Pregled po projektu: Proučavanje biomakromolekula računalnim metodama i razvoj novih algoritama (MB: MZOS-098-1191344-2860)

1.

Rastija, Vesna; Agić, Dejan; Tomić, Sanja; Nikolić, Sonja; Hranjec, Marijana; Karminski-Zamola, Grace; Abramić, Marija

Synthesis, QSAR, and molecular dynamics simulation of amidino-substituted benzimidazoles as dipeptidyl peptidase III inhibitors // Acta chimica Slovenica, 62 (2015), 4; 867-878 doi:10.17344/acsi.2015.1605 (međunarodna recenzija, članak, znanstveni)

Pristup cjelovitom tekstu rada doi fulir.irb.hr fulir.irb.hr journals.matheo.si dx.doi.org

2.

Gershberg, Jana; Radić Stojković, Marijana; Škugor, Marko; Tomić, Sanja; Rehm, Thomas H.; Rehm, Stephanie; Saha-Möller, Chantu R.; Piantanida, Ivo; Würthner, Frank

Sensing of Double-Stranded DNA/RNA Secondary Structures by Water Soluble Homochiral Perylene Bisimide Dyes // Chemistry - A European Journal, 21 (2015), 21; 7886-7895 doi:10.1002/chem.201500184 (međunarodna recenzija, članak, znanstveni)

doi onlinelibrary.wiley.com

3.

González-García, Jorge; Tomić, Sanja; Lopera, Alberto; Guijarro, Lluís; Piantanida, Ivo; García-España, Enrique

Aryl-bis-(scorpiand)-aza receptors differentiate between nucleotide monophosphates by combination of aromatic, hydrogen bond and electrostatic interactions // Organic & biomolecular chemistry, 13 (2015), 1732-1740 doi:10.1039/c4ob02084g (međunarodna recenzija, članak, znanstveni)

doi pubs.rsc.org pubs.rsc.org

4.

Brkić, Hrvoje; Kovačević, Borislav; Tomić, Sanja

Human 3-hydroxyanthranilate 3, 4-dioxygenase (3HAO) dynamics and reaction, a multilevel computational study // Molecular biosystems, 11 (2015), 3; 898-907 doi:10.1039/C4MB00668B (međunarodna recenzija, članak, znanstveni)

doi pubs.rsc.org pubs.rsc.org

5.

Grabar Branilović, Marina; Tomić, Sanja

Computational study of the IRES subdomain IIa structural plasticity and the ligand binding affinity // Chemistry towards Biology 7th Central European Conference - Book of Abstracts / Jarzembek, Krystyna (ur.) (ur.).
Katovice, 2014. str. P10-P10 (poster, međunarodna recenzija, sažetak, znanstveni)

6.

Grabar Branilović, Marina

Eksperimentalno utemeljeno modeliranje interakcija nukleinskih kiselina i malih molekula, 2014., doktorska disertacija, Prirodoslovno-matematički fakultet, Zagreb

Pristup cjelovitom tekstu rada

7.

Grabar Branilović, Marina; Tomić, Sanja

Computational study of the structural plasticity and the ligand binding affinity of the IRES subdomain IIa // Molecular biosystems, 10 (2014), 12; 3272-3279 doi:10.1039/c4mb00469h (međunarodna recenzija, članak, znanstveni)

doi pubs.rsc.org

8.

Maršavelski, Aleksandra; Lesjak, Sonja; Močibob, Marko; Weygand-Đurašević, Ivana; Tomić, Sanja

A single amino acid substitution affects the substrate specificity of the seryl-tRNA synthetase homologue // Molecular biosystems, 10 (2014), 12; 3207-3216 doi:10.1039/C4MB00416G (međunarodna recenzija, članak, znanstveni)

doi pubs.rsc.org

9.

Tomić, Antonija; Tomić, Sanja

Hunting the human DPP III active conformation : combined thermodynamic and QM/MM calculations // Dalton transactions, 43 (2014), 15503-15514 doi:10.1039/C4DT02003K (međunarodna recenzija, članak, znanstveni)

doi pubs.rsc.org

10.

Brkić, Hrvoje

Proučavanje o željezu ovisnih dioksigenaza računalnim metodama, 2014., doktorska disertacija, Prirodoslovno matematički Fakultet, Fizički odsjek, Zagreb

11.

Bertoša, Branimir; Mikleušević, Goran; Wielgus-Kutrowska, Beata; Narczyk, Marta; Hajnić, Matea; Leščić Ašler, Ivana; Tomić, Sanja; Luić, Marija; Bzowska, Agnieszka

Homooligomerization is needed for stability: a molecular modelling and solution study of E. coli purine nucleoside phosphorylase // The FEBS journal, 281 (2014), 7; 1860-1871 doi:10.1111/febs.12746 (međunarodna recenzija, članak, znanstveni)

doi

12.

Jajčanin Jozić, Nina; Tomić, Sanja; Abramić, Marija

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 (2014), 1; 43-50 doi:10.1093/jb/mvt093 (međunarodna recenzija, članak, znanstveni)

doi jb.oxfordjournals.org jb.oxfordjournals.org

13.

Marković, Marijana; Ramek, Michael; Sabolović, Jasmina

Why does the coordination mode of physiological bis(L-histidinato)copper(II) differ in the gas phase, crystal lattice and aqueous solutions? A quantum chemical study // European journal of inorganic chemistry, 17 (2014), 1; 198-212 doi:10.1002/ejic.201300746 (međunarodna recenzija, članak, znanstveni)

doi onlinelibrary.wiley.com onlinelibrary.wiley.com

14.

Aleksić, Maja; Bertoša, Branimir; Nhili, Raja; Depauw, Sabine; Martin-Kleiner, Irena; David-Cordonnier, Marie-Helene; Tomić, Sanja; Kralj, Marijeta; Karminski-Zamola, Grace

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 (2014), 267-281 doi:10.1016/j.ejmech.2013.11.010 (međunarodna recenzija, članak, znanstveni)

doi www.sciencedirect.com ac.els-cdn.com

15.

Tomić, Sanja; Brkić, Hrvoje; Grabar Branilović, Marina; Tomić, Antonija; Branimir, Bertoša; Mile, Šikić

Proteini i nukleinske kiseline u vremenu i prostoru // Bioinformatics and biological physics: proceedings of the scientific meeting / Paar, Vladimir (ur.).
Zagreb: Hrvatska akademija znanosti i umjetnosti (HAZU), 2013. str. 149-157 (pozvano predavanje, domaća recenzija, cjeloviti rad (in extenso), znanstveni)

Pristup cjelovitom tekstu rada

16.

Grabar Branilović, Marina; Maršavelski, Aleksandra; Tomić, Antonija; Tomić, Sanja

Nobelova nagrada za kemiju za 2013. godinu // Kemija u industriji : časopis kemičara i tehnologa Hrvatske, 62 (2013), 11-12; 468-471 (podatak o recenziji nije dostupan, osvrt, stručni)

fulir.irb.hr

17.

Šumanovac Ramljak, Tatjana; Despotović, Ines; Bertoša, Branimir; Mlinarić-Majerski, Kata

Synthesis and alkali metal complexation studies of novel cage-functionalized cryptands // Tetrahedron, 69 (2013), 49; 10610-10620 doi:10.1016/j.tet.2013.10.039 (međunarodna recenzija, članak, znanstveni)

doi ac.els-cdn.com www.sciencedirect.com dx.doi.org

18.

Tomić, Antonija; Tomić, Sanja

Najnovija saznanja o koordinaciji cinka i o vezanju liganda u aktivno mjesto humane DPP III – implikacije na mehanizam kemijske reakcije // XXIII. hrvatski skup kemičara i kemijskih inženjera, knjiga sažetaka / Hadžiev, Andrea ; Blažeković, Zdenko (ur.).
Zagreb: Hrvatsko društvo kemijskih inženjera i tehnologa (HDKI), 2013. str. 177-177 (poster, domaća recenzija, sažetak, znanstveni)

19.

Sabolović, Jasmina

Modeling of noncovalent interactions and self-assembly of cis- and trans-bis(L-alaninato)copper(II) in aqueous solution // ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY VOLUME 245 / AMER. CHEMICAL SOC. (ur.).
New Orleans (LA): AMER CHEMICAL SOC, 1155 16TH ST, NW, WASHINGTON, DC 20036 USA, 2013. str. PHYS-396 (poster, međunarodna recenzija, sažetak, znanstveni)

20.

Tomić, Sanja; Brkić, Hrvoje; Straganz, Grit; Buongiorno, daniela

Non-heme iron dependent enzymes – understanding transport of iron cation in acetylacetone dioxygenase from Acinetobacter johnsoii // European Biophys. J. Volume 42 Supplement 1, '9th European Biophysics Congress Abstracts' / Watts, A. (ur.).
Heidelberg: Springer, 2013. str. S184-S184 (poster, međunarodna recenzija, sažetak, znanstveni)

21.

Tomić, Sanja; Tomić, Antonija; Brkić, Hrvoje

Elucidation of metal ion-binding sites in proteins // 6th Central Europe Conference - Abstracts of scientific contributions / Roberto Rizzo (ur.).
Trst: Universita degli studi di Trieste, 2013. str. oc15-oc15 (predavanje, međunarodna recenzija, sažetak, znanstveni)

22.

Tomić, Antonija; Tomić, Sanja

Molecular Mechanics - Poisson Boltzmann Surface Area calculations using AMBER program package - application to the human dipeptidyl petidase III // Computational Electrostatics for Biological Applications - Book of Abstract
Genova, Italija, 2013. str. 39-39 (poster, međunarodna recenzija, sažetak, znanstveni)

23.

Kušević, Katarina

Računalna metoda za računanje proteinskih interakcija, 2013., diplomski rad, diplomski, Fakultet elektrotehnike i računarstva, Zagreb

Pristup cjelovitom tekstu rada

24.

Grabar Branilović, Marina; Tomić, Sanja; Tumir, Lidija-Marija; Piantanida, Ivo

The bis-phenanthridinium system flexibility and position of covalently bound uracil finely tunes the interaction with polynucleotides // Molecular biosystems, 9 (2013), 8; 2051-2062 doi:10.1039/C3MB25578F (međunarodna recenzija, članak, znanstveni)

doi pubs.rsc.org

25.

Radić Stojković, Marijana; Škugor, Marko; Tomić, Sanja; Grabar, Marina; Smrečki, Vilko; Dudek, Łukasz; Grolik, Jarosław; Eilmes, Julita; Piantanida, Ivo

Dibenzotetraaza[14]annulene – adenine conjugate recognizes complementary poly dT among ss-DNA / ss-RNA sequences // Organic & biomolecular chemistry, 11 (2013), 24; 4077-4085 doi:10.1039/c3ob40519b (međunarodna recenzija, članak, znanstveni)

doi pubs.rsc.org

26.

Tomić, Sanja; Abramić, Marija; Brkić, Hrvoje; Tomić, Antonija

Sprega kristalografije i modeliranja u proučavanju bioloških makromolekula // Kristalografija u Hrvatskoj / Popović Stanko (ur.).
Zagreb: Hrvatska akademija znanosti i umjetnosti (HAZU), 2013. str. 129-137 (predavanje, domaća recenzija, cjeloviti rad (in extenso), ostalo)

27.

Schmidt, Daniel; Bihr, Timo; Seifert, Udo; Smith, Ana-Sunčana

Coexistence of dilute and densely packed domains of ligand-receptor bonds in membrane adhesion // Europhysics Letters, 99 (2012), 3; 38003-1 doi:10.1209/0295-5075/99/38003 (međunarodna recenzija, pismo, znanstveni)

doi iopscience.iop.org

28.

Bihr, T.; Seifert, Davor; Smith, Ana-Sunčana

Nucleation of Ligand-Receptor Domains in Membrane Adhesion // Physical review letters, 109 (2012), 25; 258101, 5 doi:10.1103/PhysRevLett.109.258101 (međunarodna recenzija, članak, znanstveni)

doi journals.aps.org doi.org

29.

Tomić, Sanja; Tomić, Antonija; Gonzalez, Miguel

Molecular dynamics based studies on human DPP III revealed determinants for its broad substrate selectivity // IRENE – 'In Silico Enzyme Sesign and Screening'
Trst, Italija, 2012. (predavanje, međunarodna recenzija, sažetak, znanstveni)

30.

Šumanovac Ramljak, Tatjana; Mlinarić-Majerski, Kata; Bertoša, Branimir

Alkali metal ion complexation of adamantane functionalized diaza-bibracchial lariat ethers // Croatica chemica acta, 85 (2012), 4; 559-568 doi:10.5562/cca2100 (međunarodna recenzija, članak, znanstveni)

doi

31.

Tomić, Sanja; Grabar, Marina; Piantanida, Ivo

Molecular modeling of nucleic acid - small molecule interactions // Book of Abstracts Regional Biophysical Conference 2012 / Zakrzewska, Joanna, Živić, Miroslav, Andjus, Pavle (ur.).
Beograd: Društvo biofizičara Srbije, 2012. str. 13-13 (pozvano predavanje, međunarodna recenzija, sažetak, znanstveni)

32.

Tomić, Antonija; Tomić, Sanja

Further study of the zinc coordination in the active site of the human DPP III - ONIOM calculations // Book of abstracts, 11th Greta Pifat-Mrzljak International School of Biophysics, Biomolecular complexes and assemblies / Hozić A., Vuletić T. (ur.).
Zagreb: Institut Ruđer Bošković i Hrvatsko biofizičko društvo, 2012. str. 104-104 (poster, međunarodna recenzija, sažetak, znanstveni)

www.irb.hr

33.

Aleksić, Maja; Sović, Irena; Viskić, Marko; Bertoša, Branimir; Ester, Katja; Kralj, Marijeta; Karminski-Zamola, Grace

Synthesis, Antitumor Activity and QSAR Analysis of Heterocyclic Amides and Quinolones // ISMC 2012 XXIInd International Symposium on Medicinal Chemistry, Book of Abstracts / Ortuzar, Natalia (ur.).
Weinheim, 2012. str. 250-251 (poster, međunarodna recenzija, sažetak, znanstveni)

34.

Tus, Alan; Rakipović, Alen; Peretin, Goran; Tomić, Sanja; Šikić, Mile

BioMe : biologically relevant metals // Nucleic acids research, 40 (2012), W352-W357 doi:10.1093/nar/gks514 (međunarodna recenzija, članak, znanstveni)

doi nar.oxfordjournals.org nar.oxfordjournals.org

35.

Rakipović, Alen

BioMe - web sučelje baze biološki važnih metala, 2012., diplomski rad, diplomski, Fakultet elektrotehnike i računarstva, Zagreb

Pristup cjelovitom tekstu rada

36.

Hrvoje, Brkić; Daniela, Buongiorno; Michael, Ramek; Grit, Straganz; Sanja, Tomić

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 (2012), 5; 801-815 doi:10.1007/s00775-012-0898-8 (međunarodna recenzija, članak, znanstveni)

doi rd.springer.com

37.

Marković, Marijana; Milić, Dalibor; Sabolović, Jasmina

Modeling triple conformational disorder in a new crystal polymorph of cis-aquabis(L-isoleucinato)copper(II) // Crystal growth & design, 12 (2012), 8; 4116-4129 doi:10.1021/cg300636w (međunarodna recenzija, članak, znanstveni)

doi pubs.acs.org

38.

Tomić, Antonija; Gonzalez, Miguel; Tomić, Sanja

The large scale conformational change of the human DPP III – substrate prefers the "closed" form // Journal of chemical information and modeling, 52 (2012), 6; 1583-1594 doi:10.1021/ci300141k (međunarodna recenzija, članak, znanstveni)

doi pubs.acs.org

39.

Aleksić, Maja; Bertoša, Branimir; Nhili, Raja; Uzelac, Lidija; Jarak, Ivana; Depauw, Sabine; David-Cordonnier, Marie-Hélène; Kralj, Marijeta; Tomić, Sanja; Karminski-Zamola, Grace

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 (2012), 11; 5044-5060 doi:10.1021/jm300505h (međunarodna recenzija, članak, znanstveni)

doi pubs.acs.org

40.

Brgles, Marija; Bertoša, Branimir; Winkler, Wolfgang; Kurtović, Tihana; Allmaier, Günter; Marchetti-Deschmann, Martina; Halassy, Beata

Chromatography, mass spectrometry, and molecular modeling studies on ammodytoxins // Analytical and bioanalytical chemistry, 402 (2012), 9; 2737-2748 doi:10.1007/s00216-012-5754-8 (međunarodna recenzija, članak, znanstveni)

doi www.springerlink.com

41.

Tomić, Antonija; Tomić, Sanja

QM/MM račun koordinacije cinka u aktivnom mjestu humane DPP III / QM/MM study of the zinc coordination in the active site of the human DPP III // Knjiga sažetaka - IX. Susret mladih kemijskih inženjera / Martinez, Sanja (ur.).
Zagreb: Hrvatsko društvo kemijskih inženjera i tehnologa (HDKI), 2012. str. 173-173 (poster, domaća recenzija, sažetak, znanstveni)

42.

Vujasinović, Ines; Paravić-Radičević, Andrea; Mlinarić-Majerski, Kata; Brajša, Karmen; Bertoša, Branimir

Synthesis and biological validation of novel pyrazole derivatives with anticancer activity guided by 3D-QSAR analysis // Bioorganic & medicinal chemistry, 20 (2012), 6; 2101-2110 doi:10.1016/j.bmc.2012.01.032 (međunarodna recenzija, članak, znanstveni)

doi www.sciencedirect.com dx.doi.org

43.

Tumir, Lidija-Marija; Crnolatac, Ivo; Deligeorgiev, Todor; Vasilev, Aleksey; Kaloyanova, Stefka; Grabar Branilović, Marina; Tomić, Sanja; Piantanida, Ivo

Kinetic differentiation between homo- and alternating AT-DNA by sterically restricted phosphonium dyes // Chemistry : a European journal, 18 (2012), 13; 3859-3864 doi:10.1002/chem.201102968 (međunarodna recenzija, članak, znanstveni)

doi onlinelibrary.wiley.com

44.

Popović, Irena

Predviđanje površine dostupne otapalu iz slijeda aminokiselinskih ostataka, 2011., diplomski rad, Fakultet Elektrotehnike i računarstva, Zagreb

complex.zesoi.fer.hr

45.

Tomić, Sanja; Brkić, Hrvoje; Ramek, Michael; Buongiorno, Daniele; Straganz, Grit

Influence of The Hydrophobic Residues on The Dke1 Activity // Molecular Simulations in Biosystems and Material Science (SimBioMa)
Konstanz, Njemačka, 2011. str. 1-1 (poster, međunarodna recenzija, sažetak, znanstveni)

46.

Sanja, Tomić; Hrvoje, Brkić; Michael, Ramek; Grit, Straganz

Step Forward in Understanding Mechanism of Non-heme Fe2+ Dependent Dioxyhenase Dke1 Catalysis // Book of Abstract
Santiago de Compostela, Španjolska, 2011. str. 1-1 (predavanje, međunarodna recenzija, sažetak, znanstveni)

47.

Susanne, Fenz; Timo, Bihr; Rudolf, Merkel; Udo, Seifert; Kheya, Sengupta; Ana-Sunčana, Smith

Switching from Ultraweak to Strong Adhesion // Advanced materials, 23 (2011), 2622-2626 doi:10.1002/adma.201004097 (međunarodna recenzija, članak, znanstveni)

doi onlinelibrary.wiley.com

48.

Fenz, Susanne Franziska; Smith, Ana-Sunčana; Merkel, Rudolf; Sengupta, Kheya

Inter-membrane adhesion mediated by mobile linkers : Effect of receptor shortage // Soft matter, 7 (2011), 3; 952-962 (međunarodna recenzija, članak, znanstveni)

49.

Reister, Ellen; Bihr, Timo; Smith, Ana-Sunčana;

Two intertwined facets of adherent membranes : Membrane roughness and correlations between ligand-receptors bonds // New journal of physics, 13 (2011), 025003-1 doi:10.1088/1367-2630/13/2/025003 (međunarodna recenzija, članak, znanstveni)

doi iopscience.iop.org iopscience.iop.org

50.

Sović, Ivan

Alat za prianjanje proteina: modul za vizualizaciju, 2011., diplomski rad, diplomski, Fakultet elektrotehnike i računarstva, Zagreb

Pristup cjelovitom tekstu rada

51.

Papeš Šokčević, Lidija

Poboljšani algoritam za izbor i provjeru kvalitete najboljih multivarijacijskih modela odnosa strukture i svojstava molekula, 2011., magistarski rad, Fakultet elektrotehnike i računarstva, Zagreb

urn.nsk.hr

52.

Kušević, Katarina

Implementacija algoritma za računanje proteinskih interakcija, 2011., diplomski rad, preddiplomski, Fakultet elektrotehnike i računarstva, Zagreb

Pristup cjelovitom tekstu rada

53.

Grabar, Marina; Tomić, Sanja; Tumir Marija, Lidija; Piantanida, Ivo

Molecular modeling of new permanently charged phenanthridinium-nucleobase conjugates in complexes with double stranded polynucleotides // Ninth Triennial Congress of the World Association ot Theoretical and Computational Chemists - Book of Abstracts / Yáñez, Manuel ; Mó, Otilia (ur.).
Santiago de Compostela, 2011. (poster, sažetak, znanstveni)

54.

Tomić, Antonija; Tomić, Sanja

MD simulations showed large conformational changes of the human free DPP III // Book of Abstracts - The Conference on Molecular Simulations in Biosystems and Material Science
Konstanz, 2011. str. 72-72 (poster, međunarodna recenzija, sažetak, znanstveni)

cms.uni-konstanz.de

55.

Špoljarić, Jasminka; Tomić, Antonija; Vukelić, Bojana; Salopek-Sondi, Branka; Agić, Dejan; Tomić, Sanja; Abramić, Marija

Human Dipeptidyl Peptidase III : the Role of Asn406 in Ligand Binding and Hydrolysis // Croatica chemica acta, 84 (2011), 2; 259-268 doi:10.5562/cca1808 (međunarodna recenzija, članak, znanstveni)

doi

56.

Šimunović, Mijo; Žagrović, Bojan; Tomić, Sanja

Mechanism and thermodynamics of ligand binding to auxin amidohydrolase // Journal of molecular recognition, 24 (2011), 5; 854-861 doi:10.1002/jmr.1128 (međunarodna recenzija, članak, znanstveni)

doi onlinelibrary.wiley.com

57.

Bertoša, Branimir; Tomić, Sanja; Aleksić, Maja; Karminski-Zamola, Grace

Investigation of anticancer activity of heterocyclic amides and quinolones using 3D-QSAR analysis // Ninth Triennial Congress of the World Association ot Theoretical and Computational Chemists / Yáñez, Manuel ; Mó, Otilia (ur.).
Santiago de Compostela, 2011. (poster, međunarodna recenzija, sažetak, znanstveni)

58.

Marković, Marijana; Judaš, Nenad; Sabolović, Jasmina

Combined Experimental and Computational Study of cis-trans Isomerism in Bis(L-valinato)copper(II) // Inorganic chemistry, 50 (2011), 8; 3632-3644 doi:10.1021/ic102585f (međunarodna recenzija, članak, znanstveni)

doi pubs.acs.org dx.doi.org

59.

Tomić, Antonija; Abramić, Marija; Špoljarić, Jasminka; Agić, Dejan; Smith, David M.; Tomić, Sanja

Human Dipeptidyl Peptidase III: Insights into Ligand Binding from a Combined Experimental and Computational Approach // Journal of molecular recognition, 24 (2011), 5; 804-814 doi:10.1002/jmr.1115 (međunarodna recenzija, članak, znanstveni)

doi onlinelibrary.wiley.com

60.

Groger, Kathrin; Baretić, Domagoj; Piantanida, Ivo; Marjanović, Marko; Kralj, Marijeta; Grabar, Marina; Tomić, Sanja; Schmuck, Carsten

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 (2011), 1; 198-209 doi:10.1039/C0OB00103A (međunarodna recenzija, članak, znanstveni)

doi pubs.rsc.org

61.

Šikić, Kresimir; Tomić, Sanja; Carugo, Oliviero

Systematic comparison of crystal and NMR protein structures deposited in the protein data bank // The Open biochemistry journal, 4 (2010), 83-95 doi:10.2174/1874091X01004010083 (podatak o recenziji nije dostupan, članak, znanstveni)

doi benthamopen.com

62.

Janjić, Saša

Predviđanje mjesta sekundarne strukture protein iz slijeda aminokiselinskih ostataka, 2010., diplomski rad, Fakultet Elektrotehnike i računarstva, Zagreb

complex.zesoi.fer.hr

63.

Čanadi, Igor

Alat za prianjanje proteina: modul za pripremu prianjanja, 2010., diplomski rad, preddiplomski, Fakultet Elektrotehnike i računarstva, Zagreb

Pristup cjelovitom tekstu rada

64.

Tus, Alan

Baza podataka metala u proteinima, 2010., diplomski rad, preddiplomski, Fakultet elektrotehnike i računarstva, Zagreb

complex.zesoi.fer.hr

65.

Smith, Ana-Sunčana

Physics challenged by cells // Nature Physics, 6 (2010), 10; 726-729 doi:10.1038/nphys1798 (međunarodna recenzija, članak, znanstveni)

doi

66.

Smith, Ana-Sunčana; Fenz, Susanne Franzoska; Sengupta, Kheya

Inferring spatial organization of bonds within adhesion clusters by exploiting fluctuations of soft interfaces // Europhysics Letters, 89 (2010), 2; 28003-1 doi:10.1209/0295-5075/89/28003 (međunarodna recenzija, članak, znanstveni)

doi iopscience.iop.org

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Matija Piškorec

Multiresolution analysis of macromolecular structures, 2010., diplomski rad, diplomski, Fakultet elektrotehnike i računarstva, Zagreb

Pristup cjelovitom tekstu rada complex.zesoi.fer.hr

68.

Antulov-Fantulin, Nino

Alat za prianjanje proteina: moduli za rotaciju i vrednovanje rezultata, 2010., diplomski rad, diplomski, Fakultet elektrotehike i računarstva, Zagreb

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69.

Čolić, Dragana

Alat za prianjanje proteina: modul za utvrđivanje interakcija, 2010., diplomski rad, diplomski, Fakultet Elektrotehnike i računarstva, Zagreb

Pristup cjelovitom tekstu rada

70.

Musiani, Francesco; Bertoša, Branimir; Magistrato, Alessandra; Zambelli, Barbara; Turano, Paola; Losasso, Valeria; Micheletti, Cristian; Ciurli, Stefano; Carloni, Paolo

Computational Study of the DNA-Binding Protein Helicobacter pylori NikR: The Role of Ni2+ // Journal of chemical theory and computation, 6 (2010), 11; 3503-3515 doi:10.1021/ct900635z (međunarodna recenzija, članak, znanstveni)

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The 5th Central European Conference - Chemistry towards Biology / Abramić, Marija ; Maksić, Zvonimir ; Salopek-Sondi, Branka ; Tomić, Sanja ; Robert Vianello (ur.). Zagreb: Institut Ruđer Bošković, 2010 (zbornik)

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Bertoša, Branimir; Tomić, Sanja; Aleksić, Maja; Karminski-Zamola, Grace

QSAR analysis and proposal of new heterocyclic compounds with potential antitumor activity // The 5th Central European Conference - Chemistry towards Biology
Zagreb: Institut Ruđer Bošković, 2010. str. 66-66 (poster, međunarodna recenzija, sažetak, znanstveni)

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73.

Šimunović, Mijo

Thermodynamics of ligand binding to auxin amidohydrolase, 2010., diplomski rad, diplomski, Prirodoslovno-matematički fakultet, Zagreb

74.

Grabar, Marina; Tomić, Sanja; Tumir, Lidija-Marija; Piantanida, Ivo; Crnolatac, Ivo

Molecular modelling of phosphonium cyanine dyes in complex with DNA // Book of Abstracts of the The 5th Central European Conference - Chemistry towards Biology
Zagreb: Institut Ruđer Bošković, 2010. (poster, sažetak, znanstveni)

75.

Marković, Marijana; Sabolović, Jasmina

Molecular modeling of crystallization processes of trans and cis bis(L-valinato)copper(II) from aqueous solution // Book Of Abstracts, The 5th Central European Conference – Chemistry towards Biology / Abramić, Marija ; Maksić, Zvonimir, Salopek-Sondi, Branka ; Tomić, Sanja ; Vianello, Robert (ur.).
Zagreb: Institut Ruđer Bošković, 2010. str. 101-101 (poster, međunarodna recenzija, sažetak, znanstveni)

76.

Marković, Marijana; Judaš, Nenad; Sabolović, Jasmina

Molecular modeling in crystalline surroundings and single-crystal X-ray diffraction of trans and cis bis(L-valinato)copper(II) crystal and molecular structures // Book of Abstracts and Program, 10th International Symposium and Summer School on Bioanalysis / Matković-Čalogović, Dubravka ; Milić, Dalibor ; Prugovečki, Biserka ; Galić, Nives (ur.).
Zagreb, 2010. str. 61-61 (predavanje, međunarodna recenzija, sažetak, znanstveni)

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Grabar, Marina; Tomić, Sanja; Tumir, Lidija-Marija; Piantanida, Ivo; Crnolatac, Ivo; Deligeorgiev, Todor; Vasilev, Alexey; Kaloyanova, Stefka

Interaction of phosphonium cyanine dyes with DNA // Abstracts of the Fourth Humboldt Conference on Computational Chemistry / Petrova, P. Galina ; Vayssilov, N. Georgie (ur.).
Sofija, 2010. (poster, sažetak, znanstveni)

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Bertoša, Branimir; Aleksić, Maja; Karminski-Zamola, Grace; Tomić, Sanja

QSAR analysis of antitumor active amides and quinolones from thiophene series // International journal of pharmaceutics, 394 (2010), 1-2; 106-114 doi:10.1016/j.ijpharm.2010.05.014 (međunarodna recenzija, članak, znanstveni)

doi www.sciencedirect.com doi.org

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Tomić, Antonija; Špoljarić, Jasminka; Abramić, Marija; Tomić, Sanja

Ligand binding to human DPP III and its mutant H568N - computational analyses // Abstracts of the 6th International Workshop on New Approaches in Drug Design & Discovery "The Interactions :From Atom-Atom Contacts to Networks in System Biology" / Klebe, Gerhard ; Matter, Hans ; Sotriffer, Hans (ur.).
Marburg: University of Marburg, 2010. str. 87-87 (poster, međunarodna recenzija, sažetak, znanstveni)

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Burja, Bojan; Čimbora-Zovko, Tamara; Tomić, Sanja; Jelušić, Tihana; Kočevar, Marijan; Polanc, Slovenko; Osmak, Maja

Pyrazolone-fused combretastatins and their precursors : synthesis, cytotoxicity, antitubulin activity and molecular modeling studies // Bioorganic & medicinal chemistry, 18 (2010), 7; 2375-2387 doi:10.1016/j.bmc.2010.03.006 (međunarodna recenzija, članak, znanstveni)

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Tumir, Lidija-Marija; Grabar, Marina; Tomić, Sanja; Piantanida, Ivo

The interactions of bis-phenanthridinium – nucleobase conjugates with nucleotides: adenine conjugate recognizes UMP in aqueous medium // Tetrahedron, 66 (2010), 13; 2501-2513 doi:10.1016/j.tet.2010.01.063 (međunarodna recenzija, članak, znanstveni)

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The 3rd Adriatic Meeting on Computational Solutions in Life Sciences : book of abstracts / Babić, Darko ; Došlić, Nadja ; Smith, David ; Tomić, Sanja ; Vlahoviček, Kristian (ur.). Zagreb: Institute of Computational Life Sciences (ICLS), 2009 (zbornik)

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Grabar, Marina; Tumir, Lidija-Marija; Piantanida, Ivo; Tomić, Sanja

Computational approach to specificity of intercalators toward nucleotides // Book of Abstracts of the Tenth international summer school on biophysics - supramolecular structure and function
Rovinj, 2009. (poster, sažetak, ostalo)

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Marković, Marijana; Gomzi, Vjeran; Sabolović, Jasmina

Molecular modelling of copper(II) complexes with histidine // Book of Abstracts, Tenth International Summer School on Biophysics Supramolecular structure and function / Pifat-Mrzljak, Greta ; Zahradka, Ksenija (ur.).
Zagreb: Institut Ruđer Bošković, 2009. str. 132-132 (poster, međunarodna recenzija, sažetak, znanstveni)

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85.

Marković, Marijana; Sabolović, Jasmina

Can the MD simulations of solvated trans and cis bis(L-valinato)copper(II) molecules in aqueous solution reveal the reasons for crystallisation of specific conformers? // Book Of Abstracts, The 3rd Adriatic Meeting on Computational Solutions in the Life Sciences / Tomić, Sanja (ur.).
Zagreb: Centre for Computational Solutions in the Life Sciences, Ruđer Bošković Institute, 2009. str. 66-66 (poster, međunarodna recenzija, sažetak, znanstveni)

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86.

Grabar, Marina; Tumir, Lidija-Marija; Piantanida, Ivo; Tomić, Sanja

Computational and spectroscopic studies of intercalators and their interaction with nucleotides // Book of Abstracts of The third Adriatic Meeting on computational Solutions in the Life Sciences
Zagreb: Institut Ruđer Bošković, 2009. (poster, sažetak, ostalo)

87.

Grabar, Marina; Tumir, Lidija-Marija; Piantanida, Ivo; Tomić, Sanja

Bisphenanthridinium-nucleobase conjugates – molecular modelling and spectroscopic approach // Book of Abstracts of the EMBO Young Scientists Forum
Zagreb, 2009. (poster, sažetak, ostalo)

88.

Savić, Bojana; Tomić, Sanja; Magnus, Volker; Gruden, Kristina; Barle, Katja; Grenković, Renata; Salopek-Sondi, Branka; Jutta Ludwig-Müller

Auxin amidohydrolases from Brassica rapa cleave conjugates of indole propionic and indole butyric acid as preferable substrates: A biochemical and modeling approach // ACPD 2009, Auxins and Cytokinins in Plant Development, Book of Abstracts
Prag, 2009. str. 22-22 (predavanje, međunarodna recenzija, sažetak, znanstveni)

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Savić, Bojana; Tomić, Sanja; Magnus, Volker; Gruden, Kristina; Barle, Katja; Grenković, Renata; Ludwig-Müller, Jutta; Salopek-Sondi, Branka

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 (2009), 9; 1587-1599 doi:10.1093/pcp/pcp101 (međunarodna recenzija, članak, znanstveni)

doi academic.oup.com doi.org

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Marković, Marijana; Judaš, Nenad; Sabolović, Jasmina

MM calculations of unit cell packings of aquabis(L-valinato)copper(II) in simulated crystal lattice // EMBO Young Scientists Forum Book of Abstracts
Zagreb, Hrvatska, 2009. str. 37-37 (poster, međunarodna recenzija, sažetak, znanstveni)

www.bioinfo.hr

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Smith, Ana-Sunčana; Sackmann, Erich

Progress in mimetic studies of cell adhesion and the mechanosensing // ChemPhysChem, 10 (2009), 1; 66-78 doi:10.1002/cphc.200800683 (međunarodna recenzija, članak, znanstveni)

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Sabolović, Jasmina; Gomzi, Vjeran

Structure Prediction of Bis(amino acidato)copper(II) Complexes with a New Force Field for Molecular Modeling // Journal of Chemical Theory and Computation, 5 (2009), 7; 1940-1954 doi:10.1021/ct9000203 (međunarodna recenzija, članak, znanstveni)

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Sabolović, Jasmina

Molecular Mechanics (MM) Force Fields for Modelling of Copper(II) Amino Acid Complexes in Different Environments // AIP conference proceedings, 1102 (2009), 1; 193-199 doi:10.1063/1.3108374 (podatak o recenziji nije dostupan, conference paper, znanstveni)

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Ćaleta, Irena; Kralj, Marijeta; Marjanović, Marko; Bertoša, Branimir; Tomić, Sanja; Pavlović, Gordana; Pavelić, Krešimir; Karminski-Zamola, Grace

Novel Cyano- and Amidino- Benzothiazole Derivatives: Synthesis, Antitumor Evaluation, X-ray and QSAR Analysis // Journal of medicinal chemistry, 52 (2009), 6; 1744-1756 doi:10.1021/jm801566q (međunarodna recenzija, članak, znanstveni)

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Šikić, Mile; Tomić, Sanja; Vlahoviček, Kristian

Prediction of Protein-Protein Interaction Sites in Sequences and 3D Structures by Random Forests // Plos computational biology, 5 (2009), 1; e1000278-1 doi:10.1371/journal.pcbi.1000278 (međunarodna recenzija, članak, znanstveni)

doi fulir.irb.hr journals.plos.org

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Vujasinović, Ines; Mlinarić-Majerski, Kata; Bertoša, Branimir; Tomić, Sanja

Influence of the Rigid Spacer to Macrocyclization of Poly(thialactones): Synthesis and Computational Analysis // Journal of physical organic chemistry, 22 (2009), 5; 431-437 doi:10.1002/poc.1479 (međunarodna recenzija, članak, znanstveni)

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97.

Sović, Ivan

Vizualizacija makromolekula, 2008., diplomski rad, preddiplomski, Fakultet elektrotehnike i računarstva, Zagreb

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98.

Grabar, Marina; Tumir, Lidija-Marija; Piantanida, Ivo; Tomić, Sanja

Molecular modelling of bisphenanthridinium- nucleobase conjugates // Book of Abstracts of the MATH/CHEM/COMP - The Dubrovnik International Course on the Interfaces among Mathematics, Chemistry and Computer Sciences / A. Graovac, B. Pokrić, V. Smrečki (ur.).
Zagreb: Institut Ruđer Bošković, 2008. (poster, sažetak, ostalo)

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Grabar, Marina; Tumir, Lidija-Marija; Piantanida, Ivo; Tomić, Sanja

Molecular modelling of bisphenanthridinium- nucleobase conjugates // Book of Abstracts of the International Conference and Biophysics Summmer School From Solid State to Biophysics IV / L. Forro, D. Pavuna (ur.).
Cavtat, Hrvatska: EPFL, 2008. (poster, sažetak, ostalo)

100.

Reister Gottfried, Ellen; Sengupta, Kheya.; Lorz, Barbara; Sackmann, Erich; Seifert, Udo; Smith, Ana-Sunčana

Dynamics of Specific Vesicle-Substrate Adhesion : From Local Events to Global Dynamics // Physical Review Letters, 101 (2008), 20; 208103-1 doi:10.1103/PhysRevLett.101.208103 (međunarodna recenzija, članak, znanstveni)

doi prl.aps.org