List of Biophysics PhD Students at University of Split, Croatia
First generation: 2008/2009
1. MARIJANA MIJAKOVIĆ,
MIJAKOVIĆ MSc. Physics
[email protected]
Mentor: Franjo Sokolić
Research Interest: Microheterogenity of MultiMulti
component Liquid Mixtures Using Molecular
Dynamics
Publications: Accepted for Journal of Molecular Liquids
1. M. Mijaković, B. Kežić,
ć, L. Zoranić,
Zorani F. Sokolić,, A. Asenbaum, C. Pruner, E. Wilhelm, A.
Perera: Ethanol-Water
Water mixtures: Ultrasonic, Brillouin scattering and Molecular Dynamics
study, Journal of Molecular Liquids
2. MARIO HLEVNJAK, MSc. Molecular Biology
[email protected]
Mentor: Bojan Žagrović
Research Interest: Structural and Computational Biophysics
Publications:
1. Hlevnjak M, Zitkovic G, Zagrovic B (2010) Hydrophilicity matching – a potential
prerequisite for the formation of protein-protein
protein protein complexes int he cell. PLoS ONE 5(6):
e11169.
2. Munic V, Hlevnjak M, Erakovic Haber V (2011) Characterization of rhodamine-123, calcein
and 5(6)-carboxy-2',7'-dichlorofluorescein (CDCF) export via MRP2 (ABCC2) in MES-SA
and A549 cells. Eur J Pharm Sci 43.359-369.
3. Stepanic V, Kostrun S, Malnar I, Hlevnjak M, Butkovic K, Caleta I, Duksi M, Kragol G,
Makaruha-Stegic O, Mikac L, Ralic J, Tatic I, Tavcar B, Valko K, Zulfikari S, Munic V
(2011) Modelling cellular pharmacokinetics of 14- and 15-membered macolides with
physicochemical properties. J med Chem 54:719-733
4. Munic V, Banjanac M, Kostrun S, Nujic K, Bosnar M, Marjanovic N, Ralic J, Matijasic M,
Hlevnjak M, Erakovic Haber V (2011) Intensity of macrolide anti-inflammatory activity in
J774A.l cells positively correlates with cellular accumulation and phospholipidosis.
Pharmacol Res 64:298-307.
5. Strelec I, Ugarcic-Hardi Z, Hlevnjak M (2008) Accumulation of Amadori and Maillard
products in wheat seeds aged under different storage conditions. Croat Chem Acta 81:131137.
3. ANTONIJA KUZMANIĆ, MSc. Molecular Biology
[email protected]
Mentor: Bojan Žagrović
Research Interest: Computational Biophysics
Publications:
1. Kuzmanic A. & Zagrovic B. (2010). Determination of ensemble-average pairwise root meansquare deviation from experimental B-factors. Biophysical Journal 98(5): 861-871.
2. Kuzmanic A., Kruschel D., van Gunsteren W.F., Pannu N.S. & Zagrovic B. (2011).
Dynamics may significantly influence the estimation of interatomic distances in biomolecular
X-ray structures. Journal of Molecular Biology 2011: doi:10.1016/j.jmb.2011.05.033.
4. NADA ILIĆ, MSc. Biology and Chemistry
[email protected]
Mentor: Davor Juretić
Research Interest: Synthesis, Design and Testing of Novel
Peptide Antibiotics with High Therapeutic Index
Publications:
1. Juretić, D., Vukičević, D., Ilić, N., Antcheva, N., Tossi, A., Computational Design of Highly
Selective Antimicrobial Peptides, J. Chem. Inf. Model. 2009, 49, 2873–2882: Computational
design of highly selective antimicrobial peptides
2. Juretić, D., Vukičević, D., Petrov, D., Novković, M., Bojović, V., Lučić, B., Ilić, N., Tossi,
A., Knowledge-based computational methods for identifying or designing novel, nonhomologous antimicrobial peptides, Eur. Biophys. J. 2011, 40, 371–385, DOI
10.1007/s00249-011-0674-7: Knowledge-based computational methods for identifying or
designing novel, non-homologous antimicrobial peptides
Poster award:
1. Ilić, N., Novković, M., Guida, F., Antcheva, N., Tossi, A., Copić, T., Puizina, J., Juretić, D.,
Adepantins a new class of ab-initio designed antimicrobial peptides // AMP2010, AustraliaCroatia Workshop on Antimicrobial Peptides / http://split4.pmfst.hr/konferencija/ Faculty of
Science, University of Split, August 9-13 2010. Organisers: Juretić Davor and Frances
Separovic. Conference proceedings, 2010, 41-41.
5. JADRANKO BATISTA,
MSc. Mathematics and Physics
[email protected]
Mentor: Bono Lučić
Research Interest: Protein structure
Jadranko Batista has been working since April 2009 on validation of statistical significance, and
possibility of simplification and improvement of some structure-property models related to
bioactive molecules and proteins. All analysed models were taken from literature. Jadranko
Batista also worked on comparison between product-connectivity index and new version of
connectivity index (sum-connectivity), and obtained interesting results that will be published.
Performed researches are introductory research related to the field of his doctoral thesis
(development and application of models in structural bioinformatics of proteins). We will strictly
define the subject of his doctoral thesis soon.
Publications:
1. Lučić, Bono; Sović, Ivan; Batista, Jadranko; Skala, Karolj; Plavšić, Dejan; Vikić-Topić,
Dražen; Nikolić, Sonja; Trinajstić, Nenad. The Additive Variant of the Randić Connectivity
index. Accepted for Current Computer-Aided Drug Design.
6. SOFIA PINTO,
graduated in biomedical engineering, bioinformatics and clinical
informatics branch
[email protected]
Mentor: Kristian Vlahoviček
Research Interest: Bioinformatics
Publications:
1. Pučić, M., Pinto, S., Novokmet, M., Knežević, A., Gornik, O., Polašek, O., Vlahoviček, K.,
Wei, W., Rudd, P. M., Wright, A. F., Campbell, H., Rudan, I., and Lauc, G. (2010) Common
aberrations from normal human N‐glycan plasma profile. Glycobiology 20, 970‐975.
2. Pinto, S., Vlahoviček, K. and Buratti, E. (2011), PRO-MINE: A Bioinformatics Repository
and Analytical Tool for TARDBP Mutations. Human Mutation, 32: E1948–E1958.
doi: 10.1002/humu.21393
Second generation: 2009/2010
7. BERNARDA KEŽIĆ, MSc Physics and Mathematics
[email protected]
Mentor: Franjo Sokolić
Research interest: Structure of One-component Liquid and their
Mixture with Water Using Statistical Theory of Liquids and
Molecular Dynamics.
Publications:
1. P. Stipanović, L. Vranješ-Markić, J. Boronat, B. Kežić: Ground state of small mixed helium
and spin-polarized tritium clusters: a quantum Monte Carlo study, J. Chem. Phys. 134,
054509 (2011).
2. M. Mijaković, B. Kežić, L. Zoranić, F. Sokolić, A. Asenbaum, C. Pruner, E. Wilhelm, A.
Perera: Ethanol-Water mixtures: Ultrasonic, Brillouin scattering and Molecular Dynamics
study. Accepted in Journal of Molecular Liquids:
8. DRAŽEN PETROV, MSc Physics
[email protected]
Mentor: Bojan Žagrović
Research interest: Structural and Computational Biophysics
Publications:
1. Županović P, Kuic D, Losic Z B., Petrov D, Juretic D, Brumen M (2010) The Maximum
Entropy Production Principle and Linear Irreversible Processes Entropy 12(5):996-1005.
2. Juretić D, Vukičević D, Petrov D, Novković M, Bojović V, Lučić B, Ilić N, Tossi A. (2011)
Knowledge-based computational methods for identifying or designing novel, nonhomologous antimicrobial peptides. Eur Biophys J. 40(4):371-85.
3. Petrov D, Zagrovic B. (2011) Microscopic analysis of protein oxidative damage: effect of
carbonylation on structure, dynamics, and aggregability of villin headpiece J Am Chem Soc.
133(18):7016-24.
Third generation: 2010/2011
9. MARIJA BOROZAN, MSc. Physics and Informatics
[email protected]
Mentor: Sanja Tomić
Research interest: Computational Simulations of Protein Structure.
Molecular Dynamics Simulations. Subsets of Signal Peptides from
Amphibians and Mammals.
10. MARGITA NIMAC-KALCINA,
MSc. Medical Biochemistry
[email protected]
Mentor: Vedrana Čikeš-Čulić
Research interest: Biochemistry and Medical Biochemistry
11. MARIO NOVKOVIĆ,
MSc. Physics with Biophysics Orientation
[email protected]
Mentor: Davor Juretić
Research Interest:
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•
•
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Computational Methods in Identifying Novel Antimicrobial Peptides
Database of Amphibian Skin Bioactive Peptides
Subsets of Signal Peptides from Amphibians and Mammals
Antimicrobial Cryptides Hidden in Sequences of Highly Conserved Proteins
Publications:
1. Davor Juretić, Damir Vukičević, Dražen Petrov, Mario Novković, Viktor Bojović, Bono
Lučić, Nada Ilić, Alessandro Tossi (2011) Knowledge-based computational methods for
identifying or designing novel, non-homologous antimicrobial peptides. Eur Biophys J
40:371-385 (http://www.ncbi.nlm.nih.gov/pubmed/21274708)
Conference posters:
1. Adepantins a new class of ab-initio designed antimicrobial peptides Nada Ilić, Mario
Novković, Filomena Guida, Nikolinka Antcheva, Alessandro Tossi, Tea Copić, Jasna
Puizina, Davor Juretić AMP2010, Australia-Croatia Workshop on Antimicrobial Peptides http://split4.pmfst.hr/konferencija/ / MedILS, 21000 Split, Croatia / Organizers: Davor
Juretić and Frances Separovic / Faculty of Science, University of Split, August 9-13 2010,
Conference proceedings 41-41.