Scientific publications

dUTPase-related papers:

  1. Vértessy BG, Tóth J.
    Keeping Uracil Out of DNA: Physiological Role, Structure and Catalytic Mechanism of dUTPases. Acc Chem Res. 2008 Oct 7. [Epub ahead of print]
    PMID: 18837522

  2. Varga B, Barabás O, Takács E, Nagy N, Nagy P, Vértessy BG.
    Active site of mycobacterial dUTPase: structural characteristics and a built-in sensor. Biochem Biophys Res Commun. 2008 Aug 15;373(1):8-13. Epub 2008 Jun 2.
    PMID: 18519027

  3. Kovári J, Barabás O, Varga B, Békési A, Tölgyesi F, Fidy J, Nagy J, Vértessy
    BG. Methylene substitution at the alpha-beta bridging position within the phosphate chain of dUDP profoundly perturbs ligand accommodation into the dUTPase active site.Proteins. 2008 Apr;71(1):308-19.
    PMID: 17932923

  4. Varga B, Barabás O, Kovári J, Tóth J, Hunyadi-Gulyás E, Klement E, Medzihradszky KF, Tölgyesi F, Fidy J, Vértessy BG.
    Active site closure facilitates juxtaposition of reactant atoms for initiation of catalysis by human dUTPase. FEBS Lett. 2007 Oct 2;581(24):4783-8. Epub 2007 Sep 12.
    PMID: 17880943

  5. Tóth J, Varga B, Kovács M, Málnási-Csizmadia A, Vértessy BG.
    Kinetic mechanism of human dUTPase, an essential nucleotide pyrophosphatase enzyme. J Biol Chem. 2007 Nov 16;282(46):33572-82. Epub 2007 Sep 11.
    PMID: 17848562

  6. Németh-Pongrácz V, Barabás O, Fuxreiter M, Simon I, Pichová I, Rumlová M, Zábranská H, Svergun D, Petoukhov M, Harmat V, Klement E, Hunyadi-Gulyás E, Medzihradszky KF, Kónya E, Vértessy BG.
    Flexible segments modulate co-folding of dUTPase and nucleocapsid proteins.
    Nucleic Acids Res. 2007;35(2):495-505. Epub 2006 Dec 14.
    PMID: 17169987

  7. Németh-Pongrácz V, Snasel J, Rumlova M, Pichova I, Vértessy BG.
    Interacting partners of M-PMV nucleocapsid-dUTPase.
    Nucleosides Nucleotides Nucleic Acids. 2006;25(9-11):1197-200.
    PMID: 17065090 [PubMed - indexed for MEDLINE]

  8. Lari SU, Chen CY, Vertéssy BG, Morré J, Bennett SE.
    Quantitative determination of uracil residues in Escherichia coli DNA: Contribution of ung, dug, and dut genes to uracil avoidance.
    DNA Repair (Amst). 2006 Dec 9;5(12):1407-20. Epub 2006 Aug 14.
    PMID: 16908222

  9. Barabás O, Németh V, Vértessy BG.
    Crystallization and preliminary X-ray studies of dUTPase from Mason-Pfizer monkey retrovirus. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006 Apr 1;62(Pt 4):399-401.
    Epub 2006 Mar 25.
    PMID: 16582495

  10. Kovári J, Imre T, Szabó P, Vértessy BG.
    Mechanistic studies of dUTPases.
    Nucleosides Nucleotides Nucleic Acids. 2004 Oct;23(8-9):1475-9.
    PMID: 15571280

  11. Barabás O, Pongrácz V, Kovári J, Wilmanns M, Vértessy BG.
    Structural insights into the catalytic mechanism of phosphate ester hydrolysis by dUTPase. J Biol Chem. 2004 Oct 8;279(41):42907-15. Epub 2004 Jun 17.
    PMID: 15208312

  12. Takács E, Grolmusz VK, Vértessy BG.
    A tradeoff between protein stability and conformational mobility in homotrimeric dUTPases. FEBS Lett. 2004 May 21;566(1-3):48-54.
    PMID: 15147867

  13. Békési A, Zagyva I, Hunyadi-Gulyás E, Pongrácz V, Kovári J, Nagy AO, Erdei A, Medzihradszky KF, Vértessy BG.
    Developmental regulation of dUTPase in Drosophila melanogaster. J Biol Chem. 2004 May 21;279(21):22362-70. Epub 2004 Mar 2.
    PMID: 14996835 [PubMed - indexed for MEDLINE]

  14. Kovári J, Barabás O, Takács E, Békési A, Dubrovay Z, Pongrácz V, Zagyva I, Imre T, Szabó P, Vértessy BG.
    Altered active site flexibility and a structural metal-binding site in eukaryotic dUTPase: kinetic characterization, folding, and crystallographic studies of the homotrimeric Drosophila enzyme. J Biol Chem. 2004 Apr 23;279(17):17932-44. Epub 2004 Jan 14.
    PMID: 14724274

  15. Dubrovay Z, Gáspári Z, Hunyadi-Gulyás E, Medzihradszky KF, Perczel A, Vértessy BG.
    Multidimensional NMR identifies the conformational shift essential for catalytic competence in the 60-kDa Drosophila melanogaster dUTPase trimer. J Biol Chem. 2004 Apr 23;279(17):17945-50. Epub 2004 Jan 14.
    PMID: 14724273

  16. Barabás O, Rumlová M, Erdei A, Pongrácz V, Pichová I, Vértessy BG.
    dUTPase and nucleocapsid polypeptides of the Mason-Pfizer monkey virus form a fusion protein in the virion with homotrimeric organization and low catalytic efficiency. J Biol Chem. 2003 Oct 3;278(40):38803-12. Epub 2003 Jul 16.
    PMID: 12869552

  17. Mustafi D, Bekesi A, Vertessy BG, Makinen MW.
    Catalytic and structural role of the metal ion in dUTP pyrophosphatase. Proc Natl Acad Sci U S A. 2003 May 13;100(10):5670-5. Epub 2003 Apr 29.
    PMID: 12721364

  18. Vertessy BG, Larsson G, Persson T, Bergman AC, Persson R, Nyman PO.
    The complete triphosphate moiety of non-hydrolyzable substrate analogues is required for a conformational shift of the flexible C-terminus in E. coli dUTP pyrophosphatase. FEBS Lett. 1998 Jan 2;421(1):83-8.
    PMID: 9462846

Proteomics-related works:

  1. Gonda X, Fountoulakis KN, Juhasz G, Rihmer Z, Lazary J, Laszik A, Akiskal HS, Bagdy G.
    Association of the s allele of the 5-HTTLPR with neuroticism-related traits and temperaments in a psychiatrically healthy population.
    Eur Arch Psychiatry Clin Neurosci. 2008 Sep 19. [Epub ahead of print]
    PMID: 18806915 [PubMed - as supplied by publisher]

  2. Lörincz ML, Oláh M, Juhász G.
    Functional consequences of retinopetal fibers originating in the dorsal raphe nucleus.
    Int J Neurosci. 2008 Oct;118(10):1374-83.
    PMID: 18788023 [PubMed - indexed for MEDLINE]

  3. Juhász G, Vass G, Bozsó Z, Budai D, Penke B, Szegedi V.
    Integrin activation modulates NMDA and AMPA receptor function of CA1 cells in a dose-related fashion in vivo.
    Brain Res. 2008 Oct 3;1233:20-6. Epub 2008 May 21.
    PMID: 18762286 [PubMed - indexed for MEDLINE]

  4. Hughes SW, Errington A, Lorincz ML, Kékesi KA, Juhász G, Orbán G, Cope DW, Crunelli V.
    Novel modes of rhythmic burst firing at cognitively-relevant frequencies in thalamocortical neurons.
    Brain Res. 2008 Oct 15;1235:12-20. Epub 2008 Jun 19. Review.
    PMID: 18602904 [PubMed - indexed for MEDLINE]

  5. Baracskay P, Szepesi Z, Orbán G, Juhász G, Czurkó A.
    Generalization of seizures parallels the formation of "dark" neurons in the hippocampus and pontine reticular formation after focal-cortical application of 4-aminopyridine (4-AP) in the rat.
    Brain Res. 2008 Sep 4;1228:217-28. Epub 2008 Jun 21.
    PMID: 18602900 [PubMed - indexed for MEDLINE]

  6. Lazary J, Lazary A, Gonda X, Benko A, Molnar E, Juhasz G, Bagdy G.
    New evidence for the association of the serotonin transporter gene (SLC6A4) haplotypes, threatening life events, and depressive phenotype.
    Biol Psychiatry. 2008 Sep 15;64(6):498-504. Epub 2008 May 16.
    PMID: 18486105 [PubMed - in process]

  7. Lippai M, Csikós G, Maróy P, Lukácsovich T, Juhász G, Sass M.
    SNF4Agamma, the Drosophila AMPK gamma subunit is required for regulation of developmental and stress-induced autophagy.
    Autophagy. 2008 May 16;4(4):476-86. Epub 2008 Feb 13.
    PMID: 18285699 [PubMed - indexed for MEDLINE]

  8. Juhász G, Erdi B, Sass M, Neufeld TP.
    Atg7-dependent autophagy promotes neuronal health, stress tolerance, and longevity but is dispensable for metamorphosis in Drosophila.
    Genes Dev. 2007 Dec 1;21(23):3061-6.
    PMID: 18056421 [PubMed - indexed for MEDLINE]

  9. Papp AM, Nyilas R, Szepesi Z, Lorincz ML, Takács E, Abrahám I, Szilágyi N, Tóth J, Medveczky P, Szilágyi L, Juhász G, Juhász G.
    Visible light induces matrix metalloproteinase-9 expression in rat eye.
    J Neurochem. 2007 Dec;103(6):2224-33. Epub 2007 Sep 11.
    PMID: 17854381 [PubMed - indexed for MEDLINE]

  10. Kovács Z, Puskás L, Nyitrai G, Papp E, Császár I, Juhász G, Palkovits M.
    Suppression of spike-wave discharge activity and c-fos expression by 2-methyl-4-oxo-3H-quinazoline-3-acetyl piperidine (Q5) in vivo.
    Neurosci Lett. 2007 Aug 9;423(1):73-7. Epub 2007 Jul 4.
    PMID: 17662531 [PubMed - indexed for MEDLINE]

  11. Chang YY, Juhász G, Goraksha-Hicks P, Arsham AM, Mallin DR, Muller LK, Neufeld TP.
    Nutrient-dependent regulation of autophagy through the target of rapamycin pathway.
    Biochem Soc Trans. 2009 Feb;37(Pt 1):232-6. Review.
    PMID: 19143638 [PubMed - indexed for MEDLINE]

  12. Kékesi KA, Kovács Z, Szilágyi N, Bobest M, Szikra T, Dobolyi A, Juhász G, Palkovits M.
    Concentration of nucleosides and related compounds in cerebral and cerebellar cortical areas and white matter of the human brain.
    Cell Mol Neurobiol. 2006 Jul-Aug;26(4-6):833-44. Epub 2006 Aug 1.
    PMID: 16897364 [PubMed - indexed for MEDLINE]

  13. Szegedi V, Juhász G, Rózsa E, Juhász-Vedres G, Datki Z, Fülöp L, Bozsó Z, Lakatos A, Laczkó I, Farkas T, Kis Z, Tóth G, Soós K, Zarándi M, Budai D, Toldi J, Penke B.
    Endomorphin-2, an endogenous tetrapeptide, protects against Abeta1-42 in vitro and in vivo.
    FASEB J. 2006 Jun;20(8):1191-3. Epub 2006 Apr 24.
    PMID: 16636106 [PubMed - indexed for MEDLINE]

  14. Kovács Z, Kékesi KA, Szilágyi N, Abrahám I, Székács D, Király N, Papp E, Császár I, Szego E, Barabás K, Péterfy H, Erdei A, Bártfai T, Juhász G.
    Facilitation of spike-wave discharge activity by lipopolysaccharides in Wistar Albino Glaxo/Rijswijk rats.
    Neuroscience. 2006 Jun 30;140(2):731-42. Epub 2006 Apr 17.
    PMID: 16616432 [PubMed - indexed for MEDLINE]

  15. Gonda X, Rihmer Z, Juhasz G, Zsombok T, Bagdy G.
    High anxiety and migraine are associated with the s allele of the 5HTTLPR gene polymorphism.
    Psychiatry Res. 2007 Jan 15;149(1-3):261-6. Epub 2006 Nov 17.
    PMID: 17113652 [PubMed - indexed for MEDLINE]

  16. Lörincz M, Oláh M, Baracskay P, Szilágyi N, Juhász G.
    Propagation of spike and wave activity to the medial prefrontal cortex and dorsal raphe nucleus of WAG/Rij rats.
    Physiol Behav. 2007 Feb 28;90(2-3):318-24. Epub 2006 Nov 14.
    PMID: 17107694 [PubMed - indexed for MEDLINE]

  17. Klinker EJ, Jackson TA, Jensen MP, Stubna A, Juhász G, Bominaar EL, Münck E, Que L Jr.
    A tosylimido analogue of a nonheme oxoiron(IV) complex.
    Angew Chem Int Ed Engl. 2006 Nov 13;45(44):7394-7. No abstract available.
    PMID: 17039556 [PubMed - indexed for MEDLINE]

Bioinformatics works:

Gabor Ivan, Zoltan Szabadka, Vince Grolmusz: Cysteine and Tryptophan Anomalies Found when Scanning all the Binding Sites in the Protein Data Bank, (preliminary version). To appear in the International Journal of Bioinformatics Research and Applications.

Gabor Ivan, Vince Grolmusz: Revealing the density-based clustering structure of the SwissProt database (poster) Page 606 of Abstract book, International Congress of Mathematicians 2010 Hyderabad, India, 19th-27th August, 2010

Gabor Ivan, Zoltan Szabadka, Vince Grolmusz: A Hybrid Clustering of Protein Binding Sites(preliminary version). FEBS Journal Vol. 277, No. 6. pp. 1494-1502 (2010)

Rafael Ördög, Vince Grolmusz: Frequently appearing spherically aligned substructers in proteins 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Boston, MA July 11-13, 2010

Gabor Ivan, Daniel Banky, Vince Grolmusz: Refining the protein interaction network generated by NASCENT using sequence alignment 18th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Boston, MA July 11-13, 2010

Gabor Ivan, Vince Grolmusz: Designing universal oligonucleotides for DNA/nanoparticle conjugates (lecture by Gabor Ivan) Nanotech Conference and Expo 2010, Anaheim, California/USA, 21st-25th June, 2010

Arpad Toth, Daniel Banky, Vince Grolmusz: Mathematical modeling and computer simulation of Brownian motion and hybridization of nanoparticle-bioprobe-polymer complexes in the low concentration limit Nanotech Conference and Expo 2010, Anaheim, California/USA, 21st-25th June, 2010

Rafael Ördög Vince Grolmusz: On Delaunay simplices containing functional groups Nanotech Conference and Expo 2010, Anaheim, California/USA, 21st-25th June, 2010

Gabor Ivan, Zoltan Szabadka, Vince Grolmusz: On the asymmetry of the residue compositions of the binding sites on protein surfaces;  Journal of Bioinformatics and Computational Biology, Vol. 7. No. 6. (2009) pp. 931-938.

Gabor Ivan, Vince Grolmusz: Revealing the density-based clustering structure of the SwissProt database (poster) 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Stockholm, Sweden, 27th June - 2nd July, 2009

Gabor Ivan, Daniel Banky, Vince Grolmusz: Finding new drug candidates against Mycobacterium tuberculosis using protein-protein interaction networks (poster) 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Stockholm, Sweden, 27th June - 2nd July, 2009

Gabor Ivan, Zoltan Szabadka, Rafael Ördög, Vince Grolmusz: Decomp: a PDB decomposition tool (talk by Gabor Ivan) 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) Stockholm, Sweden, 27th June - 2nd July, 2009

Rafael Ördög, Vince Grolmusz: WikiPDB- A community for enhancing the PDB, (talk by Rafael Ördög). 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Stockholm, Sweden, 27th June - 2nd July, 2009

Daniel Banky, Rafael Ördög, Vince Grolmusz: NASCENT: An Automatic Protein Interaction Network Generation Tool, (talk by Daniel Banky). 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Stockholm, Sweden, 27th June - 2nd July, 2009

Rafael Ördög, Zoltan Szabadka, Vince Grolmusz: DECOMP: A PDB decomposition tool on the web, Bioinformation Vol. 3 No. 10. pp. 413-414 (2009)

Daniel Banky, Rafael Ördög, Vince Grolmusz: NASCENT: An automatic protein interaction network generation tool for non-model organisms. Bioinformation Vol. 3 No. 8. pp. 361-363 (2009)

Rafael Ördög, Vince Grolmusz: On the bond graphs in the Delaunay-tetrahedra of the simplicial decomposition of spatial protein structures; Proceedings of the International Workshop on Practical Applications of Computational Biology & Bioinformatics (IWPACBB'09) LNCS 5518, University of Salamanca, June 10-12, 2009. Also available as a personal preprint version.

Gabor Ivan, Zoltan Szabadka, Rafael Ördög, Vince Grolmusz, Gabor Naray-Szabo: Four Spatial Points That Define Enzyme Families, Biochemical and Biophysical Research Communications, Vol. 383, No. 4, pp. 417-420, (2009) doi:10.1016/j.bbrc.2009.04.022; also available as a personal preprint version.

K. Hill, C.B. Penzes, B.G. Vertessy, Z. Szabadka, V. Grolmusz, É.Kiss: Amphiphilic Nature of New Antitubercular Drug Candidates and Their Interaction with Lipid Monolayer, Progr Colloid Polym Sci (2008) 135: 87-92, DOI 10.1007/2882_2008_117

Rafael Ördög, Zoltán Szabadka, Vince Grolmusz: A community portal for a better PDB. 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Toronto, Canada July 19-July 23, 2008.

Rafael Ördög, Vince Grolmusz
Evaluating Genetic Algorithms in Protein-Ligand Docking, Lecture Notes in Computer Science, Volume 4983/2008, page 402-413

Zoltán Szabadka, Rafael Ördög, Vince Grolmusz
The Ramachandran Map of More Than 6,500 Perfect Polypeptide Chains, Biophysical Reviews and Letters, Vol 2, No. 3 (2007), pp. 1-5

Rafael Ördög, Zoltán Szabadka, Vince Grolmusz
Analyzing the Simplicial Decomposition of Spatial Protein Structures; 6th International Conference on Bioinformatics (InCoB 2007), Hong Kong University of Science and Technology, Hong Kong, 27th-30th August, 2007; Journal version: BMC Bioinformatics, 2008, 9(Suppl 1):S11(doi:10.1186/1471-2105-9-S1-S11) (http://www.biomedcentral.com/1471-2105/9/S1/S11)

Zoltán Szabadka, Gábor Iván, Vince Grolmusz
Being a Binding-Site: Characterizing Residue-Composition of Binding Sites on Proteins 6th International Conference on Bioinformatics (InCoB 2007), Hong Kong University of Science and Technology, Hong Kong, 27th-30th August, 2007. Journal version: Bioinformation 2(5), 216-221 (2007), http://www.bioinformation.net/002/004800022007.htm

Gábor Iván
An Optimized Distance Function for Comparison of Protein Binding Sites, Brazilian Symposium on Bioinformatics (BSB), Angra dos Reis, Brazil, 29th-31th August, 2007, Lecture Notes in Computer Science Volume 4643/2007, pp. 93-100, http://www. springerlink.com/content/k14617662gm623g7/

  • Gábor Iván
    Studying Binding Sites of Protein-Ligand Complexes using Data-Mining Algorithms; SEFI and IGIP Joint Annual Conference, Miskolc, Hungary, 1st-4th July, 2007

    • Zoltán Szabadka, Gábor Iván, Vince Grolmusz
    Analyzing the Residue-Composition of Metal Binding Sites in the Whole Protein Data Bank. Mol. Biol. Cell 17(suppl), 535. (CD-ROM) (Appeared in the Proceedings of the 46th Annual Meeting of the American Society of Cell Biology

    Zoltán Szabadka, Vince Grolmusz
    High Throughput Processing of the Structural Information of the Protein Data Bank, Journal of Molecular Graphics and Modeling, 25 (2007) pp. 831-836 http://dx.doi.org/10 .1016/j.jmgm.2006.08.004

  • Zoltán Szabadka, Vince Grolmusz
    Building a Structured PDB: The RS-PDB Database, Proceedings of the 28th IEEE EMBS Annual International Conference, New York City, Aug. 30-Sept 3, 2006., pp. 5755-5758.

    • Zoltán Szabadka, Vince Grolmusz
    Re-Structuring the PDB, European Conference on Operational Research (EURO 2006), July 2-5, 2006, Reykjavik, Iceland

    Ördög Rafael, Vince Grolmusz
    Optimizing the running-structure of genetic-based docking algorithms, 21st European Conference on Operational Research (EURO 2006), July 2-5, 2006, Reykjavik, Iceland



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