Research Groups

Sandor Pongor

Protein Structure and Bioinformatics

Former Group Leader

Sandor Pongor

Education

Technical University, Budapest, Hungary, Diploma in Chemical Engineering (biological technologies), 1974
Technical University, Budapest, Hungary, PhD in Biochemistry, 1978
Hungarian Academy of Sciences, Budapest, Hungary, Doctor of Sciences, 1989
Szent István University, Gödöllö, Hungary, Doctor Habilitatus, 1998

Career History

1990-2015, Senior Scientist and Group Leader of the Protein Structure and Bioinformatics Laboratory of the ICGEB, Trieste.
1989-1994 Director, Institute for Biochemistry and Protein Research, Agricultural Biotechnology Center, Gödöllö, Hungary
1986-1990 Research Director, Agricultural Biotechnology Center, Gödöllö, Hungary
1984-1985 Research Associate, Cornell University, Ithaca, NY, USA
1982-1983 Research Associate, Rockefeller University, New York, NY, USA
1974-1981 Ph.D. Student, Research Associate, Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary

Teaching Activity

Since 1992, organizer of the summer course: Bioinformatics: Computer Methods in Molecular Biology as well as other practical and theoretical courses in bioinformatics (over 1100 students since 1992).
Since 2001, Szent-Györgyi Professor in Bioinformatics, Biological Research Center and University of Szeged, Hungary.
Since 1997 lecturer in Proteome Boinformatics in the PhD Course of Molecular Genetics of the International School for Advanced Studies (ISAS) of Trieste, Italy.
Since 1988 Adjunct Professor in Biochemistry, Szent István University, Gödöllö, Hungary.

Scientific Activity

His research focuses on the principles of stability and specificity in molecular recognition systems. The first area of interest is bioinformatics (evolution of network models, classification by machine learning techniques, databases). The second area of interest concerns the specificity of protein/DNA interactions, disulfide bond formation with particular reference to signal transduction events such as the Notch signalling network, as well as to pharmaceutical applications. On the theoretical side, his Group is interested in the problems of scientific knowledge-representation as applied to genome, proteome and structural analysis.
Over 200 papers published, 2 books and 4 patents.

Other Activities

Member of Academia Europaea, the Hungarian Academy of Sciences, the International Society of Computational Biology, the Italian and the Hungarian Bioinformatics Societies. His Group operates the bioinformatics and the peptide synthesis core facilities at ICGEB, Trieste.
Member of the Editorial Board of Databases (Oxford University Press).
1996-1997 Chairman, European Molecular Biology Network (EMBnet).

Selected 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

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, In press

Sonego, P., Kocsor, A., Pongor, S. 2008. Receiver Operating Characteristics (ROC) Analysis: Applications to the classification of biological sequences and 3D structures. Briefings in Bioinformatics, 9, 198-209

Ángyán, A., Perczel, A., Pongor, S., Gáspári, Z. 2008. Fast protein fold estimation from NMR-derived distance restraints. Bioinformatics 24, 272-275

Kocsor, A., Busa-Fekete, R., Pongor S. 2008. Protein Classification Based on Propagation on  Unrooted Binary Trees. Peptide and Protein Lett. 15, 428-434

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., Jack A.M. Leunissen, J.A.M., Pongor, S. 2007. A Protein Classification Benchmark collection for machine learning. Nucl. Acids. Res. 35, D232-236

Kaján, L., Kertész-Farkas, A., Coinete Franklin, D.R., Kocsor, A., Pongor, S. 2006. Application of a simple log likelihood ratio approximant to protein sequence classification. Bioinformatics 22, 2865-2869

Popovic, M., Coglievina, M., Guarnaccia, C., Verdone, G., Esposito, G., Pintar, A., Pongor, S. 2006. Gene synthesis, expression, purification, and characterisation of human Jagged-1 intracellular region. Protein Expr. Purif. 47, 398-404

Ágoston, V., Cemazar, M., Kaján, L., Pongor, S. 2005. Graph representation of oxidative folding pathways. BMC Bioinformatics 6, 19

Ágoston, V., Csermely, P., Pongor, S. 2005. Weak hits confuse complex systems. Physical Review E, Stat Nonlin Soft Matter Phys. 71, 051909

Moss, D.S., Jelaska, S., Pongor, S., editors. Essays in Bioinformatics. IOS Press, Amsterdam 11-31

Csermely, P., Ágoston, V., Pongor, S. 2005. The efficiency of multi-target drugs: The network approach may help drug design. Trends Pharmacol. Sci. 26, 178-182

Gáspári, L., Vlahovicek, K., Pongor, S. 2005. Efficient recognition of protein folds in protein 3-D structures by the improved PRIDE algorithm. Bioinformatics 21, 3322-3323

Kocsor, A., Kertész-Farkas, A., Kaján, L., Pongor, S. 2005. Application of compression-based distance measures to protein sequence classification: a methodological study. Bioinformatics, 22, 407-412

Moss, D.S., Jelaska, S., Pongor, S., editors. 2005. Essays in Bioinformatics. IOS Press, Amsterdam, 251 pages.

Pintar, A., Pongor, S. 2005. The “first in-last out” hypothesis on protein folding revisited. Proteins 60, 584-590

Zahariev, S., Guarnaccia, C., Zanuttin, F., Pintar, A., Esposito, G., Maravic, G., Krust, B., Hovanessian, A.G., Pongor, S. 2005. Synthesis and comparative studies of the arginine and Nw,Nw-dimethylarginine forms of the human nucleolin glycine/arginine rich domain. J. Pept. Sci. 11, 17-28

Cemazar, M., Zahariev, S., Pongor, S., Hore, P.J. 2004. Oxidative folding process: from disulfide species to conformations of amino acid residues in Amarathus a-amylase inhibitor. J. Biol. Chem. 279, 16697-16705

Guarnaccia C., Pintar A., Pongor S. 2004. Exon 6 of human Jagged-1 encodes an autonomously folding unit. FEBS Lett. 574(1-3):156-160

Guarnaccia C., Raman B., Zahariev S., Simoncsits A., Pongor S. 2004. DNA-mediated assembly of weakly interacting DNA-binding protein subunits: in vitro recruitment of phage 434 repressor and yeast GCN4 DNA-binding domains. Nucl. Acids Res. 32, 4992-5002

Zahariev S., Guarnaccia C., Lamba D., Cemazar M., Pongor S. 2004. Solvent-free synthesis of azole carboximidamides and one pot preparation of guanidines from amines. J. Pept. Sci. 10, (S2):151

Cemazar, M., Zakhariev, S., Lopez, J.J., Carugo, O., Jones, J.A., Hore, P.J., Pongor, S. 2002. Oxidative folding intermediates with non-native disulfide bridges between adjacent cystein residues. Proc. Natl. Acad. Sci. USA. 100, 5754-5759

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