Computer Simulation, Protein Structure/Function
Biophysics and Systems Pharmacology [BSP]
PhD, Etvs Lornd University
, New York University
Specific Clinical/Research Interest:
Computer simulation of aqueous systems; methodology and biomolecular applications
Summary of Research Studies:
Research in my laboratory centers on developing computational techniques for the modeling and understanding of complex molecular systems such as proteins and nucleic acids in their aqueous environments. The methods developed are applied to problems of interest in structural biology. Methodological developments focus on novel techniques to calculate free energy from computer simulations, on extending the range of applicability of grand-canonical ensemble simulations, on enhancing Monte Carlo sampling algorithms and on developing novel approaches to the analysis and visualization of macromolecular structures and computer simulation results. These techniques are applied to the calculation of the solvent contribution to conformational free energy differences between various conformation of polypeptides, drug candidates; probing ionic solvation; modeling lipid bilayers. In addition, ligand-protein interactions are studied by docking tecniques and by molecular dynamics. Recent work showed that grand-canonical ensemble simulations can be used to predict sites for derivatizing a ligand in order to enhance its binding affinity.
Jin YJ, Cai CY, Mezei M, Ohlmeyer M, Sanchez R, Burakoff SJ. Identification of a novel binding site between HIV type 1 Nef C-terminal flexible loop and AP2 required for Nef-mediated CD4 downregulation. AIDS research and human retroviruses 2013 Apr; 29(4).
Dixit SB, Mezei M, Beveridge DL. Studies of base pair sequence effects on DNA solvation based on all-atom molecular dynamics simulations. Journal of biosciences 2012 Jul; 37(3).
Cui M, Mezei M, Osman R. Prediction of protein loop structures using a local move Monte Carlo approach and a grid-based force field. Protein Eng. Des. Sel 2008; 21: 729-735.
Pan C, Mezei M, Mujtaba S, Muller M, Zeng L, Li J, Wang Z, Zhou MM. Structure-guided optimization of small molecules inhibiting human immunodeficiency virus 1 tat association with the human coactivator p300/CREB binding protein-associated factor. J. Med. Chem 2007; 50: 2285-2288.
Speidel JA, Banfelder JR, Mezei M. Automatic Control of Solvent Density in Grand Canonical Ensemble Monte Carlo Simulations. J. Chem. Theory and Comp 2006; 2: 1429-1434.
Mezei M, Filizola M. TRAJELIX: A computational tool for the geometric characterization of protein helices during molecular dynamics simulations. J. Computer-Aided Molecular Design 2006; 20: 97-107.
Mezei M, Fleming PJ, Srinivasan R, Rose GD. The solvation free energy of the peptide backbone is conformation-dependent. Proteins 2004; 55: 502-507.
Mezei M. A novel fingerprint for the characterization of protein folds. Prot. Engng 2003; 16: 713-715.
Mezei M. A new method for mapping macromolecular topography. J. Mol. Graph. Model 2003; 21: 463-472.
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Dr.Mezei did not report having any of the following types of financial relationships with industry during 2015 and/or 2016: consulting, scientific advisory board, industry-sponsored lectures, service on Board of Directors, participation on industry-sponsored committees, equity ownership valued at greater than 5% of a publicly traded company or any value in a privately held company. Please note that this information may differ from information posted on corporate sites due to timing or classification differences.
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