Gáspári, Zoltán
Associate professor (bioinformatics)
Faculty of Information Technology & Bionics, PPCU
Phone: +36-1-886-4780
E-mail: gaspari.zoltan itk.ppke.hu
  Official page (in Hungarian)   Research   Programs & services   Publications   ResearchGate profile
Research directions
  • Analysis of the protein network of the PSD

    The postsynaptic density (PSD) is a complex network of proteins located beneath the postsynaptic membrane. It contains a number of multivalent scaffold proteins that are organized into different layers and link membrane receptors to the cytoskeleton. The PSD is capable of dynamic reorganization, is characteristically different in specific neuron types and is involved in the molecular processes of learning and memory. We are using experimental and computational approaches to characterize selected proteins in detail and the network formation in general.

  • Generation and analysis of dynamic biomolecular ensembles to understand partner binding and structural evolution

    Recently developed computational tools allow for the generation of 'dynamic structural ensembles' corresponding to a set of conformers whose diversity reflects the experimentally determined internal dynamics of the molecule at a given time scale. The emphasis is on the correspondence with experimental data, which can be achieved using additional restraints, derived primarily from NMR spectroscopy, that are characteristic of the internal mobility. Such restraints are usually applied to multiple replicas of the simulated molecule simultaneously, requiring modifications and extensions of commonly available molecular dynamics software. The conformer sets resulting from such calculations serve as an atomic-detail model of the dynamic nature of the biomolecule and can be used to interpret biomolecular processes at high resolution.

Programs & webservers

Web servers & databases
PSINDB The PostSynaptic INteraction DataBase contains data on postsynaptic proteins, their binding partners and interacting regions, wherever possible.
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


Google Scholar profile
PubMed results
Official list at The Hungarian Scientific Bibliography (MTMT)
ResearcherID: D-9594-2011
ScopusID: 6602902051
ORCID: 0000-0002-8692-740X