Publikacije

2013

1. Luo Jinghui, Yu Chien-Hung, Yu Huixin, Borštnar Rok, Kamerlin Shina Caroline Lynn, Gräslund Astrid, Abrahams Jan-Pieter, Wärmländer Sebastian K. T. S., Cellular polyamines promote amyloid-beta (A [beta] ) peptide fibrillation and modulate the aggregation pathways, ACS chemical neuroscience, 2013, str. A-I, DOI

2. Kolšek Katra, Sollner Dolenc Marija, Mavri Janez, Computational study of reactivity of bisphenol A-3,4-quinone with deoxyadenosine and glutathione, Chemical research in toxicology, 2013, vol. 26, no. 1, str. 106-111, DOI, Full Text

3. Zidar Jernej, Pavlin Matic, Mihelič Igor, Ogorelec Primož, Plavec Janez, Mavri Janez, Stability and reactivity of progressively methylolated melamine derivatives, Computational and theoretical chemistry, 2013, vol. 1006, str. 85-91, DOI, Full Text

4. Molčanov Krešimir, Kojić-Prodić Biserka, Babić Darko, Stare Jernej, Face-to-face stacking of dianionic quinoid rings in crystals of alkali salts of 2,5-dihydroxyquinone in view of [pi]-system polarization : Elektronski vir, CrystEngComm, 2013, vol. 15, iss. 1, str. 135-143, DOI, Full Text

5. Minovski Nikola, Perdih Andrej, Novič Marjana, Šolmajer Tomaž, Cluster-based molecular docking study for in silico identification of novel 6-fluoroquinolones as potential inhibitors against mycobacterium tuberculosis, Journal of computational chemistry, 2013, vol. 34, no. 9, str. 790-801, DOI

6. Glušič Martina, Stare Jernej, Grdadolnik Jože, Vianello Robert, Binding of cadmium dication to glutathione facilitates cysteine SH deprotonation : a computational DFT study, Journal of inorganic biochemistry, 2013, vol. 119, str. 90-94, DOI

7. Mavri Janez, Can the chemical reactivity of an ultimate carcinogen be related to its carcinogenicity? : an application to propylene oxide, Toxicology in vitro, 2013, vol. 27, no. 1, str. 479-485, DOI

8. Pogorelčnik Barbara, Perdih Andrej, Šolmajer Tomaž, Recent advances in the development of catalytic inhibitors of human DNA topoisomerase II[alpha] as novel anticancer agents, Current medicinal chemistry, 2013, vol. 20, no. 5, str. 694-709

9. Pogorelčnik Barbara, Perdih Andrej, Šolmajer Tomaž, Recent developments of DNA poisons - human DNA topoisomerase II[alpha] inhibitors - as anticancer agents, Current pharmaceutical design, 2013, vol. 19, iss. 13, str. 2474-2488, DOI

2012

1. Brvar Matjaž, Perdih Andrej, Hodnik Vesna, Renko Miha, Anderluh Gregor, Jerala Roman, Šolmajer Tomaž, In silico discovery and biophysical evaluation of novel 5-(2-hydroxybenzylidene) rhodanine inhibitors of DNA gyrase B, Bioorganic & Medicinal Chemistry, 2012, vol. 20, iss. 8, str. 2572-2580, Full Text

2. Erić Slavica, Ke Song, Barata Teresa, Šolmajer Tomaž, Stanković Jelena, Juranić Zorica, Savić Vladimir M., Zloh Mire, Target fishing and docking studies of the novel derivatives of aryl-aminopyridines with potential anticancer activity, Bioorganic & Medicinal Chemistry, 2012, vol. 20, issue 17, str. 5220-5228, DOI, Full Text

3. Perdih Andrej, Šolmajer Tomaž, MurD ligase from Escherichia coli: C-terminal domain closing motion, Computational and theoretical chemistry, 2012, vol. 979, str. 73-81, DOI, Full Text

4. Vianello Robert, Repič Matej, Mavri Janez, How are biogenic amines metabolized by monoamine oxidases?, European journal of organic chemistry, 2012, vol. 2012, iss. 36, str. 7057-7065, DOI

5. Abdallah Hassan H., Mavri Janez, Repič Matej, Lee Vannajan Sanghiran, Wahab Habibah A., Chemical reaction of soybean flavonoids with DNA : a computational study using the implicit solvent model, International journal of molecular sciences, 2012, vol. 13, no. 2, str. 1269-1283, Full Text

6. Tratar-Pirc Elizabeta, Zidar Jernej, Bukovec Peter, A computational study of calcium(II) and copper(II) ion binding to the hyaluronate molecule, International journal of molecular sciences, 2012, vol. 13, no. 9, str. 12036-12045, DOI

7. Borštnar Rok, Repič Matej, Kamerlin Shina Caroline Lynn, Vianello Robert, Mavri Janez, Computational study of the pK[sub]a values of potential catalytic residues in the active site of monoamine oxidase B, Journal of chemical theory and computation, 2012, vol. 8, iss. 10, str. 3864-3870, DOI, Full Text

8. Djerdj Igor, Popović Jasminka, Stare Jernej, Ambrožič Gabriela, Škapin Srečo D., Kozlevčar Bojan, Pajić Damir, Jagličić Zvonko, Crnjak Orel Zorica, Nanocrystalline hybrid inorganic-organic one-dimensional chain systems tailored with 2- and 3-phenyl ring monocarboxylic acids, Journal of materials chemistry, 2012, vol. 22, no. 20, str. 10255-10265, DOI

9. Brvar Matjaž, Perdih Andrej, Renko Miha, Anderluh Gregor, Turk Dušan, Šolmajer Tomaž, Structure-based discovery of substituted 4,5`-bithiazoles as novel DNA gyrase inhibitors, Journal of medicinal chemistry, 2012, vol. 55, issue 14, str. 6413-6426, DOI, Full Text

10. Minovski Nikola, Perdih Andrej, Šolmajer Tomaž, Combinatorially-generated library of 6-fluoroquinolone analogs as potential novel antitubercular agents : a chemometric and molecular modeling assessment, Journal of molecular modeling, 2012, vol. 18, no. 5, str. 1735-1753, DOI, Full Text

11. Kearley G. J., Stare Jernej, Kutteh Ramzi, Daemen Luke L., Hartl Monika A., Eckert Jürgen, Methyl dynamics flattens barrier to proton transfer in crystalline tetraacetylethane, The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2012, vol. 116, no. 9, str. 2283-2291, Full Text

12. Brela Mateusz Zbigniew, Stare Jernej, Pirc Gordana, Sollner Dolenc Marija, Boczar Marek, Wojcik Marek Janusz, Mavri Janez, Car-parrinello simulation of the vibrational spectrum of a medium strong hydrogen bond by two-dimensional quantization of the nuclear motion: application to 2-hydroxy-5-ntrobenzamide, The journal of physical chemistry. B, Materials, surfaces, interfaces & biophysical, 2012, vol. 116, issue 15, str. 4510-4518, DOI, Full Text

13. Pirc Gordana, Mavri Janez, Novič Marjana, Stare Jernej, Virtually nonexistent correlation between the OH stretching frequency and the instantaneous geometry in the short hydrogen bond of sodium hydrogen bis(sulfate) : advanced chemometrics analysis, The journal of physical chemistry. B, Materials, surfaces, interfaces & biophysical, 2012, vol. 116, issue 24, str. 7221-7231, DOI, Full Text

14. Vianello Robert, Mavri Janez, Microsolvation of the histamine monocation in aqueous solution : the effect on structure, hydrogen bonding ability and vibrational spectrum, New journal of chemistry, 2012, vol. 36, issue 4, str. 954-962, Full Text

15. Perdih Andrej, Roy Choudhury Amrita, Župerl Špela, Sikorska Emilia, Zhukov Igor, Šolmajer Tomaž, Novič Marjana, Structural analysis of a peptide fragment of transmembrane transporter protein bilitranslocase, PloS one, 2012, vol. 7, iss. 6, str. e38967-1-e38967-14, Full Text

16. Kolšek Katra, Mavri Janez, Sollner Dolenc Marija, Reactivity of bisphenol A-3,4-quinone with DNA. A quantum chemical study, Toxicology in vitro, 2012, vol. 26, no. 1, str. 102-106, DOI, Full Text

17. Pirc Gordana, Mavri Janez, Stare Jernej, Program package for numerical solving time-independent Schrödinger equation for vibrational problems: Inclusion of coordinate dependent reduced masses, Vibrational Spectroscopy, 2012, vol. 58, str. 153-162, DOI

18. Jukič Marko, Perdih Andrej, Šolmajer Tomaž, Integriran pristop iskanja spojin vodnic naravnega izvora z uporabo eksperimentalnih in računalniško podprtih metod = Integrated approach in the search of novel natural products as lead compounds using experimental and computer-based approaches, Farmacevtski vestnik, 2012, vol. 63, no. 1, str. 54-63

19. Barrozo Alexandre, Borštnar Rok, Marloie Gaël, Kamerlin Shina Caroline Lynn, Computational protein engineering : bridging the gap between rational design and laboratory evolution, International journal of molecular sciences, 2012, vol. 13, no. 10, str. 12428-12460, DOI

2011

1. Stare Jernej, A highly accurate, analytic potential energy surface of the hydrogendifluoride anion in the gas phase, Acta chimica slovenica, 2011, vol. 58, no. 3, str. 501-508, Full Text

2. Stare Jernej, Hartl Monika, Daemen Luke, Eckert Jürgen, The very short hydrogen bond in the pyridine N-oxide - trichloroacetic acid complex: an inelastic neutron scattering and computational study, Acta chimica slovenica, 2011, vol. 58, no. 3, str. 521-527, Full Text

3. Minovski Nikola, Jezierska-Mazzarello Aneta, Vračko Marjan, Šolmajer Tomaž, Investigation of 6-fluoroquinolones activity against Mycobacterium tuberculosis using theoretical molecular descriptors : a case study, Central European Journal of Chemistry, 2011, vol. 9, no. 5, str. 855-866, DOI

4. Borštnar Rok, Repič Matej, Kržan Mojca, Mavri Janez, Vianello Robert, Irreversible inhibition of monoamine oxidase B by the antiparkinsonian medicines rasagiline and selegiline : a computational study, European journal of organic chemistry, 2011, vol. 2011, issue 32, str. 6419-6433, DOI

5. Kržan Andrej, Mavri Janez, Atomic volume as a descriptor for carbon electronic structure and stability, Journal of organic chemistry, 2011, vol. 76, issue 6, str. 1891-1893, DOI

6. Biliškov Nikola, Kojić-Prodić Biserka, Mali Gregor, Molčanov Krešimir, Stare Jernej, A partial proton transfer in hydrogen bond O-H [times] [times] [times] O in crystals of anhydrous potassium and rubidium complex chloranilates, The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2011, vol. 115, no. 14, str. 3154-3166

7. Zidar Jernej, Merzel Franci, Probing amyloid-beta fibril stability by increasing ionic strengths, The journal of physical chemistry. B, Condensed matter, materials, surfaces, interfaces & biophysical, 2011, vol. 115, no. 9, str. 2075-2081, DOI

8. Stare Jernej, Mavri Janez, Grdadolnik Jože, Zidar Jernej, Maksić Zvonimir B., Vianello Robert, Hydrogen bond dynamics of histamine monocation in aqueous solution : Car-Parrinello molecular dynamics and vibrational spectroscopy study, The journal of physical chemistry. B, Condensed matter, materials, surfaces, interfaces & biophysical, 2011, vol. 115, no. 19, str. 5999-6010, DOI

9. Minovski Nikola, Vračko Marjan, Šolmajer Tomaž, Quantitative structure-activity relationship study of antitubercular fluoroquinolones, Molecular diversity, 2011, vol. 15, no. 2, str. 417-426, DOI

10. Perdih Andrej, Sollner Dolenc Marija, Recent advances in the synthesis of unnatural [alpha]-amino acids - an updated version, Current organic chemistry, 2011, vol. 15, no. 22, str. 3750-3799, Full Text

2010

1. Minovski Nikola, Šolmajer Tomaž, Chemometrical exploration of combinatorially generated drug-like space of 6-fluoroquinolone analogs : a QSAR study, Acta chimica slovenica, 2010, vol. 57, no. 3, str. 529-540

2. Brvar Matjaž, Perdih Andrej, Oblak Marko, Peterlin-Mašič Lucija, Šolmajer Tomaž, In silico discovery of 2-amino-4-(2,4-dihydroxyphenyl)thiazoles as novel inhibitors of DNA gyrase B, Bioorganic & Medicinal Chemistry Letters, 2010, vol. 20, iss. 3, str. 958-962, DOI, Full Text

3. Perdih Andrej, Sollner Dolenc Marija, Small molecule antagonists of integrin receptors, Current medicinal chemistry, 2010, vol. 17, no. 22, str. 2371-2392

4. Štefane Bogdan, Perdih Andrej, Pevec Andrej, Šolmajer Tomaž, Kočevar Marijan, The participation of 2H-pyran-2-ones in [4+2] cycloadditions : an experimental and computational study, European journal of organic chemistry, 2010, vol. 2010, issue 30, str. 5870-5883, DOI

5. Pirc Gordana, Stare Jernej, Mavri Janez, Car-Parrinello simulation of hydrogen bond dynamics in sodium hydrogen bissulfate, The Journal of chemical physics, 2010, vol. 132, no. 22, str. 224506-1-224506-7, DOI

6. Perdan-Pirkmajer Katja, Mavri Janez, Kržan Mojca, Histamine (re)uptake by astrocytes : an experimental and computational study, Journal of molecular modeling, 2010, letn. 6, št. 1, str. 1151-1158, DOI

7. Borštnar Rok, Roy Choudhury Amrita, Stare Jernej, Novič Marjana, Mavri Janez, Calculation of pK [sub] a values of carboxylic acids : application to bilirubin, Journal of Molecular Structure. Theochem, 2010, vol. 947, no. 1-3, str. 76-82, DOI, Full Text

8. Perdih Andrej, Kotnik Miha, Oblak Marko, Šolmajer Tomaž, Uporaba računalniške kemije pri načrtovanju in iskanju novih spojin vodnic = The use of computational chemistry in the design and screening of novel lead compounds, Farmacevtski vestnik, 2010, let. 61, št. 4, str. 195-202

9. Kamerlin Shina Caroline Lynn, Mavri Janez, Warshel Arieh, Examining the case for the effect of barrier compression on tunneling vibrationally enhanced catalysis, calalytic entropy and related issues, FEBS letters, 2010, vol. 584, no. 13, str. 2759-2766, DOI

10. Kolšek Katra, Zidar Jernej, Sollner Dolenc Marija, Mavri Janez, Kvantno kemijsko modeliranje elementarne S[subN]1 in S[subN]2 reakcije v vodni raztopini, Kemija v šoli in družbi, 2010, let. 22, št. 4, str. 12-16

2009

1. Paukner Susanne, Hesse Lars, Preželj Andrej, Šolmajer Tomaž, Urleb Uroš, In vitro activity of LK-157, a novel tricyclic carbapenem as broad-spectrum beta-lactamase inhibitor, Antimicrobial agents and chemotherapy, 2009, no. 2, vol. 53, str. 505-511

2. Perdih Andrej, Kovač Andreja, Wolber Gerhard, Blanot Didier, Gobec Stanislav, Šolmajer Tomaž, Discovery of novel benzene 1,3-dicarboxylic acid inhibitors of bacterial MurD and MurE ligases by structure-based virtual screening approach, Bioorganic & Medicinal Chemistry Letters, 2009, vol. 19, no. 10, str. 2668-2673, DOI, Full Text

3. Xu Dong, Stare Jernej, Cooksy Andrew L., Solving the vibrational Schrödinger equation on an arbitrary multidimensional potential energy surface by the finite element method, Computer physics communications, 2009, vol. 180, no. 11, str. 2079-2094

4. Kržan Mojca, Mavri Janez, Carcinogenicity of styrene oxide : calculation of chemical reactivity, Croatica chemica acta, 2009, vol. 82, no. 1, str. 317-322

5. Stare Jernej, Henson Neil J., Eckert Jürgen, Mechanistic aspects of propene epoxidation by hydrogen peroxide. Catalytic role of water molecules, external electric field, and zeolite framework of TS-1, Journal of chemical information and modeling, 2009, vol. 49, issue 4, str. 833-846

6. Perdih Andrej, Bren Urban, Šolmajer Tomaž, Binding free energy calculations of N-sulphonyl-glutamic acid inhibitors of MurD ligase, Journal of molecular modeling, 2009, vol. 15, no. 8, str. 983-996

7. Zidar Jernej, Merzel Franci, Hodošček Milan, Rebolj Katja, Sepčić Kristina, Maček Peter, Janežič Dušanka, Liquid-ordered phase formation in cholesterol/sphingomyelin bilayers : all-atom molecular dynamics simulations, The journal of physical chemistry. B, Condensed matter, materials, surfaces, interfaces & biophysical, 2009, vol. 113, no. 48, str. 15795-15802

8. Mohaček-Grošev Vlasta, Grdadolnik Jože, Stare Jernej, Hadži Dušan, Identification of hydrogen bond modes in polarized Raman spectra of single crystals of [alpha]-oxalic acid dihydrate, Journal of Raman spectroscopy, 2009, issue 11, vol. 40, str. 1605-1614, DOI

9. Perdih Andrej, Hodošček Milan, Šolmajer Tomaž, MurD ligase from E. coli : tetrahedral intermediate formation study by hybrid quantum mechanical/molecular mechanical replica path method, Proteins, 2009, vol. 74, no. 3, str. 744-759, DOI, Full Text

2008

1. Pirc Gordana, Stare Jernej, Titanium site preference problem in the TS-1 zeolite catalyst : a periodic Hartree-Fock study, Acta chimica slovenica, 2008, vol. 55, no. 4, str. 951-959

2. Galeša Katja, Bren Urban, Kranjc Agata, Mavri Janez, Carcinogenicity of acrylamide : a computational study, Journal of agricultural and food chemistry, 2008, vol. 56, no. 18, str. 8720-8727, DOI, Full Text

3. Zidar Jernej, Tratar-Pirc Elizabeta, Hodošček Milan, Bukovec Peter, Copper(II) ion binding to cellular prion protein, Journal of chemical information and modeling, 2008, vol. 48, no. 2, str. 283-287

4. Humljan Jan, Kotnik Miha, Contreras-Martel Carlos, Blanot Didier, Urleb Uroš, Dessen Andréa, Šolmajer Tomaž, Gobec Stanislav, Novel naphthalene-N-sulfonyl-d-glutamic acid derivatives as inhibitors of MurD, a key peptidoglycan biosynthesis enzyme, Journal of medicinal chemistry, 2008, vol. 51, no. 23, str. 7486-7494

5. Zega Anamarija, Srčič Stanko, Mavri Janez, Bešter-Rogač Marija, Molecular interactions of 1,4-dihydropyridine derivatives with selected organic solvents : a volumetric, spectroscopic and computational study, Journal of molecular structure, 2008, issues 1/3, vol. 875, str. 354-363

6. Bren Urban, Kržan Andrej, Mavri Janez, Microwave catalysis through rotationally hot reactive species, The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2008, vol. 112, no. 2, str. 166-171

7. Stare Jernej, Panek Jaroslaw J., Eckert Jürgen, Grdadolnik Jože, Mavri Janez, Hadži Dušan, Proton dynamics in the strong chelate hydrogen bond of crystalline picolinic acid n-oxide. A new computational approach and infrared, Raman and INS study, The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2008, vol. 112, no. 7, str. 1576-1586

8. Piccoli Paula, Koetzle Thomas, Schultz Arthur, Zhurova Elizabeth, Stare Jernej, Pinkerton Alan, Eckert Jürgen, Hadži Dušan, Variable temperature neutron diffraction and X-ray charge density studies of tetraacetylethane, The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2008, vol. 112, no.29, str. 6667-6677

9. Mavri Janez, Liu Hanbin, Olsson Mats H. M., Warshel Arieh, Simulation of tunneling in enzyme catalysis by combining a biased propagation approach and the quantum classical path method : application to lipoxygenase, The journal of physical chemistry. B, Condensed matter, materials, surfaces, interfaces & biophysical, 2008, issue 19, vol. 112, str. 5950-5954, DOI, Full Text

10. Pumpernik Danilo, Oblak Borut Tone, Borštnik Branko, Replication slippage versus point mutation rates in short tandem repeats of the human genome, Molecular genetics and genomics, 2008, vol. 279, no. 1, str. 53-61

11. Mlinšek Gregor, Friedrich Reiner, Šolmajer Tomaž, Thrombin inhibitors with novel azaphenylalanine scaffolds and a new P1 binding pocket functionality : structural analysis of binding, Acta chimica slovenica, 2008, vol. 55, no. 4, str. 739-751