Projects since 2013
Coordinator
2007 – 2013. MZOŠ project „Computational study of bio-macromolecules and development of new
algorithms‟ (098-1191344-2860)
2012 – 2015 'Alexander von Humboldt, Research Group Linkage' programm: 'Study of plant
enzymes from metallopeptidase families M20 and M49‟
2014 – 2017 HRZZ project: 'Flexibility, activity and structure correlations in the dipeptidyl
peptidase III family' (01.07.2014-30.06.2017)
2016 – 2017 Bilateral project with Austria (Karl Gruber, TU, Graz), 'An Interdisciplinary
Study on Atypical Dipeptidyl Peptidases III (DPPs III) Structure and Dynamics '.
2018 – 2022 HRZZ project: 'Biological relevance of dipeptidyl peptidase III and its impact on
human health' (IP-2018-01-2936)
Paricipant
2013-2016: FP7-REGPOT-2012-2013-1 „Enhancement of the InnovationPotential in SEE
through new Molecular Solutions in Research and Development‟

Awards
1991-1992. NUFFIC fellowship, Rijkuniversiteit, Utrecht, Netherland
1996-1998 Alexander von Humboldt research fellowship
2012. RuĊer Bošković Institute award for scientific publication

“Biomacromolecules Crystalography and Modeling” (Luić, Tomić,) Faculty of Natural Sciences and
Mathematics, at University of Zagreb, Graduate study, “Molecular modelling of biomacromolecules”
(Faculty of Natural Sciences and Mathematics, at University of Zagreb, University of Split and
University of Osjek, PhD studies in Biochemistry & Biophysics, “Computational Chemistry” at
University of Rijeka, Department for Biotehnology, Doctorate study)

Knjige i poglavlja u knjigama

Poglavlja u knjigama

• Tomić, S. (2003) Enantioselectivity of Burkholderia cepacia lipase towards primary and secondary alcohols: molecular modelling and 3D QSAR analysis. U: M. Ford, D. Livingstone, J. Dearden, H. van de Waterbeemd (ur.) Designing drugs and crop protectants: processes, problems and solutions. Oxford, UK, Blackwell Publishing Ltd, str. 326-328.

• Tomić, S., Nillson, L. & Wade, R. (2000) Combine and Free-Wilson QSAR analysis of nuclear receptor-DNA binding. U: Gudertofte, K. & Jorgensen, F. (ur.) Molecular Modeling and Prediction of Bioactivity. New York, Kluwer Academic/Plenum Publishers, str. 269-270.

Radovi u časopisima

Znanstveni i pregledni radovi

• Tomić, A., Karačić, Z. & Tomić, S. (2023) Influence of Mutations of Conserved Arginines on Neuropeptide Binding in the DPP III Active Site. Molecules, 28 (4), 1976, 17 doi:10.3390/molecules28041976.

  doiwww.mdpi.comfulir.irb.hr

• Karačić, Z., Šupljika, F., Tomić, A., Brkljačić, L., Tomašić Paić, A., Ćehić, M. & Tomić, S. (2022) Neuropeptides, substrates and inhibitors of human dipeptidyl peptidase III, experimental and computational study — A new substrate identified. International journal of biological macromolecules, 220, 1390-1401 doi:10.1016/j.ijbiomac.2022.09.119.

  doi

• Matić, S., Tomašić Paić, A., Sobočanec, S., Pinterić, M., Pipalović, G., Martinčić, M., Matovina, M. & Tomić, S. (2022) Interdisciplinary study of the effects of dipeptidyl-peptidase III cancer mutations on the KEAP1-NRF2 signaling pathway. International journal of molecular sciences, 23 (4), 1994, 15 doi:10.3390/ijms23041994.

  doiwww.mdpi.comwww.ncbi.nlm.nih.govfulir.irb.hr

• Zonjić, I., Tumir, L., Crnolatac, I., Šupljika, F., Racané, L., Tomić, S. & Radić Stojković, M. (2022) Recognition of ATT Triplex and DNA:RNA Hybrid Structures by Benzothiazole Ligands. Biomolecules, 12 (3), 1600173, 20 doi:10.3390/biom12030374.

  doiwww.mdpi.comdoi.orgfulir.irb.hr

• Tomić, A. & Tomić, S. (2022) Demystifying DPP III Catalyzed Peptide Hydrolysis—Computational Study of the Complete Catalytic Cycle of Human DPP III Catalyzed Tynorphin Hydrolysis. International journal of molecular sciences, 23 (3), 1858, 24 doi:10.3390/ijms23031858.

  doiwww.mdpi.comdoi.orgfulir.irb.hr

• Ban, Ž., Karačić, Z., Tomić, S., Amini, H., Marder, T. & Piantanida, I. (2021) Triarylborane Dyes as a Novel Non‐Covalent and Non‐Inhibitive Fluorimetric Markers for DPP III Enzyme. Molecules, 26, 4816, 20 doi:10.3390/molecules26164816.

  doiwww.mdpi.comdoi.orgfulir.irb.hr

• Trnski, D., Sabol, M., Tomić, S., Štefanac, I., Mrčela, M., Musani, V., Rinčić, N., Kurtović, M., Petrić, T., Levanat, S. & Ozretić, P. (2021) SHH-N non-canonically sustains androgen receptor activity in androgen-independent prostate cancer cells. Scientific reports, 11 (1), 14880, 11 doi:10.1038/s41598-021-93971-6.

  doiwww.nature.comdoi.orgfulir.irb.hr

• Tomić, A., Brkić, H., Matić, A. & Tomić, S. (2021) Unravelling the inhibitory zinc ion binding site and the metal exchange mechanism in human DPP III. PCCP. Physical chemistry chemical physics, 23, 13267-13275 doi:10.1039/D1CP01302E.

  doi

• Agić, D., Karnaš, M., Šubarić, D., Lončarić, M., Tomić, S., Karačić, Z., Bešlo, D., Rastija, V., Molnar, M., Popović, B. & Lisjak, M. (2021) Coumarin derivatives act as novel inhibitors of human dipeptidyl peptidase III: combined in vitro and in silico study. Pharmaceuticals, 14 (6), 540, 19 doi:10.3390/ph14060540.

  doiwww.mdpi.comfulir.irb.hr

• Lončar, B., Perin, N., Mioč, M., Boček, I., Grgić, L., Kralj, M., Tomić, S., Radić Stojković, M. & Hranjec, M. (2021) Novel amino substituted tetracyclic imidazo[4,5-b]pyridine derivatives: Design, synthesis, antiproliferative activity and DNA/RNA binding study. European journal of medicinal chemistry, 217, 113342, 18 doi:10.1016/j.ejmech.2021.113342.

  doi

• Ferger, M., Ban, Ž., Krošl, I., Tomić, S., Dietrich, L., Lorenzen, S., Rauch, F., Sieh, D., Friedrich, A., Griesbeck, S., Kenđel, A., Miljanić, S., Piantanida, I. & Marder, T. (2021) Aryl-diyne linkers in bis-triarylborane cations control fluorimetric and Raman sensing of various DNA and RNA. Chemistry : a European journal, 27, 5142-5159 doi:10.1002/chem.202005141.

  doichemistry-europe.onlinelibrary.wiley.comdoi.orgfulir.irb.hr

• Matić, S., Kekez, I., Tomin, M., Bogár, F., Šupljika, F., Kazazić, S., Hanić, M., Jha, S., Brkić, H., Bourgeois, B., Madl, T., Gruber, K., Macheroux, P., Matković-Čalogović, D., Matovina, M. & Tomić, S. (2021) Binding of dipeptidyl peptidase III to the oxidative stress cell sensor Kelch-like ECH-associated protein 1 is a two-step process. Journal of biomolecular structure & dynamics, 39 (18), 6870-6881 doi:10.1080/07391102.2020.1804455.

  doi

• Ban, Ž., Griesbeck, S., Tomić, S., Nitsch, J., Marder, T. & Piantanida, I. (2020) A quadrupolar bis‐triarylborane chromophore as a fluorimetric and chirooptic probe for simultaneous and selective sensing of DNA, RNA and proteins. Chemistry : a European journal, 26, 2195-2203 doi:10.1002/chem.201903936.

  doionlinelibrary.wiley.comdoi.orgfulir.irb.hr

• Ćehić, M., Suć Sajko, J., Karačić, Z., Piotrowski, P., Šmidlehner, T., Jerić, I., Schmuck, C., Piantanida, I. & Tomić, S. (2020) The guanidiniocarbonylpyrrole - fluorophore conjugates as theragnostic tools for DPP III monitoring and inhibition. Journal of biomolecular structure & dynamics, 38 (13), 3790-3800 doi:10.1080/07391102.2019.1664936.

  doi

• Tomić, A., Horvat, G., Ramek, M., Agić, D., Brkić, H. & Tomić, S. (2019) New zinc ion parameters suitable for classical MD simulations of zinc metallo-peptidases. Journal of chemical information and modeling, 59 (8), 3437-3453 doi:10.1021/acs.jcim.9b00235.

  doi

• Bistrović Popov, A., Stolić, I., Krstulović, L., Taylor, M., Kelly, J., Tomić, S., Tumir, L., Bajić, M. & Raić-Malić, S. (2019) Novel symmetric bis-benzimidazoles: Synthesis, DNA/RNA binding and antitrypanosomal activity. European journal of medicinal chemistry, 173, 63-75 doi:10.1016/j.ejmech.2019.04.007.

  doi

• Tomin, M. & Tomić, S. (2019) Oxidase or peptidase? A computational insight into a putative aflatoxin oxidase from Armillariella tabescens. Proteins, 87 (5), 390-400 doi:10.1002/prot.25661.

  doi

• Tomin, M., Tomić, A., Kovačević, B. & Tomić, S. (2018) The Mechanism of Peptide Hydrolysis Catalysed by Dipeptidyl Peptidase III from Bacteroides thetaiotaomicron. Croatica chemica acta, 91 (2), 187-193 doi:10.5562/cca3343.

  doihrcak.srce.hrfulir.irb.hr

• Kazazić, S., Karačić, Z., Sabljić, I., Agić, D., Tomin, M., Abramić, M., Dadlez, M., Tomić, A. & Tomić, S. (2018) Conservation of the conformational dynamics and ligand binding within M49 enzyme family. RSC Advances, 8 (24), 13310-13322 doi:10.1039/c7ra13059g.

  doipubs.rsc.orgpubs.rsc.orgfulir.irb.hr

• Šmidlehner, T., Karačić, Z., Tomić, S., Schmuck, C. & Piantanida, I. (2018) Fluorescent cyanine-guanidiniocarbonyl-pyrrole conjugate with pH-dependent DNA/RNA recognition and DPP III fluorescent labelling and inhibition properties. Monatshefte für Chemie, 149 (7), 1307-1313 doi:10.1007/s00706-018-2192-0.

  doi

• Sabljić, I., Tomin, M., Matovina, M., Sučec, I., Tomašić Paić, A., Tomić, A., Abramić, M. & Tomić, S. (2018) The first dipeptidyl peptidase III from a thermophile: Structural basis for thermal stability and reduced activity. PLoS One, 13 (2), e0192488, 25 doi:10.1371/journal.pone.0192488.

  doifulir.irb.hrfulir.irb.hr

• Hromić-Jahjefendić, A., Jajčanin Jozić, N., Kazazić, S., Grabar Branilović, M., Karačić, Z., Schrittwieser, J., Das, K., Tomin, M., Oberer, M., Gruber, K., Abramić, M. & Tomić, S. (2017) A novel Porphyromonas gingivalis enzyme: An atypical dipeptidyl peptidase III with an ARM repeat domain. PLoS One, 12 (11), e0188915, 27 doi:10.1371/journal.pone.0188915.

  doifulir.irb.hr

• Tomin, M. & Tomić, S. (2017) Dynamic properties of dipeptidyl peptidase III from Bacteroides thetaiotaomicron and the structural basis for its substrate specificity – a computational study. Molecular biosystems, 13, 2407-2417 doi:10.1039/c7mb00310b.

  doi

• Matovina, M., Agić, D., Abramić, M., Matić, S., Karačić, Z. & Tomić, S. (2017) New findings about human dipeptidyl peptidase III based on mutations found in cancer. RSC Advances, 7 (58), 36326-36334 doi:10.1039/C7RA02642K.

  doi

• Agić, D., Brkić, H., Tomić, S., Karačić, Z., Špoljarević, M., Lisjak, M., Bešlo, D. & Abramić, M. (2017) Validation of flavonoids as potential dipeptidyl peptidase III inhibitors: experimental and computational approach. Chemical biology & drug design, 89 (4), 619-627 doi:10.1111/cbdd.12887.

  doi

• Gundić, M., Tomić, A., Wade, R., Matovina, M., Karačić, Z., Kazazić, S. & Tomić, S. (2016) Human DPP III – Keap1 Interactions : A Combined Experimental And Computational study. Croatica chemica acta, 89 (2), 217-228 doi:10.5562/cca2916.

  doihrcak.srce.hr

• Tomić, A., Kovačević, B. & Tomić, S. (2016) Concerted nitrogen inversion and hydrogen bonding to Glu451 are responsible for protein-controlled suppression of the reverse reaction in the human DPP III. Physical Chemistry Chemical Physics, 18 (39), 27245-27256 doi:10.1039/C6CP04580D.

  doi

• Matić, J., Šupljika, F., Tir, N., Piotrowski, P., Schmuck, C., Abramić, M., Piantanida, I. & Tomić, S. (2016) Guanidiniocarbonyl-pyrrole -aryl conjugates as inhibitors of human dipeptidyl peptidase III: combined experimental and computational study. RSC Advances, 6, 83044-83052 doi:10.1039/c6ra16966j.

  doi

• Crnolatac, I., Rogan, I., Majić, B., Tomić, S., Deligeorgiev, T., Horvat, G., Makuc, D., Plavec, J., Pescitelli, G. & Piantanida, I. (2016) Small molecule probes finely differentiate between various ds- and ss-DNA and RNA by fluorescence, CD and NMR response. Analytica chimica acta, 940, 128-135 doi:10.1016/j.aca.2016.08.021.

  doi

• Smolko, A., Šupljika, F., Martinčić, J., Jajčanin-Jozić, N., Grabar- Branilović, M., Tomić, S., Ludwig- Müller, J., Piantanida, I. & Salopek- Sondi, B. (2016) The role of conserved Cys residues in Brassica rapa auxin amidohydrolase: the Cys139 is crucial for the enzyme activity and the Cys320 regulates enzyme stability. Physical Chemistry Chemical Physics, 18 (13), 8890-8900 doi:10.1039/c5cp06301a.

  doi

• Rastija, V., Agić, D., Tomić, S., Nikolić, S., Hranjec, M., Karminski-Zamola, G. & Abramić, M. (2015) Synthesis, QSAR, and molecular dynamics simulation of amidino-substituted benzimidazoles as dipeptidyl peptidase III inhibitors. Acta chimica Slovenica, 62 (4), 867-878 doi:10.17344/acsi.2015.1605.

  doifulir.irb.hrfulir.irb.hrjournals.matheo.sidx.doi.org

• Tomić, A., Berynskyy, M., Wade, R. & Tomić, S. (2015) Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding. Molecular biosystems, 11, 3068-3080 doi:10.1039/c5mb00465a.

  doi

• Gershberg, J., Radić Stojković, M., Škugor, M., Tomić, S., Rehm, T., Rehm, S., Saha-Möller, C., Piantanida, I. & Würthner, F. (2015) Sensing of Double-Stranded DNA/RNA Secondary Structures by Water Soluble Homochiral Perylene Bisimide Dyes. Chemistry - A European Journal, 21 (21), 7886-7895 doi:10.1002/chem.201500184.

  doi

• González-García, J., Tomić, S., Lopera, A., Guijarro, L., Piantanida, I. & García-España, E. (2015) Aryl-bis-(scorpiand)-aza receptors differentiate between nucleotide monophosphates by combination of aromatic, hydrogen bond and electrostatic interactions. Organic & biomolecular chemistry, 13, 1732-1740 doi:10.1039/c4ob02084g.

  doi

• Brkić, H., Kovačević, B. & Tomić, S. (2015) Human 3-hydroxyanthranilate 3, 4-dioxygenase (3HAO) dynamics and reaction, a multilevel computational study. Molecular biosystems, 11 (3), 898-907 doi:10.1039/C4MB00668B.

  doi

• Grabar Branilović, M. & Tomić, S. (2014) Computational study of the structural plasticity and the ligand binding affinity of the IRES subdomain IIa. Molecular biosystems, 10 (12), 3272-3279 doi:10.1039/c4mb00469h.

  doi

• Maršavelski, A., Lesjak, S., Močibob, M., Weygand-Đurašević, I. & Tomić, S. (2014) A single amino acid substitution affects the substrate specificity of the seryl-tRNA synthetase homologue. Molecular biosystems, 10 (12), 3207-3216 doi:10.1039/C4MB00416G.

  doi

• Tomić, A. & Tomić, S. (2014) Hunting the human DPP III active conformation : combined thermodynamic and QM/MM calculations. Dalton transactions, 43, 15503-15514 doi:10.1039/C4DT02003K.

  doi

• Bertoša, B., Mikleušević, G., Wielgus-Kutrowska, B., Narczyk, M., Hajnić, M., Leščić Ašler, I., Tomić, S., Luić, M. & Bzowska, A. (2014) Homooligomerization is needed for stability: a molecular modelling and solution study of E. coli purine nucleoside phosphorylase. The FEBS journal, 281 (7), 1860-1871 doi:10.1111/febs.12746.

  doi

• Jajčanin Jozić, N., Tomić, S. & Abramić, M. (2014) Importance of the three basic residues in the vicinity of the zinc-binding motives for the activity of the yeast dipeptidyl peptidase III. Journal of biochemistry, 155 (1), 43-50 doi:10.1093/jb/mvt093.

  doi

• Aleksić, M., Bertoša, B., Nhili, R., Depauw, S., Martin-Kleiner, I., David-Cordonnier, M., Tomić, S., Kralj, M. & Karminski-Zamola, G. (2014) Anilides and quinolones with nitrogen-bearing substituents from benzothiophene- and thienothiophene- series: synthesis, photochemical synthesis, cytostatic evaluation, 3D-derived QSAR analysis and DNA-binding properties. European journal of medicinal chemistry, 71, 267-281 doi:10.1016/j.ejmech.2013.11.010.

  doi

• Grabar Branilović, M., Tomić, S., Tumir, L. & Piantanida, I. (2013) The bis-phenanthridinium system flexibility and position of covalently bound uracil finely tunes the interaction with polynucleotides. Molecular biosystems, 9 (8), 2051-2062 doi:10.1039/C3MB25578F.

  doi

• Radić Stojković, M., Škugor, M., Tomić, S., Grabar, M., Smrečki, V., Dudek, Ł., Grolik, J., Eilmes, J. & Piantanida, I. (2013) Dibenzotetraaza[14]annulene – adenine conjugate recognizes complementary poly dT among ss-DNA / ss-RNA sequences. Organic & biomolecular chemistry, 11 (24), 4077-4085 doi:10.1039/c3ob40519b.

  doi

• Tus, A., Rakipović, A., Peretin, G., Tomić, S. & Šikić, M. (2012) BioMe : biologically relevant metals. Nucleic acids research, 40, W352-W357 doi:10.1093/nar/gks514.

  doi

• Hrvoje, B., Daniela, B., Michael, R., Grit, S. & Sanja, T. (2012) Dke1 – Structure, Dynamics and Function, A Theoretical and Experimental Study Elucidated the Role of the Binding Site Shape and the H-Bonding Network in Catalysis. Journal of biological inorganic chemistry, 17 (5), 801-815 doi:10.1007/s00775-012-0898-8.

  doi

• Tomić, A., Gonzalez, M. & Tomić, S. (2012) The large scale conformational change of the human DPP III – substrate prefers the "closed" form. Journal of chemical information and modeling, 52 (6), 1583-1594 doi:10.1021/ci300141k.

  doi

• Aleksić, M., Bertoša, B., Nhili, R., Uzelac, L., Jarak, I., Depauw, S., David-Cordonnier, M., Kralj, M., Tomić, S. & Karminski-Zamola, G. (2012) Novel Substituted Benzothiophene- and Thienothiophene-carboxanilides and quinolones : Synthesis, Photochemical Synthesis, DNA–binding Properties, Antitumor evaluation and 3D-derived QSAR analysis. Journal of medicinal chemistry, 55 (11), 5044-5060 doi:10.1021/jm300505h.

  doi

• Tumir, L., Crnolatac, I., Deligeorgiev, T., Vasilev, A., Kaloyanova, S., Grabar Branilović, M., Tomić, S. & Piantanida, I. (2012) Kinetic differentiation between homo- and alternating AT-DNA by sterically restricted phosphonium dyes. Chemistry : a European journal, 18 (13), 3859-3864 doi:10.1002/chem.201102968.

  doi

• Špoljarić, J., Tomić, A., Vukelić, B., Salopek-Sondi, B., Agić, D., Tomić, S. & Abramić, M. (2011) Human Dipeptidyl Peptidase III : the Role of Asn406 in Ligand Binding and Hydrolysis. Croatica chemica acta, 84 (2), 259-268 doi:10.5562/cca1808.

  doihrcak.srce.hr

• Šimunović, M., Žagrović, B. & Tomić, S. (2011) Mechanism and thermodynamics of ligand binding to auxin amidohydrolase. Journal of molecular recognition, 24 (5), 854-861 doi:10.1002/jmr.1128.

  doi

• Tomić, A., Abramić, M., Špoljarić, J., Agić, D., Smith, D. & Tomić, S. (2011) Human Dipeptidyl Peptidase III: Insights into Ligand Binding from a Combined Experimental and Computational Approach. Journal of molecular recognition, 24 (5), 804-814 doi:10.1002/jmr.1115.

  doi

• Groger, K., Baretić, D., Piantanida, I., Marjanović, M., Kralj, M., Grabar, M., Tomić, S. & Schmuck, C. (2011) Guanidiniocarbonyl-pyrrole-aryl conjugates as nucleic acid sensors: switch of binding mode and spectroscopic responses by introducing additional binding sites into the linker. Organic & biomolecular chemistry, 9 (1), 198-209 doi:10.1039/C0OB00103A.

  doi

• Šikić, K., Tomić, S. & Carugo, O. (2010) Systematic comparison of crystal and NMR protein structures deposited in the protein data bank. The Open biochemistry journal, 4, 83-95 doi:10.2174/1874091X01004010083.

  doi

• Bertoša, B., Aleksić, M., Karminski-Zamola, G. & Tomić, S. (2010) QSAR analysis of antitumor active amides and quinolones from thiophene series. International journal of pharmaceutics, 394 (1-2), 106-114 doi:10.1016/j.ijpharm.2010.05.014.

  doi

• Burja, B., Čimbora-Zovko, T., Tomić, S., Jelušić, T., Kočevar, M., Polanc, S. & Osmak, M. (2010) Pyrazolone-fused combretastatins and their precursors : synthesis, cytotoxicity, antitubulin activity and molecular modeling studies. Bioorganic & medicinal chemistry, 18 (7), 2375-2387 doi:10.1016/j.bmc.2010.03.006.

  doi

• Tumir, L., Grabar, M., Tomić, S. & Piantanida, I. (2010) The interactions of bis-phenanthridinium – nucleobase conjugates with nucleotides: adenine conjugate recognizes UMP in aqueous medium. Tetrahedron, 66 (13), 2501-2513 doi:10.1016/j.tet.2010.01.063.

  doifulir.irb.hr

• Savić, B., Tomić, S., Magnus, V., Gruden, K., Barle, K., Grenković, R., Ludwig-Müller, J. & Salopek-Sondi, B. (2009) Auxin amidohydrolases from Brassica rapa cleave the alanine conjugate of indolepropionic acid as a preferable substrate: a biochemical and modeling approach. Plant and cell physiology, 50 (9), 1587-1599 doi:10.1093/pcp/pcp101.

  doi

• Banjanac, M., Tatić, I., Ivezić, Z., Tomić, S. & Dumić, J. (2009) Pyrimido-Pyrimidines : A Novel Class of Dihydrofolate Reductase Inhibitors. Food technology and biotechnology, 47 (3), 236-245.

• Ćaleta, I., Kralj, M., Marjanović, M., Bertoša, B., Tomić, S., Pavlović, G., Pavelić, K. & Karminski-Zamola, G. (2009) Novel Cyano- and Amidino- Benzothiazole Derivatives: Synthesis, Antitumor Evaluation, X-ray and QSAR Analysis. Journal of medicinal chemistry, 52 (6), 1744-1756 doi:10.1021/jm801566q.

  doi

• Šikić, M., Tomić, S. & Vlahoviček, K. (2009) Prediction of Protein-Protein Interaction Sites in Sequences and 3D Structures by Random Forests. Plos computational biology, 5 (1), e1000278-1 doi:10.1371/journal.pcbi.1000278.

  doifulir.irb.hr

• Vujasinović, I., Mlinarić-Majerski, K., Bertoša, B. & Tomić, S. (2009) Influence of the Rigid Spacer to Macrocyclization of Poly(thialactones): Synthesis and Computational Analysis. Journal of physical organic chemistry, 22 (5), 431-437 doi:10.1002/poc.1479.

  doi

• Mihel, J., Šikić, M., Tomić, S., Jeren Branko & Vlahoviček, K. (2008) PSAIA - Protein Structure and Interaction Analyzer. BMC structural biology, 8, 21, 11 doi:10.1186/1472-6807-8-21.

  doibmcstructbiol.biomedcentral.comdoi.orgpubmed.ncbi.nlm.nih.govfulir.irb.hr

• Dokmanić, I., Šikić, M. & Tomić, S. (2008) Metals in proteins: correlation between the metal-ion type, coordination number and the amino-acid residues involved in the coordination. Acta crystallographica. Section D, Biological crystallography, 64 (3), 257-263 doi:10.1107/S090744490706595X.

  doi

• Luić, M., Štefanić, Z., Ceilinger, I., Hodošček, M., Janežić, D., Lenac, T., Leščić Ašler, I., Šepac, D. & Tomić, S. (2008) Combined X-Ray Diffraction and QM/MM Study of the Burkholderia cepacia Lipase-Catalyzed Secondary Alcohol Esterification. The journal of physical chemistry. B, Condensed matter, materials, surfaces, interfaces & biophysical, 112 (16), 4876-4883 doi:10.1021/jp077717u.

  doi

• Hernandez-Folgado, L., Schmuck, C., Tomić, S. & Piantanida, I. (2008) A novel pyrene-guanidiniocarbonyl-pyrrole cation efficiently differentiates between ds-DNA and ds-RNA by two independent, sensitive spectroscopic methods. Bioorganic & Medicinal Chemistry Letters, 18, 2977-2981 doi:10.1016/j.bmcl.2008.03.060.

  doi

• Bertoša, B., Kojić-Prodić, B., Wade, R. & Tomić, S. (2008) Mechanism of Auxin Interaction with Auxin Binding Protein (ABP1): A Molecular Dynamics Simulation Study. Biophysical journal, 94 (1), 27-37 doi:10.1529/biophysj.107.109025.

  doi

• Tomić, S., Bertoša, B., Wang, T. & Wade, R. (2007) COMBINE Analysis of the Specificity of Binding of Ras Proteins to their Effectors. Proteins Structure, Function, and Bioinformatics, 67 (2), 435-447. (https://www.bib.irb.hr/313287).

• Tomašić, A., Bertoša, B., Tomić, S., Šoškić, M. & Magnus, V. (2007) Binding behavior of amino acid conjugates of indole-3-acetic acid to immobilized human serum albumin. Journal of Chromatography. A, 1154 (1-2), 240-249.

• Tumir, L., Piantanida, I., Žinić, M., Juranović Cindrić, I., Meić, Z., Kralj, M. & Tomić, S. (2006) Synthesis of phenanthridinium bis-nucleobase conjugates, interactions with poly U, nucleotides and in vitro antitumor activity of mono- and bis-nucleobase conjugates. European Journal of Medicinal Chemistry, 41 (10), 1153-1166.

• Tomić, S. & Ramek, M. (2006) Quantum Mechanical Study of Burkholderia cepacia Lipase Enantioselectivity. Journal of Molecular Catalysis B: Enzymatic, 38, 139-147.

• Tumir, L., Piantanida, I., Juranović, I., Meić, Z., Tomić, S. & Žinić, M. (2005) Recognition of homo-polynucleotides containing adenine by phenanthridinium bis-uracil conjugate in aqueous media.. Chemical communications, - (20), 2561-2563.

• Wang, T., Tomić, S., Gabdoulline, R. & Wade, R. (2004) How Optimal Are the Binding Energetics of Barnase and Barstar?. Biophysical journal, 87, 1618-1630.

• Ramek, M. & Tomić, S. (2004) Ab initio Hartree-Fock Investigation of 2-Methylindole-3-acetic Acid. Croatica chemica acta, 77 (1-2), 371-376.

• Tomić, S., Bertoša, B., Kojić-Prodić, B. & Kolosvary, I. (2004) Stereoselectivity of Burkholderia cepacia lipase towards secondary alcohols: molecular modelling and 3D QSAR approach. Tetrahedron: Asymmetry, 15, 1163-1172.

• Bertoša, B., Kojić-Prodić, B., Ramek Michael, Piperaki, Stavroula, Tsantili-Kakoulidou, Anna, Wade, R. & Tomić, S. (2003) A new approach to predict the biological activity of molecules based on similarity of their interaction fields and the logP and logD values: application to auxins. Journal of Chemical Information Computer Sciences, 43, 1532-1541.

• Antolić, S., Dolušić, E., Kožić, E., Kojić-Prodić, B., Magnus, V., Ramek, M. & Tomić, S. (2003) Auxin activity and molecular structure of 2-alkylindole-3-acetic acids. Plant Growth Regulation, 39 (3), 235-252.

• Tomić, S. & Kojić-Prodić, B. (2002) A Quantitative Model for Predicting Enzyme Enantioselectivity: Application to Burkholderia cepacia lipase and 3-(Aryloxy)-1, 2-propanediol Derivatives. Journal of Molecular Graphics and Modeling, 21 (3), 241-252.

• Ramek, M. & Tomić, S. (2001) Ab initio Hartree-Fock investigation of 1-H-pyrrolo[3, 2-b]pyridine-3-yl acetic acid. Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy, 57, 1951-1957.

• Tomić, S. & Wade, R. (2001) COMBINE analysis of nuclear receptor-DNA binding specifity: Comparison of two datasets. Croatica Chemica Acta, 74, 295-314.

• Ljubović, E., Tomić, S., Kojić-Prodić, B. & Šunjić, V. (2001) Current Approach to Study of Biocatalytic Reactions: Experiment and Molecular Modeling of Lipase Catalysed Reactions. Kemija u Industriji, 50 (3), 139-156.

• Tomić, S., Dobovičnik, V., Šunjić, V. & Kojić-Prodić, B. (2001) Enantioselectivity of the Pseudomonas cepacia lipase towards 2-methyl-3-(or 4)-arylalkanols: an approach based on stereoelectronic theory and the molecular modeling. Croatica Chemica Acta, 74, 343-357.

• Luić, M., Tomić, S., Leščić, I., Ljubović, E., Šepac, D., Šunjić, V., Vitale, L., Saenger, W. & Kojić-Prodić, B. (2001) Complex of Burkholderia cepacia lipase with transition state analogue of 1-phenoxy-2-acetoxybutane, Biocatalytic, structural and modelling study.. European Journal of Biochemistry, 268 (14), 3964-3973.

• Tomić, S., Nillson, L. & Wade, R. (2000) Nuclear receptor-DNA binding specificity : a combine and Free-Wilson QSAR ananlysis. Journal of medicinal chemistry, 43 (9), 1780-1792.

• Tomic, S., Chughtai, N. & Ali, S. (1999) SOCS-1, -2, -3: selective targets and functions downstream of the prolactin receptor. Molecular and Cellular Endocrinology, 158 (1-2), 45-54 doi:10.1016/s0303-7207(99)00180-x.

  doi

• Tomic, S., Chughtai, N. & Ali, S. (1999) SOCS-1, -2, -3: selective targets and functions downstream of the prolactin receptor. Molecular and Cellular Endocrinology, 158 (1-2), 45-54 doi:10.1016/s0303-7207(99)00180-x.

  doi

• Ramek, M. & Tomić, S. (1999) Quantum chemical conformational analysis of the auxin phytohormone 4-methyl-3-indole acetic acid. International journal of quantum chemistry, 75 (6), 1003-1008.

• Kojić-Prodić, B., Magnus, V., Antolić, S., Tomić, S. & Salopek-Sondi, B. (1999) Structure/activity correlations for auxins. Acta botanica Croatica, 58, 27-37.

• Tomić, S., Gabdoulline, R., Kojić-Prodić, B. & Wade, R. (1998) Classification of auxin related compounds based on similarity of their interaction fields: extension to a new set of compounds.. Internet journal of chemistry, 1.

• Ramek, M. & Tomić, S. (1998) RHF conformational analysis of the auxin phytohormones n-ethyl-indole-3-acetic acid (n=4, 5, 6).. International journal of quantum chemistry, 70 (6), 1169-1175.

• Ramek, M. & Tomić, S. (1998) Ab Initio RHF investigation of mono- and dihalogenated indole-3-acetic acid (IAA) phytohormones.. Theochem : journal of molecular structure, 454, 167-173.

• Tomić, S., Gabdoulline, R., Kojić-Prodić, B. & Wade, R. (1998) Classification of auxin plant hormones by interaction property similarity indices.. Journal of computer-aided molecular design, 12, 63-79.

• Tomić, S., Ramek, M. & Kojić-Prodić, B. (1998) Combined Ab Initio SCF and molecular mechanics studies of propionic and isobutyric acids and their indole derivatives related to the phytohormone auxin (Indole-3-acetic acid).. Croatica chemica acta, 71, 511-525.

• Antolić, S., Kojić-Prodić, B., Magnus, V., Salopek, B. & Tomić, S. (1997) Structure-activity correlations for ring-alkylated derivatives of indole-3-acetic acid. Plant physiology, 114 (3), 158-158.

• Antolić, S., Kojić-Prodić, B., Tomić, S., Nigović, B., Magnus, V. & Cohen, J. (1996) Structural studies on monofluorinated derivatives of the phytohormone indole-3-acetic acid (auxin). Acta crystallographica. Section B, Structural science, 52 (4), 651-661 doi:10.1107/S0108768195016302.

  doi

• Ramek, M., Tomić, S. & Kojić-Prodić, B. (1996) Comparative ab initio SCF conformational study of phytohormones (auxins) 4-chloro-indole-3-acetic acid and indole-3-acetic acid. International journal of quantum chemistry, 60 (8), 1727-1733 doi:10.1002/(SICI)1097-461X(1996)60:83.0.CO ; 2-#.

  doi

• Tomić, S., Kojić-Prodić, B., Magnus, V., Laćan, G., Duddeck, H. & Hiegemann, M. (1995) Synthesis and conformational analysis of plant hormone (auxin) related compound, 2-(indol-3-yl)ethyl β -D-galactopyranoside and its 2, 3, 4, 6-tetra-O-acetyl derivative. Carbohydrate research, 279, 1-19 doi:10.1016/0008-6215(95)00245-6.

  doi

• Ramek, M., Tomić, S. & Kojić-Prodić, B. (1995) Systematic Ab Initio SCF Conformational Analysis of Indol-3-ylacetic Acid Phytohormone (Auxin): Comparison with Experiment and Molecular Mechanics Calculations. International journal of quantum chemistry, 56 (22), 75-81 doi:10.1002/qua.560560708.

  doi

• Tomić, S., van Eijck, B., Kojić-Prodić, B., Kroon, J., Magnus, V., Nigović, B., Ilić, N., Duddeck, H. & Hiegemann, M. (1995) Synthesis and Conformational Analysis of Plant Hormone (auxin) Related Compounds, 2-(indol-3-yl)ethyl and 2-(phenyl)ethyl β -D-xylopyranosides and their 2, 3, 4-tri-O-acetyl Derivatives. Carbohydrate research, 270 (1), 11-32 doi:10.1016/0008-6215(95)00037-T.

  doi

• Tomić, S., van Duijneveldt, F., Kroon-Batenburg, L. & Kojić-Prodić, B. (1995) Molecular Mechanics and SCF MO Conformational Analysis of Indol-3-ylacetic Acid, Phytohormone. Croatica Chemica Acta, 68 (1), 205-214.

  hrcak.srce.hr

• Tomić, S., van Eijck, B., Kroon, J., Kojić-Prodić, B., Laćan, G., Magnus, V., Duddeck, H. & Hiegemann, M. (1994) Synthesis and Conformational Analysis of 2-(indol-3-yl) ethyl α -L-arabinopyranoside and its 2, 3, 4-tri-O-acetyl derivative. Carbohydrate research, 259 (2), 175-190.

• Keglević, D., Kojić-Prodić, B., Banić, Z., Tomić, S. & Puntarec, V. (1993) Synthesis and Conformational Analysis of Muramic Acid δ - Lactam Structures and Their -O-(2-Acetamido-2-deoxy- α -D-glucopyranosyl) Derivatives, Characteristic of Bacterial Spore Peptidoglycan. Carbohydrate research, 241, 131-152 doi:10.1016/0008-6215(93)80101-J.

  doi

• Kojić-Prodić, B., Nigović, B., Puntarec, V., Tomić, S. & Magnus, V. (1993) Structural comparison of Biologically Active and Inactive Conjugates of alpha-Amino Acids and the Plant Growth Hormone (Auxin) Indole-3-acetic Acid. Acta crystallographica. Section B, Structural science, 49, 367-374.

• Kojić-Prodić, B., Danilović, Ž., Puntarec, V., Tomić, S. & Šušković, B. (1991) Crystal and Molecular Structure of (4S, 5S)-6-Ammonium-6-deoxy-3-O-ascorbate. Croatica Chemica Acta, 64 (3), 311-317.

  hrcak.srce.hr

• Kojić-Prodić, B., Nigović, B., Tomić, S., Ilić, N., Magnus, V., Giba, Z., Konjević, R. & Duax, W. (1991) Structural studies on 5-(n-alkyl)-substituted derivatives of the plant hormone indole-3-acetic acid. Acta crystallographica. Section B, Structural science, 47, 1010-1019 doi:10.1107/S0108768191008996.

  doi

• Kušec, R., Nikolić, V., Tomić, S., Hančević, J., Davila, S. & Valković, V. (1990) Trace elements in periosteal callus and cortical bone after plating for fracture. Periodicum biologorum. Supplement, 92 (3), 325-327.

• Tomić, S., Lakatoš, J. & Valković, V. (1989) Analysis of Trace Elements in Hair of Pregnant Women Using XRF Spectroscopy. X-Ray Spectrometry, 18 (2), 73-76 doi:10.1002/xrs.1300180208.

  doi

• Orlić, I., Tomić, S., Makjanić, J., Jakšić, M. & Valković, V. (1987) A Modified Approach to Quantitative XRF Analysis of Thick Targets. X-ray spectrometry, 16 (3), 125-130 doi:10.1002/xrs.1300160307.

  doi

• Tomić, S., Valković, V., Budnar, M., Starc, V. & Šmit, Ž. (1987) Comparison of XRF and PIXE on aerosol samples. Nuclear instruments & methods in physics research. Section B, Beam interactions with materials and atoms, 24-25 (2), 609-612 doi:10.1016/S0168-583X(87)80207-0.

  doi

• Nagj, M., Makjanić, J., Orlić, I., Tomić, S. & Valković, V. (1986) Determination of Uranium in Sea Water by X-Ray Fluorescence Spectroscopy. Journal of radioanalytical and nuclear chemistry, 97 (2), 373-380 doi:10.1007/BF02035683.

  doi

• Tomić, S., Krmpotić-Nemanić, J. & Valković, V. (1986) X-ray fluorescence of (irregularly shaped) bone sample materials. Nuclear instruments & methods in physics research. Section B, Beam interactions with materials and atoms, 18 (1-6), 71-76 doi:10.1016/S0168-583X(86)80014-3.

  doi

• Tomić, S., Nagj, M. & Raos, D. (1985) Determination of Heavy Metal in Drinking Water by X-Ray Spectroscopy. International journal of environmental analytical chemistry, 23, 87-94 doi:10.1080/03067318508076437.

  doi

Radovi u zbornicima skupova

Znanstveni radovi u zbornicima skupova

• Tomić, S., Brkić, H., Grabar Branilović, M., Tomić, A., Branimir, B. & Mile, Š. (2013) Proteini i nukleinske kiseline u vremenu i prostoru. U: Paar, V. (ur.)Bioinformatics and biological physics: proceedings of the scientific meeting. (https://www.bib.irb.hr/689340).

• Šikić, K. & Tomić, Sanja, Jeren, Branko (2008) Identifying protein flexibility by NMA. U: Arabnia, H. (ur.)Proceedings of the 2008 International Conference on Bioinformatics & Computational Biology.

• Šikić, K., Tomić, S. & Jeren, B. (2008) The protein secondary structure flexibility. U: Arabnia, H. (ur.)Proceedings of the 2008 International Conference on Bioinformatics & Computational Biology.