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2022

1. Herlah Barbara, Hoivik Andrej, Jamšek Luka, Valjavec Katja, Yamamoto Norio, Hoshino Tyuji, Kranjc Krištof, Perdih Andrej. Design, Synthesis and Evaluation of Fused Bicyclo[2.2.2]octene as a Potential Core Scaffold for the Non-Covalent Inhibitors of SARS-CoV-2 3CLpro Main Protease. Pharmaceuticals,  2022, vol. 15 iss. 5, [article no.] 539. Full Text

2. Maršavelski Aleksandra, Mavri Janez, Vianello Robert, Stare Jernej. Why Monoamine Oxidase B Preferably Metabolizes N-Methylhistamine over Histamine: Evidence from the Multiscale Simulation of the Rate-Limiting  Step. International journal of molecular sciences, 2022, vol. 23, iss. 3, [article no.] 1910. Full text

3. Vitorović-Todorović Maja, Cvijetić Ilija, Zloh Mile, Perdih Andrej. Molecular recognition of acetylcholinesterase and its subnanomolar reversible inhibitor: a molecular simulations study.  Journal Biomolecular Structure and Dynamics, 2022 vol. 40, 4, 1671-1691. Full text

4. Hok Lucija, Rimac Hrvoje, Mavri Janez, Vianello Robert. COVID-19 infection and neurodegeneration: Computational evidence for interactions between the SARS-CoV-2 spike protein and monoamine oxidase enzymes. Computational and Structural Biotechnology Journal2022, vol. 20, 1254-1263. Full text

5. Prašnikar Eva, Borišek, Jure, Perdih Andrej. Celična senescenca : nova terapevtska tarča pri zdravljenju s starostjo povezanih boleznih= Cell senescence : a new therapeutic target for the treatment of age-related diseases. Farmacevtski vestnik,  2022, vol. 73, 40 - 53. Full text

2021

1. Janežič, Matej, Valjavec, Katja, Bergant Loboda, Kaja, Herlah, Barbara, Ogris, Iza, Kozorog, Mirijam, Podobnik, Marjetka, Golič Grdadolnik, Simona, Wolber, Gerhard, Perdih, Andrej. Dynophore-based approach in virtual screening: a case of human DNA topoisomerase IIα. International journal of molecular sciences. 2021, vol. 22, iss. 24, [article no.] 13474 Full text

2. Prah Alja, Mavri Janez, Stare Jernej. An electrostatic duel: subtle differences in the catalytic performance of monoamine oxidase A and B isoenzymes elucidated at the residue level using quantum computations. Phys Chem Chem Phys2021, vol 23. 26459-26467 Full text

3. Prašnikar, Eva, Perdih, Andrej, Borišek, Jure. All-atom simulations reveal a key interaction network in the HLA-E/NKG2A/CD94 immune complex fine-tuned by the nonameric peptide. Journal of chemical information and modeling. 2021, vol. 61, iss. 7, str. 3593-3603. Full text

4. Kavčič, Hana, Umek, Nejc, Vintar, Neli, Mavri, Janez. Local anesthetics transfer relies on pH differences and affinities toward lipophilic compartments. Journal of physical organic chemistry. 2021, vol 34. e4275 Full link

5. Prašnikar, Eva, Perdih, Andrej, Borišek, Jure. Nonameric peptide orchestrates signal transduction in the activating HLA-E/NKG2C/CD94 immune complex as revealed by all-atom simulations. International journal of molecular sciences. 2021, vol. 22, iss. 13, [article no.] 6670. Full text

6. Stevanović S,  Marjanović DS, Trailović SM, Zdravković N, Perdih A, Nikolić K. Potential modulating effect of the Ascaris suum nicotinic acetylcholine receptor (nAChR) by compounds GSK575594A, diazepam and flumazenil discovered by structure-based virtual screening approach Molecular and Biochemical Parasitology, 2021, 242, 111350. Full text

7. Kavčič, Hana, Umek, Nejc, Pregeljc, Domen, Vintar, Neli, Mavri, Janez. Local anesthetics transfer across the membrane : reproducing octanol-water partition coefficients by solvent reaction field methodsActa chimica slovenica2021, vol. 68, Full Text

8. Kenda, Maša, Vegelj, Jan, Herlah, Barbara, Perdih, Andrej, Přemysl Mladěnka, Sollner Dolenc, Marija. Evaluation of firefly and renilla luciferase inhibition in reporter-gene assays: a case of Isoflavonoids.International journal of molecular sciences. 2021, vol. 22, no. 13, [article no.] 6927. Full text

9. Prašnikar Eva, Borišek, Jure, Perdih Andrej. Senescent cells as promising targets to tackle age-related diseases, Aging Research Reviews 2021, vol. 66, 101251. Full text

10. Prašnikar, Eva, Borišek, Jure, Perdih, Andrej. Staranje, celična senescenca in zdravljenje s starostjo povezanih bolezni.Proteus : ilustriran časopis za poljudno prirodoznanstvo. 2021, 83, [št.] 7, str. 295, 314-322. Full text

2020

1.Bergant Loboda Kaja, Janežič Matej, Štampar, Martina, Žegura, Bojana, Filipič, Metka, Perdih, Andrej. Substituted 4,5'-Bithiazoles as Catalytic Inhibitors of Human DNA Topoisomerase IIαJournal of chemical information and modeling2020, vol 60, str. 3662–3678. Full text

2. Prah Alja, Ogrin Peter, Mavri Janez, Stare Jernej. Nuclear quantum effects in enzymatic reactions: simulation of the kinetic isotope effect of phenylethylamine oxidation catalyzed by monoamine oxidase APhys Chem Chem Phys2020, vol 13, str. 6838-6847.Full text

3.Bergant Loboda, Kaja, Valjavec Katja, Štampar, Martina, Wolber, Gerhard, Žegura, Bojana, Filipič, Metka, Sollner Dolenc, Marija, Perdih, Andrej. Design and synthesis of 3,5-substituted 1,2,4-oxadiazoles as catalytic inhibitors of human DNA topoisomerase IIα,. Bioorganic chemistry 2020, vol. 99, str. 103828-1-103828-19. Full text

4. Kump J Karson, Miao Lei , Mady AS Ahmed, Ansari H Nurul, Shrestha K Uttar, Yang Yuting, Pal Mohan, Liao Chenzong, Perdih Andrej, Abulwerdi A Fardokht, Chinnaswamy Krishnapriya, Meagher L Jeniffer, Carlson M Jacob, Khanna May, Stuckey A Jeanne, Nikolovska-Coleska Zaneta. Discovery and Characterization of 2,5-Substituted Benzoic Acid Dual Inhibitors of the Anti-Apoptotic Mcl-1 and Bfl-1 Proteins.Journal of medicinal chemistry, 2020, vol. 63, str. 2489-2510. Full text

5. Pintar, Sara, Borišek, Jure, Usenik, Aleksandra, Perdih, Andrej, Turk, Dušan. Domain sliding of two Staphylococcus aureus N-acetylglucosaminidases enables their substrate-binding prior to its catalysis. Communications biology2020, vol. 3, str. 178-1-178-9. Full text

6. Pregeljc, Domen, Teodorescu-Prijoc, Diana, Vianello, Robert, Umek, Nejc, Mavri, Janez. How important is the use of cocaine and amphetamines in the development of Parkinson disease? A computational study. Neurotoxicity research2020, vol. 37, str. 724-731.Full text

7. Tandarič, Tana, Prah, Alja, Stare, Jernej, Mavri, Janez, Vianello, Robert. Hydride abstraction as the rate-limiting step of the irreversible inhibition of monoamine oxidase B by rasagiline and selegiline: a computational empirical valence bond studyInternational journal of molecular sciences. 2020, vol. 21, str. 6151-1-6151-13. Full text

8. Kržan Mojca, Keuschler Jan, Mavri, Janez, Vianello Robert,  Relevance of Hydrogen Bonds for the Histamine H2 Receptor-Ligand Interactions: A Lesson from Deuteration Biomolecules 2020, 10, 196. Full text

9. Hok Lucija, Mavri, Janez, Vianello Robert, The Effect of Deuteration on the H2 Receptor Histamine Binding Profile: A Computational Insight into Modified Hydrogen Bonding Interactions Molecules2020, vol. 25, str. 6017. Full text

10. Stare, Jernej, Gradišek, Anton, Seliger, Janez. Nuclear quadrupole resonance supported by periodic quantum calculations : a sensitive tool for precise structural characterization of short hydrogen bonds. PCCP. Physical chemistry chemical physics : a journal of European chemical societies. 2020, vol. 22, iss. 47, str. 27681-27689. Full text

2019

1. Prah, Alja, Frančišković, Eric, Mavri, Janez, Stare, Jernej. Electrostatics as the driving force behind the catalytic function of the monoamine oxidase a enzyme confirmed by quantum computationsACS catalysis2019, vol. 9, str. 1231-1240.Full text

2. Bergant  Kaja, Janežič Matej, Valjavec Katja, Sosič Izidor, Pajk Stane, Štampar Martina, Žegura Bojana, Gobec Stanislav, Filipič Metka, Perdih Andrej. Structure-guided optimization of 4,6-substituted-1,3,5-triazin-2(1H)-ones as catalytic inhibitors of human DNA topoisomerase IIαEuropean Journal of Medicinal Chemistry2019, vol. 175, str. 330-348. Full text

3. Sencanski Milan, Glisic Sanja, Šnajder Marko, Veljkovic Nevena, Poklar Ulrih Nataša, Mavri Janez & Vrecl Milka, Computational design and characterization of nanobody-derived peptides that stabilize the active conformation of the β2-adrenergic receptor (β2-AR) Scientific reports2019, vol. 9, str. 16555. Full text

4. Brela Mateusz Z., Prah Alja, Boczar Marek, Stare Jernej, Mavri Janez. Path integral calculation of the hydrogen/deuterium kinetic isotope effect in monoamine oxidase A-catalyzed decomposition of benzylamine. Molecules2019, vol. 24, str. 4359. Full text

5. Szutkowski, Kosma, Sikorska, Emilia, Bakanovych, Iulia, Roy Choudhury, Amrita, Perdih, Andrej, Jurga, Stefan, Novič, Marjana, Zhukov, Igor. Structural analysis and dynamic processes of the transmembrane segment inside different micellar environments-implications for the TM4 fragment of the bilitranslocase proteinInternational journal of molecular sciences2019, vol. 20, iss. 17, str. 4172-1-4172-21.Full text

6. Vitorović-Todorović D Maja, Worek Franz, Perdih Andrej, Bauk Đ Sonja, Vujatović B Tamara, Cvijetić N Ilija. The in vitro protective effects of the three novel nanomolar reversible inhibitors of human cholinesterases against irreversible inhibition by organophosphorous chemical warfare agents. Chem-Biol. Interact.2019, 309, 108714. Full text

7. Ivanovski, Vladimir, Mayerhőfer, Thomas G., Stare, Jernej, Klanjšek Gunde, Marta, Grdadolnik, Jože. Analysis of the polarized IR reflectance spectra of the monoclinic α-oxalic acid dihydrateSpectrochimica acta. Part A, Molecular and biomolecular spectroscopy2019, vol. 218, str. 1-8. Full text

8. Valjavec Katja, Perdih Andrej Razvoj zdravilnih učinkovin in metode računalniško podprtega načrtovanja, Proteus2019, 8/81, str. 398-406. Full text

2018

1. Mandy, Ahmed S.A., Liao, Chenzhong, Bajwa, Naval, Kump, Karson J., Abulwerdi, Fardokht A., Lev, Katherine, Miao, Lei, Grigsby, Sierrah M., Perdih, Andrej, Stuckey, Jeanne A., Du, Yuhong, Fu, Haian, Nikolovska-Coleska, Žaneta. Discovery of Mcl-1 inhibitors from integrated high throughput and virtual screeningScientific reports2018, vol. 8, str. 10210-1-10210-15. Full text

2. Borišek, Jure, Pintar, Sara, Ogrizek, Mitja, Turk, Dušan, Perdih, Andrej, Novič, Marjana. A water-assisted catalytic mechanism in glycoside hydrolases demonstrated on the Staphylococcus aureus autolysin EACS catalysis2018, vol. 8, no. 5, str. 4334-4345. Full text

3. Borišek, Jure, Pintar, Sara, Ogrizek, Mitja, Golič Grdadolnik, Simona, Hodnik, Vesna, Turk, Dušan, Perdih, Andrej, Novič, Marjana. Discovery of (phenylureido)piperidinyl benzamides as prospective inhibitors of bacterial autolysin E from Staphylococcus aureus. Journal of enzyme inhibition and medicinal chemistry, 2018, vol. 33, str. 1239-1247.Full text

4, Albreht Alen, Vovk, Irena, Mavri, Janez, Marco-Contelles, José, Ramsay, Rona R. Evidence for a cyanine link between propargylamine drugs and monoamine oxidase clarifies the inactivation mechanism. Frontiers in chemistry, 2018, vol. 6, str. 169-1-169-11.Full text

5. Vižintin, Alen, Bitenc, Jan, Kopač Lautar, Anja, Pirnat, Klemen, Grdadolnik, Jože, Stare, Jernej, Randon-Vitanova, Anna, Dominko, Robert. Probing electrochemical reactions in organic cathode materials via in operando infrared spectroscopy. Nature communications2018, vol. 9, str. 1-7. Full text

6. Stevanović, Strahinja, Perdih, Andrej, Sencanski, Milan, Glisic, Sanja, Duarte, Margarida, Tomás, Ana M., Sena, Filipa V., Sousa, Filipe M., Pereira, Manuela M., Šolmajer, Tomaž. In silico discovery of a substituted 6-methoxy-quinalidine with leishmanicidal activity in Leishmania infantumMolecules, 2018, vol. 23, iss. 4, str. 1-17. Full text

7. Pregeljc, Domen, Jug, Urška, Mavri, Janez, Stare, Jernej. Why does the Y326I mutant of monoamine oxidase B decompose an endogenous amphetamine at a slower rate than the wild type enzyme? Reaction step elucidated by multiscale molecular simulations. PCCP. Physical chemistry chemical physics : a journal of European chemical societies, 2018, vol. 20, iss. 6, str. 4181-4188. Full text

8. Stare, Jernej, Meden, Anton, Hadži, Dušan. Structure determination by joint effort of X-ray powder diffraction and quantum calculations : crystal structure and short hydrogen bonding in pentadecafluorooctanoic acid hydrateCroatica chemica acta2018, vol. 91, str. 209-220. Full text

9. Bergant, Kaja, Janežič, Matej, Perdih, Andrej. Bioassays and in silico methods in the identification of human DNA topoisomerase IIa inhibitorsCurrent medicinal chemistry2018, vol. 25, str. 3284-3316. Full text

10. Valjavec, Katja, Bavcon, Sara, Perdih, Andrej. DNA topoizomeraze pomembne tarče protirakavih zdravilnih učinkovinKemija.net, ISSN 1854-7419, 2018, št. 1, str. 1-7.

2017

1. Ričko, Sebastijan, Meden, Anže, Ivancic, Anže, Perdih, Andrej, Štefane Bogdan, Bogdan, Svete Jurij,  Grošelj Uroš. Organocatalyzed deracemisation of Δ2-pyrrolin-4-ones. Advanced Synthesis & Catalysis2017, vol. 359, iss. 13, str. 2288-2296. Full text

2. Kisovec, Matic, Rezelj, Saša, Knap, Primož, Cajnko, Miša Mojca, Caserman, Simon, Flašker, Ajda, Žnidaršič, Nada, Repič, Matej, Mavri, Janez, Ruan, Yi, Scheuring, Simon, Podobnik, Marjetka, Anderluh , Gregor. Engineering a pH responsive pore forming proteinScientific reports2017, vol. 7, str. 42231-1-42231-13 Full text

3. Jug, Urška, Pregeljc, Domen, Mavri, Janez, Vianello, Robert, Stare, Jernej . Elementary SN2 reaction revisited. Effects of solvent and alkyl chain length on kinetics of halogen exchange in haloalkanes elucidated by Empirical Valence Bond simulationComputational and theoretical chemistry, 2017, str. 1-6. Full text

4. Janežič, Matej, Pogorelčnik, Barbara, Brvar, Matjaž, Šolmajer, Tomaž, Perdih, Andrej. 3-substituted-1H-indazoles as catalytic inhibitors of the human DNA topoisomerase II [alpha]. ChemistrySelect, 2017, vol. 2, str. 480-488. Full text

5. Usenik, Aleksandra, Renko, Miha, Mihelič, Marko, Lindič, Nataša, Borišek, Jure, Perdih, Andrej, Pretnar, Gregor, Műller, Uwe, Turk, Dušan. The CWB2 cell wall-anchoring module is revealed by the crystal structures of the Clostridiumdifficile cell wall proteins Cwp8 and Cwp6Structure, 2017, vol. 25, iss. 3, str. 514-521. Full text

6. Oanca, Gabriel, Stare, Jernej, Vianello, Robert, Mavri, Janez. Multiscale simulation of monoamine oxidase catalyzed decomposition of phenylethylamine analogsEuropean Journal of Pharmacology2017, str. 1-5.Full text

7. Bergant, Kaja, Perdih, Andrej. Zaviralci in stabilizatorji interakcij med proteini = Inhibitors and stabilizators of protein-protein interactionsFarmacevtski vestnik 2017, 68, št. 3, str. 224-233. Full text

2016 

1. Eniyan Kandasamy, Kumar Anuradha, Rayasam Geetha Vani, Perdih, Andrej, Bajpai, Urmi. Development of a one-pot assay for screening and identification of Mur pathway inhibitors in Mycobacterium tuberculosisScientific reports, 2016, vol. 6, str. 35134-1-35134-12, Full text

2Mavri Janez, Matute Ricardo A, Chu Zhen T, Vianello Robert. Path integral simulation of the H/D kinetic isotope effect in monoamine oxidase B catalyzed decomposition of dopamineThe journal of physical chemistry. B, Condensed matter, materials, surfaces, interfaces & biophysical, 2016, vol. 120, iss. 14, str. 3488-3492, Full text

3. Ričko Sebastijan, Svete Jurij, Štefane Bogdan, Perdih Andrej, Golobič Amalija, Meden Anže, Grošelj Uroš. 1,3-diamine-derived bifunctional organocatalyst prepared from camphorAdvanced Synthesis & Catalysis, 2016, vol. 358, iss. 23, str. 3786-3796, Full text

4.  Poberžnik Matic, Purg Miha, Repič Matej, Mavri Janez, Vianello Robert. Empirical valence bond simulations of the hydride-transfer step in the monoamine oxidase A catalyzed metabolism of noradrenalineThe journal of physical chemistry. B, Condensed matter, materials, surfaces, interfaces & biophysical, 2016, vol. 120, iss. 44, str. 11419-11427, Full text

5. Oanca Gabriel, Purg Miha, Mavri Janez, Shih Jean C., Stare Jernej. Insights into enzyme point mutation effect by molecular simulation : phenylethylamine oxidation catalyzed by monoamine oxidase APCCP. Physical chemistry chemical physics, 2016, vol. 18, iss. 19, str. 13346-13356. Full text

6. Kržan Mojca, Vianello Robert, Maršavelski Aleksandra, Repič Matej, Zakšek Maja, Kotnik Kristina, Fijan Estera, Mavri, Janez. The quantum nature of drug-receptor interactions : deuteration changes binding affinities for histamine receptor ligandsPloS one, 2016, vol. 11, iss. 5, e0154002-1-e0154002-16. Full text

7.  Vianello Robert, Domene, Carmen, Mvri, Janez. The use of multiscale molecular simulations in understanding a relationship between the structure and function of biological systems of the brain : the application to monoamine oxidase enzymesFrontiers in neuroscience, 2016, vol. 10, art. 327, str. 1-24. Full text

8.Pavlin, Matic, Repič, Matej, Vianello, Robert, Mavri, Janez. The chemistry of neurodegeneration : kinetic data and their implicationsMolecular neurobiology, 2016, vol. 53, iss. 5, str. 3400-3415. Full text

2015

1. Pogorelčnik Barbara, Janežič Matej, Sosič Izidor, Gobec Stanislav, Šolmajer Tomaž, Perdih Andrej, 4,6- substituted-1,3,5-triazin-2(1H)-ones as monocyclic catalytic inhibitors of human DNA topoisomerase II [alpha] targeting the ATP binding siteBioorganic & Medicinal Chemistry, 2015, vol. 23, iss. 15, str. 4218-4229, Full text

2. Al-Asri Jamil, Fazekas Erika, Lehoczki Gábor, Perdih Andrej, Görick Cornelia, Melzig Matthias F., Gyémánt Gyöngyi, Wolber Gerhard, Mortier Jérémie, From carbohydrates to drug-like fragments : rational development of novel [alpha] -amylase inhibitorsBioorganic & Medicinal Chemistry, 2015, vol. 23, iss. 20, str. 6725-6732, Full text

3. Boldyreva Elena V., Arkhipov Sergey G., Drebushchak Tatiana N., Drebushchak Valeri A., Losev Evgeniy A., Matvienko Alexander A., Minkov Vasily S., Rychkov D. A., Seryotkin Yurii V., Stare Jernej, Zakharov Boris A., Isoenergetic polymorphism : the puzzle of tolazamide as a case studyChemistry, 2015, str. 1-11, Full text

4. Pogorelčnik Barbara, Brvar Matjaž, Žegura Bojana, Filipič Metka, Šolmajer Tomaž, Perdih Andrej, Discovery of mono- and disubstituted 1H-pyrazolo[3,4]pyrimidines and 9H-purines as catalytic inhibitors of human DNA topoisomerase II [alpha], ChemMedChem, 2015, vol. 10, iss. 2, str. 345-359, Full text

5. Plošnik Alja, Vračko Marjan, Mavri Janez, Computational study of binding affinity to nuclear receptors for some cosmetic ingredientsChemosphere, 2015, vol. 135, str. 325-334, Full text

6. Perdih Andrej, Hrast Martina, Pureber Kaja, Barreteau Hélène, Golič Grdadolnik Simona, Kocjan Darko, Gobec Stanislav, Šolmajer Tomaž, Wolber Gerhard, Furan-based benzene mono- and dicarboxylic acid derivatives as multiple inhibitors of the bacterial Mur ligases (MurC-MurF) : experimental and computational characterizationJournal of computer-aided molecular design, 2015, vol. 29, iss. 6, str. 541-560, Full text 

7. Pavlin Matic, Repič Matej, Vianello Robert, Mavri Janez, The chemistry of neurodegeneration : kinetic data and their implicationsMolecular neurobiology, 2015, str. [1-16], Full text

8. Martinčič Rok, Mravljak Janez, Švajger Urban, Perdih Andrej, Anderluh Marko, Novič Marjana, In silico discovery of novel potent antioxidants on the basis of pulvinic acid and coumarine derivatives and their experimental evaluationPloS one, 2015, vol. 10, no. 10, str. 1-27, e0140602, Full text 

9. Pogorelčnik Barbara, Janežič Matej, Perdih Andrej, Zaviralci DNA topoizomeraze II [alfa] - pomembne tarče protirakavih učinkovin = Inhibitors of DNA topoisomerase II [alpha] - an important target of anticancer therapyFarmacevtski vestnik, 2015, letn. 66, št. 4, str. 326-333. Full text

2014

1. Molčanov Krešimir, Babić Darko, Kojić-Prodić Biserka, Stare Jernej, Maltar-Strmečki Nadica, Androš Lidija, Spin-coupling in dimers of 2,3-dicyano-5,6-dichlorosemiquinone radical anions in the crystalline state, Acta crystallographica. Section B, Structural science, crystal engineering and materials, 2014, vol. 70, iss. 1, str. 181-190, Full text

2. Pogorelčnik Barbara, Brvar Matjaž, Zajc Irena, Filipič Metka, Šolmajer Tomaž, Perdih Andrej, Monocyclic 4-amino-6-(phenylamino)-1,3,5-triazines as inhibitors of human DNA topoisomerase II [alpha], Bioorganic & Medicinal Chemistry Letters, 2014, vol. 24, iss. 24, str. 5762-5768, Full text

3. Perdih Andrej, Hrast Martina, Barreteau Hélène, Gobec Stanislav, Wolber Gerhard, Šolmajer Tomaž, Benzene-1,3-dicarboxylic acid 2,5-dimethylpyrrole derivatives as multiple inhibitors of bacterial Mur ligases (MurC-MurF), Bioorganic & Medicinal Chemistry, 2014, vol. 22, iss.15, str. 4124-4134, Full text

4. Avbelj Monika, Wolz Olaf-Oliver, Fekonja Ota, Benčina Mojca, Repič Matej, Mavri Janez, Krüger Jens, Schärfe Charlotta, Delmiro-Garcia Magno, Panter Gabriela, Kohlbacher Oliver, Weber Alexander N. R., Jerala Roman, Activation of lymphoma-associated MyD88 mutations via allostery-induced TIR domain oligomerizationBlood, 2014, vol. 124, iss. 26, str. 3896-3904, Full text

5. Pirc Gordana, Stare Jernej, Mavri Janez, Vianello Robert, Hydrogen bond dynamics of histamine monocation in aqueous solution : how geometric parameters influence the hydrogen bond strengthCroatica chemica acta, 2014, vol. 87, no. 4, str. 397-405, I-IV, Full text

6. Kapustin Eugene A., Minkov Vasily S., Stare Jernej, Boldyreva Elena V., One hydrogen bond-two ways to build a structure, The role of N-H[...]O hydrogen bonds in crystal structures of N,N-dimethylglycineCrystal growth & design, 2014, vol. 14, iss. 4, str. 1851-1864, Full text

7. Kolšek Katra, Mavri Janez, Sollner Dolenc Marija, Gobec Stanislav, Turk Samo, Endocrine disruptome - an open source prediction tool for assessing endocrine disruption potential through nuclear receptor bindingJournal of chemical information and modeling, 2014, vol. 54, iss. 4, str. 1254-1267, Full text

8. Perdih Andrej, Hrast Martina, Barreteau Hélène, Gobec Stanislav, Wolber Gerhard, Šolmajer Tomaž, Inhibitor design strategy based on an enzyme structural flexibility : a case of bacterial MurD ligaseJournal of chemical information and modeling, 2014, vol. 54, iss. 5, str. 1451-1466, Full text

9. Stare Jernej, Hadži Dušan, Cooperativity assisted shortening of hydrogen bonds in crystalline oxalic acid dihydrate : DFT and NBO model studiesJournal of chemical theory and computation, 2014, vol. 10, iss. 4, str. 1817-1823, Full text

10. Repič Matej, Purg Miha, Vianello Robert, Mavri Janez, Examining electrostatic preorganization in monoamine oxidases A and B by structural comparison and pK [sub] a calculations, The journal of physical chemistry. B, Condensed matter, materials, surfaces, interfaces & biophysical, 2014, vol. 118, iss. 16, str. 4326-4332, Full text

11. Bruce-Smith Ian F., Zakharov Boris A., Stare Jernej, Boldyreva Elena V., Pulham Colin R., Structural properties of nickel dimethylglyoxime at high pressure : single-crystal X-ray diffraction and DFT studiesThe journal of physical chemistry. C, Nanomaterials and interfaces, 2014, vol. 118, iss. 42, str. 24705-24713, Full text

12. Molčanov Krešimir, Stare Jernej, Vener Mikhail V., Kojić-Prodić Biserka, Mali Gregor, Grdadolnik Jože, Mohaček-Grošev Vlasta, Nitranilic acid hexahydrate, a novel benchmark system of the Zundel cation in an intrinsically asymmetric environment : spectroscopic features and hydrogen bond dynamics characterised by experimental and theoretical methodsPCCP. Physical chemistry chemical physics, 2014, vol. 16, iss. 3, str. 998-1007, Full text

13. Repič Matej, Vianello Robert, Purg Miha, Duarte Fernanda, Bauer Paul, Kamerlin Shina Caroline Lynn, Mavri Janez, Empirical valence bond simulations of the hydride transfer step in the monoamine oxidase B catalyzed metabolism of dopamineProteins, 2014, vol. 82, iss. 12, str. 3347-3355, Full text

14. Mavri Janez, Nobelova nagrada za kemijo 2013 : razvoj večnivojskih modelov za simulacije kompleksnih molekulskih sistemovProteus, 2014, letn. 76, [št.] 5, str. 216-220, 235.


2013

1. Pavlin Matic, Mavri Janez, Repič Matej, Vianello Robert, Quantum-chemical approach to determining the high potency of clorgyline as an irreversible acetylenic monoamine oxidase inhibitor, 15th Amine Oxidase Conference : Re-Examining Amines : [16 to 18 July 2012, Toulouse, France], 2013, vol. 120, iss. 6, str. 875-882, Full full

2. Roy Choudhury Amrita, Perdih Andrej, Župerl Špela, Sikorska Emilia, Šolmajer Tomaž, Jurga Stefan, Zhukov Igor, Novič Marjana, Structural elucidation of transmembrane transporter protein bilitranslocase : conformational analysis of the second transmembrane region TM2 by molecular dynamics and NMR spectroscopyBiochimica et biophysica acta, Biomembranes, 2013, vol. 1828, iss. 11, str. 2609-2619, Full text

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

4. 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, Full text

5. 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 polarizationCrystEngComm, 2013, vol. 15, iss. 1, str. 135-143, Full text

6. Škedelj Veronika, Perdih Andrej, Brvar Matjaž, Kroflič Ana, Dubbée Vincent, Savage Victoria, O'Neill Alex J., Šolmajer Tomaž, Bešter-Rogač Marija, Blanot Didier, Hugonnet Jean-Emmanuel, Magnet Sophie, Arthur Michel, Mainardi Jean-Luc, Stojan Jure, Zega Anamarija, Discovery of the first inhibitors of bacterial enzyme D-aspartate ligase from Enterococcus faecium (Asl [sub] fm), European Journal of Medicinal Chemistry, 2013, vol. 67, str. 208-220, Full text

7. 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, Full text

8. Perdih Andrej, Wolber Gerhard, Šolmajer Tomaž, Molecular dynamics simulation and linear interaction energy study of D-Glu-based inhibitors of the MurD ligaseJournal of computer-aided molecular design, 2013, vol. 27, iss. 8, str. 723-738, Full text

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

10. Erić Slavica, Šolmajer Tomaž, Kotnik Miha, Zloh Mire, Agbaba Danica, Study of the selectivity of [alpha] [sub] 1-adrenergic antagonists by molecular modeling of [alpha] [sub] 1a-, [alpha] [sub] 1b-, and [alpha] [sub] 1d-adrenergic receptor subtypes and docking simulationsMonatshefte für Chemie, 2013, vol. 144, iss. 6, str. 903-912, Full text

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

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

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

14. Mavri Janez, Biomolekularne simulacije - pot do novih zdravil : Nobelova nagrada za kemijo 2013Delo, 2013, leto 55, št. 241, str. 14, Full Text

15. Purg Miha, Repič Matej, Mavri Janez, Računalniško modeliranje S[spodaj]N2 reakcije z metodo empirične valenčne vezi (EVB), Kemija v šoli in družbi, 2013, letn. 25, št. 2, str. 10-18

16. Munda Barbara, Perdih Andrej, Pogled v svet atomov in molekul s pomočjo računalnika - molekulsko modeliranjeSpatula, 2013, št. 61, str. 7-11

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 BBioorganic & 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 activityBioorganic & Medicinal Chemistry, 2012, vol. 20, issue 17, str. 5220-5228, Full text

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

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 modelInternational journal of molecular sciences, 2012, vol. 13, no. 2, str. 1269-1283, Full Text

6. 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 BJournal of chemical theory and computation, 2012, vol. 8, iss. 10, str. 3864-3870, Full text

7. 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 acidsJournal of materials chemistry, 2012, vol. 22, no. 20, str. 10255-10265, Full text

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

9. 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, Full text

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

11. 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, Full text

12. 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 analysisThe journal of physical chemistry. B, Materials, surfaces, interfaces & biophysical, 2012, vol. 116, issue 24, str. 7221-7231, Full text

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

14. 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

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

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

17. 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 approachesFarmacevtski vestnik, 2012, letn. 63, š. 1, str. 54-63 Full text

2011

1. Stare Jernej, A highly accurate, analytic potential energy surface of the hydrogendifluoride anion in the gas phaseActa 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 studyActa 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 studyCentral European Journal of Chemistry, 2011, vol. 9, no. 5, str. 855-866, Full text

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 studyEuropean journal of organic chemistry, 2011, vol. 2011, issue 32, str. 6419-6433, Full text

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

6. Pahovnik David, Reven Sebastjan, Grdadolnik Jože, Borštnar Rok, Mavri Janez, Žagar Ema, Determination of the interaction between glimepiride and hyperbranched polymers in solid dispersionsJournal of pharmaceutical sciences, 2011, vol. 100, iss. 11, str. 4700-4709, Full text

7. 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 chloranilatesThe journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2011, vol. 115, no. 14, str. 3154-3166

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 studyThe journal of physical chemistry. B, Condensed matter, materials, surfaces, interfaces & biophysical, 2011, vol. 115, no. 19, str. 5999-6010, Full text

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

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

2010

1. 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 BBioorganic & Medicinal Chemistry Letters, 2010, vol. 20, iss. 3, str. 958-962, Full text

2. Perdih Andrej, Sollner Dolenc Marija, Small molecule antagonists of integrin receptorsCurrent medicinal chemistry, 2010, vol. 17, no. 22, str. 2371-2392 Full text

3. 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 studyEuropean journal of organic chemistry, 2010, vol. 2010, issue 30, str. 5870-5883, Full text

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

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

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

7. Borštnar Rok, Roy Choudhury Amrita, Stare Jernej, Novič Marjana, Mavri Janez, Calculation of pK [sub] a values of carboxylic acids : application to bilirubinJournal of Molecular Structure. Theochem, 2010, vol. 947, no. 1-3, str. 76-82, 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 compoundsFarmacevtski vestnik, 2010, let. 61, št. 4, str. 195-202. Full text

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 issuesFEBS letters, 2010, vol. 584, no. 13, str. 2759-2766. Full text

10. Kolšek Katra, Zidar Jernej, Sollner Dolenc Marija, Mavri Janez, Kvantno kemijsko modeliranje elementarne S[subN]1 in S[subN]2 reakcije v vodni raztopiniKemija 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 inhibitorAntimicrobial agents and chemotherapy, 2009, no. 2, vol. 53, str. 505-511. Full text

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 approachBioorganic & Medicinal Chemistry Letters, 2009, vol. 19, no. 10, str. 2668-2673. 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 methodComputer physics communications, 2009, vol. 180, no. 11, str. 2079-2094. Full text

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

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-1Journal of chemical information and modeling, 2009, vol. 49, issue 4, str. 833-846 Full text

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

7. 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. Full text

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

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