Gáspári, Zoltán
Associate professor (bioinformatics)
Faculty of Information Technology & Bionics, PPCU
Phone: +36-1-886-4780
E-mail: gaspari.zoltan itk.ppke.hu
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Research directions
Programs & webservers

Web servers
CoNSEnsX+ A web server for the analysis of the correspondonce of protein structural ensembles reflecting internal dynamics to measured NMR parameters. Contains a simple (greedy) algorithm for selecting a sub-ensemble that corresponds best to user-selected parameters
CSAHserver 2.5 A web server for the prediction of single α-helices in protein sequences
PRIDE2 & PRIDE-NMR PRIDE2 is a fast protein structure comparison method. PRIDE-NMR allows protein fold estimation based on intrabackbone NMR distance restraints
S2 restraining for GROMACS 4.5.5 These modifications allow ensemble restraining using experimentally determined S2 order parameters in GROMACS as an implementation of the approach described in Best & Vendruscolo 2004. Also supports pairwise averaging of NOE distance restraints over replicas (similar to the concept of the MUMO approach, Richter et al. 2007). The current 4.5.5 version contains a basic AMD scheme for the dihedral energy term (Wang & McCammon 2012). This version was used in the Fizil et al. 2015 paper.
S2 restraining for GROMACS 3.1.1

  • Bertalan Kovács, Nóra Zajácz-Epresi, Zoltán Gáspári:
    Ligand-dependent intra- and interdomain motions in the PDZ12 tandem regulate binding interfaces in postsynaptic density protein-95
    FEBS Lett. (2019), doi:10.1002/1873-3468.13626
    [free full text]

  • Annamária Kiss-Tóth, Laszlo Dobson, Bálint Péterfia, Annamária F. Ángyán, Balázs Ligeti, Gergely Lukács, Zoltán Gáspári:
    Occurrence of ordered and disordered structural elements in postsynaptic proteins supports optimization for interaction diversity
    Entropy (2019) 21: 761
    [free full text]

  • Zita Harmat, András L. Szabó, Orsolya Tőke, Zoltán Gáspári:
    Different modes of barrel opening suggest a complex pathway of ligand binding in human gastrotropin
    PLoS ONE (2019) 14: e0216142
    [free full text]

  • Pablo Mier, Lisanna Paladin, Stella Tamana, Sophia Petrosian, Borbála Hajdu-Soltész, Annika Urbanek, Aleksandra Gruca, Dariusz Plewczynski, Marcin Grynberg, Pau Bernadó, Zoltán Gáspári, Christos A. Ouzounis, Vasilis J. Promponas, Andrey V. Kajava, John M. Hancock, Silvio C. E. Tosatto, Zsuzsanna Dosztányi, Miguel A. Andrade-Navarro:
    Disentangling the complexity of low complexity proteins
    Briefings in Bioinformatics (2019), doi:10.1093/bib/bbz007
    [free full text]

  • Ákos Kovács, Dániel Dudola, László Nyitray, Gábor Tóth, Zoltán Nagy, Zoltán Gáspári:
    Detection of single alpha-helices in large protein sequence sets using hardware acceleration
    J. Struct. Biol. (2018) 204:109-116.

  • Sándor Boros, Zoltán Gáspári, Gyula Batta:
    Accurate NMR determinations of protonżproton distances
    Annu. Rep. NMR (2018) 94:1-39.

  • Anna Huber, Dorottya Hajdu, Doris Bratschun-Khan, Zoltán Gáspári, Mihayl Varbanov, Stéphanie Philippot, Ádám Fizil, András Czajlik, Zoltán Kele, Christoph Sonderegger, László Galgóczy, Andrea Bodor, Florentine Marx, Gyula Batta:
    New antimicrobial potential and structural properties of PAFB: a cationic, cysteine-rich protein from Penicillium chrysogenum Q176
    Sci. Rep. (2018) 8:1751
    [free full text]

  • Dániel Dudola, Bertalan Kovács, Zoltán Gáspári:
    The CoNSEnsX+ web server for the analysis of protein structural ensembles reflecting experimentally determined internal dynamics
    J. Chem. Inf. Model. (2017) 57:1728-1734.

  • András Czajlik, Bertalan Kovács, Perttu Permi, Zoltán Gáspári:
    Fine-tuning the extent and dynamics of binding cleft opening as a potential general regulatory mechanism in parvulin-type peptidyl prolyl isomerases
    Sci. Rep. (2017) 7:44504
    [free full text]

  • Christoph Sonderegger, Ádám Fizil, Laura Burtscher, Dorottya Hajdu, Alberto Muńoz, Zoltán Gáspári, Nick D. Read, Gyula Batta, Florentine Marx:
    D19S mutation of the cationic, cysteine-rich protein PAF: novel insights into its structural dynamics, thermal unfolding and antifungal function
    PLoS ONE (2017) 12:e0169920
    [free full text]

  • Dániel Dudola, Gábor Tóth, László Nyitray, Zoltán Gáspári:
    Consensus prediction of charged single alpha-helices with CSAHserver
    Zhou, Kloczkowski, Faraggi, Yang (eds): Prediction of Protein Secondary Structure
    Methods Mol Biol Vol. 1847, Springer, 2017, pp. 25-34.
    [abstract] [CSAHserver 2.0]

  • László Dobson, László Nyitray, Zoltán Gáspári:
    A conserved charged single alpha-helix with a putative steric role in paraspeckle formation
    RNA (2015) 21:2023-2029
    [abstract] [free full text]

  • László Gráf, Tamás Molnár, József Kardos, Zoltán Gáspári, Gergely Katona:
    The role of structural flexibility and stability in the interaction of serine proteases with their inhibitors
    Curr. Prot. Pept. Sci. (2015) 6:521-531

  • Ádám Fizil, Zoltán Gáspári, Terézia Barna, Florentine Marx, Gyula Batta:
    "Invisible" conformers of an antifungal disulfide protein revealed by constrained cold & heat unfolding, CEST-NMR experiments and molecular dynamics calculations
    Chem. Eur. J. (2015) 21:5136-5144
    [free full text]

  • Annamária F. Ángyán, Csaba Ortutay, Zoltán Gáspári:
    Are proposed early genetic codes capable of encoding viable proteins?
    J. Mol. Evol. (2014) 78:263-274
    [final publication at Springer] [preprint version]

  • Krisztina Hegedűs, Péter Nagy, Zoltán Gáspári, Gábor Juhász:
    The putative HORMA domain protein Atg101 dimerizes and is required for starvation-induced and selective autophagy in Drosophila
    BioMed Res. Int. (2014) Article ID 470482
    [free full text]

  • Zoltán Gáspári:
    Is five percent too small? Analysis of the overlaps between disorder, coiled coil and collagen predictions in complete proteomes
    Proteomes (2014) 2:72-83
    [free full text]

  • Annamária F. Ángyán, Zoltán Gáspári:
    Ensemble-based interpretations of NMR structural data to describe protein internal dynamics
    Molecules (2013) 18:10548-10567
    [free full text]

  • Annamária F. Ángyán, András Perczel, Zoltán Gáspári:
    Estimating intrinsic structural preferences of de novo emerging random-sequence proteins: is aggregation the main bottleneck?
    FEBS Lett. (2012) 586:2468-2472.
    [abstract] [free full text]

  • Zoltán Gáspári, Dániel Süveges, András Perczel, László Nyitray, Gábor Tóth:
    Charged single alpha-helices in proteomes revealed by a consensus prediction approach.
    Biochem. Biophys. Acta - Proteins and Proteomics (2012) 1824:637-646.
    [abstract] [full text (preprint version)] [CSAH prediction server]

  • Zoltán Gáspári, László Nyitray:
    Coiled coils as possible models for protein structure evolution
    Biomol. Concepts (2011) 2:199.210

  • Annamária F. Ángyán, Balázs Szappanos, András Perczel, Zoltán Gáspári:
    CoNSEnsX: an ensemble view of protein structures and NMR-derived experimental data
    BMC Strut. Biol. (2010) 10:39
    [abstract] [free full text] [CoNSEnsX web server]

  • András Láng, Balázs Major, Katalin Szilágyi, Zoltán Gáspári, Péter Gál, Péter Závodszky, András Perczel:
    Interaction between separated consecutive complement control modules of human C1r: implications for dimerization of the full-length protease.
    FEBS Lett. (2010) 584:4565-4569.
    [abstract] [free full text]

  • Zoltán Gáspári, András Perczel:
    Protein dynamics as reported by NMR
    Annu. Rep. NMR Vol. 71, pp. 35-75 (ed.: Graham Webb), Academic Press

  • Zoltán Gáspári, Annamária F. Ángyán, Somdutta Dhir, Dino Franklin, András Perczel, Alessandro Pintar, Sándor Pongor:
    Probing dynamic protein ensembles with atomic proximity measures
    Curr. Prot. Pept. Sci. (2010) 11:512-522.

  • Somdutta Dhir, Mircea Pacurar, Dino Franklin, Zoltán Gáspári, Attila Kertész-Farkas, Frank Eisenhaber, Sándor Pongor:
    Detecting atypical examples of known domain types by sequence similarity searching: The SBASE domain library approach
    Curr. Prot. Pept. Sci. (2010) 11:538-549.

  • Balázs Szappanos, Dániel Süveges, László Nyitray, András Perczel, Zoltán Gáspári:
    Folded-unfolded cross-predictions and protein evolution: the case study of coiled-coils
    FEBS Lett. (2010) 584:1623-1627.
    [abstract] [free full text]

  • Zoltán Gáspári, Péter Várnai, Balázs Szappanos, András Perczel:
    Reconciling the lock-and-key and dynamic views of canonical serine protease inhibitor action
    FEBS Lett. (2010) 584:203-206.
    [abstract] [free full text]

  • Gyula Batta, Teréz Barna, Zoltán Gáspári, Szabolcs Sándor, Katalin E. Kövér, Ulrike Binder, Bettina Sarg, Lydia Kaiserer, Anil Kumar Chhillar, Andrea Eigentler, Éva Leiter, Nikoletta Hegedüs, István Pócsi, Herbert Lindner, Florentine Marx:
    Functional aspects of the solution structure and dynamics of PAF, a highly stable antifungal protein from Penicillium chrysogenum
    FEBS J. (2009) 276:2875-2890.
    [abstract] [full text]

  • Dániel Süveges, Zoltán Gáspári, Gábor Tóth, László Nyitray:
    Charged single α-helix: a versatile protein structural motif
    Proteins (2009) 74:905-916.

  • Zoltán Gáspári, Gábor Pál, and András Perczel:
    A redesigned genetic code for selective labeling in protein NMR
    BioEssays (2008) 30:772-780.

  • Edit Kassai-Jáger, Csaba Ortutay, Gábor Tóth, Tibor Vellai and Zoltán Gáspári:
    Distribution and evolution of short tandem repeats in closely related bacterial genomes
    Gene (2008) 410(1): 146-153.
    [abstract] [full text (preprint version)] [online supplementary material]

  • Annamária F. Ángyán, András Perczel, Sándor Pongor and Zoltán Gáspári:
    Fast protein fold estimation from NMR-derived distance restraints
    Bioinformatics (2008) 24(2):272-275.
    [abstract] [free full text] [PRIDE-NMR web server @ PPCU]

  • Zoltán Gáspári, Csaba Ortutay and Gábor Tóth:
    Divergent microsatellite evolution in the human and chimpanzee lineages
    FEBS Lett (2007) 581(13):2523-2526.
    [abstract] [free full text] [accompanying website: SSRDB]

  • Borbála Szenthe, András Patthy, Zoltán Gáspári, Adrienna Katalin Kékesi, László Gráf and Gábor Pál:
    When the surface tells what lies beneath: Combinatorial phage-display mutagenesis reveals complex network of surface-core interactions in the pacifastin protease inhibitor family
    J. Mol. Biol. (2007) 370(1):63-79.

  • Paolo Sonego, Mircea Pacurar, Somdutta Dhir, Attila Kertész-Farkas, András Kocsor, Zoltán Gáspári, Jack Leunissen and Sándor Pongor:
    A Protein Classification Benchmark collection for machine learning
    Nucleic Acids Res. 35(Database issue):D232-D236
    [abstract] [free full text] [The Protein Classification Benchmark Collection]

  • Zoltán Gáspári, Borbála Szenthe, András Patthy, William M. Westler, László Gráf and András Perczel:
    Local binding with globally distributed changes in a small protease inhibitor upon enzyme binding
    FEBS J. 273(8):1831-1842.
    [abstract] [free full text]

  • Zoltán Gáspári, Kristian Vlahovicek and Sándor Pongor:
    Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm.
    Bioinformatics, 21(15):3322-3323.
    [abstract] [free full text] [PRIDE2 web server @ PPCU]

  • András Perczel, Zoltán Gáspári and Imre G. Csizmadia:
    Structure and stability of β-pleated sheets.
    J. Comput. Chem., 26(11):1155-1168.

  • Zoltán Gáspári, Ilona Hudáky, András Czajlik and András Perczel:
    Is there an excuse for the non-conformist? Notes on the calculated energies, abundance and atom-atom contacts of alanine conformers in proteins.
    J. Mol. Struct. (THEOCHEM), 675(1-3):141-148.

  • Zsófia Dubrovay, Zoltán Gáspári, Éva Hunyadi-Gulyás, Katalin F. Medzihradszky, András Perczel and Beáta G. Vértessy:
    Multidimensional NMR identifies the conformational shift essential for catalytic competence in the 60 kDa Drosophila melanogaster dUTPase trimer
    J. Biol. Chem., 279(17): 17945-17950.
    [abstract] [free full text]

  • Borbála Szenthe, Zoltán Gáspári, Attila Nagy, András Perczel and László Gráf:
    Same fold with different mobility: backbone dynamics of small protease inhibitors from the desert locust, Schistocerca gregaria
    Biochemistry (2004) 43(12): 3376-3384.

  • Zoltán Gáspári, Csaba Ortutay and András Perczel:
    A simple fold with variations: the pacifastin inhibitor family
    Bioinformatics, (2004) 20 (4): 448-451.
    [abstract] [free full text]

  • Ilona Hudáky, Zoltán Gáspári, Oliviero Carugo, Masa Cemazar, Sándor Pongor and András Perczel:
    Vicinal disulfide bridge conformers by experimental methods and by ab initio and DFT molecular computations
    Proteins, (2004) 55(1): 152-168.

  • Csaba Ortutay, Zoltán Gáspári, Gábor Tóth, Edit Jáger, Gábor Vida, László Orosz and Tibor Vellai:
    Speciation in Chlamydia: Genome-wide phylogenetic analyses identified a reliable set of acquired genes
    J. Mol. Evol. 57(6): 672-680.

  • Zoltán Mucsi, Zoltán Gáspári, György Orosz and András Perczel:
    Structure-oriented rational design of chymotrypsin inhibitor models
    Protein Eng. (2003) 16(9): 673-681.
    [abstract] [free full text]

  • Oliviero Carugo, Masa Cemazar, Sotir Zahariev, Ilona Hudáky, Zoltán Gáspári, András Perczel and Sándor Pongor:
    Vicinal disulfide turns
    Protein Eng. (2003) 16(9): 637-639.
    [abstract] [free full text]

  • István Bágyi, Balázs Balogh, András Czajlik, Olivér Éliás, Zoltán Gáspári, Viktor Gergely, Ilona Hudáky, Péter Hudáky, Adrián Kalászi, László Károlyházy, Katalin Keserű, Róbert Kiss, Gábor Krajsovszky, Barbara Láng, Tamás Nagy, Ákos Rácz, Aletta Szentesi, Tamás Tábi, Pál Tapolcsányi, Judit Vaik, Joseph C. P. Koo, Gregory A. Chass, Ödön Farkas, András Perczel and Péter Mátyus:
    Generation and analysis of the conformational potential energy surfaces of N-acetyl-N-methyl-L-alanine-N'-methylamide. An exploratory ab initio study
    J. Mol. Struct. (THEOCHEM) (2003) 625(1-3): 121-136.

  • Zoltán Gáspári, András Patthy, László Gráf and András Perczel:
    Comparative structure analysis of proteinase inhibitors from the desert locust, Schistocerca gregaria
    Eur J Biochem. (2002) 269(2): 527-537.
    [free full text]
    Structures determined (RCSB PDB): [1KGM] [1KIO] [1KJ0]

  • Gábor Tóth, Zoltán Gáspári and Jerzy Jurka:
    Microsatellites in different eukaryotic genomes: survey and analysis
    Genome Res. (2000) 10(7):967-981.
    [abstract] [free full text] [supplementary material: SSRDB]


Publication list at MTMT
ResearcherID: D-9594-2011
ScopusID: 6602902051
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