass Type I Proteins: The Case of the Notch Ligand Delta-4. J Proteome Res. 7, 2496-2506
Popovic, M., De Biasio, A., Pintar, A., Pongor, S. 2007. The intracellular region of the Notch ligand Jagged-1 gains partial structure upon binding to synthetic membranes. FEBS J 274, 5325-5336
Sonego, P., Pacurar, M., Dhir, S., Kertész-Farkas, A, Kocsor, A., Gáspári, Z., Leunissen, J.A.M., Pongor, S. 2007. A Protein Classification Benchmark collection for machine learning. Nucl. Acids. Res. D232-236
Zahariev, S., Guarnaccia, C., Zanuttin, F., Pintar, A., Esposito, G., Maravic, G., Krust, B., Hovanessian, A.G., Pongor, S. 2005. Efficient synthesis and comparative studies of the arginine and Nomega,Nomega-dimethylarginine forms of the human nucleolin glycine/arginine rich domain. J Pept Sci. 11, 17-28
Csermely, P., Ágoston, V., Pongor S. 2005. The efficiency of multi-target drugs: The network approach may help drug design. Trends Pharmacol Sciences, 26, 178-182
