Publications
2026
2025
1. Stevanović Kristina, Herlah Barbara, Pavlin Matic, Perdih Andrej. Asymmetric T-segment binding and gate dynamics govern the final stages of the type IIA topoisomerase catalytic cycle. International Journal of Biological Macromolecules. 2025, 270, 147216. Full text
2. Isaković Stefan, Senćanski Milan, Perović Vladimir, Stevanović Kristina, Prodić Ivana. Bioinformatic Selection of Mannose-Specific Lectins from Allium genus as SARS-CoV-2 Inhibitors Analysing Protein–Protein Interaction. Life. 2025, 15, 162. Full text
3. Kałka Andrzej, Novotný Aleš, Stare Jernej. Rescaling of Point Charges as a Way to Improve the Simple-to-Use Electrostatic Embedding Scheme Developed to Explore Enzyme Activity with QM-Oriented Software. Journal of Chemical Information and Modeling. 2025, 65, 8653-8663. Full text
4. Ljubič Martin, Sollner Dolenc Marija, Borišek Jure, Perdih Andrej. Water-based pharmacophore modeling in kinase inhibitor design : a case study on Fyn and Lyn protein kinases. Journal of Chemical Information and Modeling. 2025, 65, 9747-9761. Full text
5. Rajić Martina, Stare Jernej. Investigation of Electrostatic Effects on Enyzme Catalysis : Insights from Computational Simulations of Monoamine Oxidase A Pathological Variants Leading to the Brunner Syndrome. Journal of Chemical Information and Modeling. 2025, 65, 3439-3450. Full text
6. Oanca Gabriel, Prah Alja, Åqvist Johan, Mavri Janez. L-DOPA-Containing Protein Autoxidation : An Empirical Valence Bond Simulation of the Rate-Limiting Step. Journal of Physical Chemistry B. 2025, 129, 12422-12431. Full text
7. Smrkolj Vladimir, Kralj Jakob, Mavri Janez, Umek Nejc. Spatiotemporal dynamics of local anesthetic diffusion in nerve revealed by a 2D computational model. Biophysical Journal. 2025, 124, 3706-3716. Full text
8. Meden Anže, Žnidaršič Neža, Knez Damijan, Wang Yuanyuan, Xu Ziwei, Yang Huajing, Zhang Weiting, Pišlar Anja, Perdih Andrej, Kranjc Brezar Simona, Grgurevič Neža, Pajk Stane, Sun Haopeng, Gobec Stanislav. Pleiotropic prodrugs for both symptomatic and disease-modifying treatment of Alzheimer’s disease. Acta Pharmaceutica Sinica B. 2025, 15, 4807-4828. Full text
9. Perdih Andrej. Topoisomerases as Targets for Novel Drug Discovery. Pharmaceuticals. 2025, 18, 1693. Full text
10. Glisic Sanja, Stevanovic Kristina, Perdih Andrej, Bukreyeva Natalya, Maruyama Junki, Perovic Vladimir, López-Serrano Sergi, Darji Ayub, Radosevic Draginja, Sencanski Milan, Veljkovic Veljko, Bruno Botta, Mori Mattia, Paessler Slobodan. Influenza a Virus Inhibition : Evaluating Computationally Identified Cyproheptadine Through In Vitro Assessment. International Journal of Molecular Sciences. 2025, 26, 5962. Full text
11. Zupan Patricija, Kralj Jakob, Nolimal Niko, Čekada Gregor, Smrkolj Vladimir, Umek Nejc, Mavri Janez, Slapničar Miha. Farmakokinetični model kanabinoidov. Kemija v šoli in družbi. 2025, št. 1.
12. Herlah Barbara, Perdih Andrej. Računalniški mikroskop : raziskovanje skrivnosti atomskih svetov z molekulskimi simulacijami. Alternator : misliti znanost. 2025, št. 7. Full text
2024
1. Herlah Barbara, Janežič Matej, Ogris Iza, Golič Grdadolnik Simona, Kološa Katja, Žabkar Sonja, Žegura Bojana, Perdih Andrej. Nature-inspired substituted 3-(imidazol-2-yl) morpholines targeting human topoisomerase IIα : Dynophore-derived discovery. Biomedicine & Pharmacotherapy. 2024, 175, 116676. Full text
2. Herlah Barbara, Pavlin Matic, Perdih Andrej. Molecular choreography : unveiling the dynamic landscape of type IIA DNA topoisomerases before T-segment passage through all-atom simulations. International Journal of Biological Macromolecules. 2024, 269, 131991. Full text
3. Herlah Barbara, Goričan Tjaša, Strašek Benedik Nika, Golič Grdadolnik Simona, Sosič Izidor, Perdih Andrej. Simulation- and AI-directed optimization of 4,6-substituted 1,3,5-triazin-2(1H)-ones as inhibitors of human DNA topoisomerase Iiα.Computational and Structural Biotechnology Journal. 2024, 23, 2995-3018. Full text.
4. Rajić Martina, Prah Alja, Stare Jernej. Deciphering the Two-Step Hydride Mechanism of Monoamine Oxidase Flavoenzymes. ACS Omega. 2024, 9, 43046-43057. Full text
5. Prah Alja, Mavri Janez. L-DOPA Autoxidation : An Empirical Valence Bond Simulation of the Reactive Step. Journal of Physical Chemistry. 2024, 128, 8355-8361. Full text
6. Stare Jernej. Oxidation of Flavin by Molecular Oxygen : Computational Insights into a Possible Radical Mechanism. ACS Omega. 2024, 9, 23431-23441. Full text
7. Ljubič Martin, Perdih Andrej, Borišek Jure. All-Atom Simulations Reveal the Effect of Membrane Composition on the Signaling of the NKG2A/CD94/HLA-E Immune Receptor Complex. Journal of Chemical Information and Modeling. 2024, 64, 9374–9387. Full text
8. Senćanski Milan, Glišić Sanja, Kubale Valentina, Cotman Marko, Mavri Janez, Vrecl Milka. Computational modeling and characterization of peptides derived from nanobody complementary-determining region 2 (CDR2) targeting active-state conformation of the β2-adrenergic receptor (β2AR). Biomolecules. 2024, 14, 423. Full text
9. Stare Jernej, Grdadolnik Jože, Mason Sax, Albinati Alberto, Eckert Juergen, 4‑Methoxypicolinic Acid N‑Oxide : One of the Shortest Hydrogen Bonds Known Characterized by Neutron Diffraction, Inelastic Neutron Scattering, Infrared Spectroscopy, and Periodic DFT Calculations. ACS Omega. 2024, 9, 38116–38125. Full text
10. Prašnikar Eva, Ljubič Martin, Perdih Andrej, Borišek Jure. Machine learning heralding a new development phase in molecular dynamics simulations. Artificial Intelligence Review. 2024, 57, 102. Full text
2023
1. Pavlin Matic, Herlah, Barbara, Valjavec Katja, Perdih Andrej. Unveiling the Interdomain Dynamics of Type II DNA Topoisomerase through All-Atom Simulations : Implications for Understanding its Catalytic Cycle. Computational and Structural Biotechnology Journal. 2023, 21, 3746-3759. Full text
2. Smrkolj Vladimir, Pregeljc Domen, Kavčič Hana, Umek Nejc, Mavri Janez. Micro-pharmacokinetics of lidocaine and bupivacaine transfer across a myelinated nerve fiber. Computers in Biology and Medicine. 2023, 165, 107375. Full text
3. Cvijetić Ilija, Herlah Barbara, Marinković Aleksandar, Perdih Andrej, Snežana K. Bjelogrlić. Phenotypic discovery of thiocarbohydrazone with anticancer properties and catalytic inhibition of human DNA topoisomerase IIα. Pharmaceuticals. 2023, 16, 341. Full text
4. Kavčič Hana, Jug Urška, Mavri Janez, Umek Nejc. Antioxidant activity of lidocaine, bupivacaine, and ropivacaine in aqueous and lipophilic environments : an experimental and computational study. Frontiers in Chemistry. 2023, 11, 1208843. Full text
5. Ljubič Martin, Prašnikar Eva, Perdih Andrej, Borišek Jure. All-Atom Simulations Reveal the Intricacies of Signal Transduction upon Binding of the HLA-E Ligand to the Transmembrane Inhibitory CD94/NKG2A Receptor. Journal of Chemical Information and Modeling. 2023, 63, 3486-3499. Full text
6. Lojevec Hartl Simona, Žakelj Simon, Sollner Dolenc Marija, Smrkolj Vladimir, Mavri Janez. How azide ion/hydrazoic acid passes through biological membranes : an experimental and computational study. The Protein Journal. 2023, 42, 229-238. Full text
7. Phuong Vu Lan, Diehl Claudia J., Casement Ryan, Bond Adam G., Steinebach Christian, Strašek Nika, Bricelj Aleša, Perdih Andrej, Schnakenburg Gregor, Sosič Izidor. Expanding the structural diversity at the phenylene core of ligands for the von hippel–lindau E3 ubiquitin ligase : development of highly potent hypoxia-inducible factor-1α stabilizers. Journal of Medicinal Chemistry. 2023, 66, 12776-12811. Full text
8. Meden Anže, Knez Damijan, Brazzoloto Xavier, Modeste Fabrice, Perdih Andrej, Pišlar Anja, Zorman Maša, Zorić Maja, Denic Milica, Pajk Stane, Živin Marko, Nachalon Florian, Gobec Stanislav. Pseudo-irreversible butyrylcholinesterase inhibitors : SAR, kinetic, computational, and crystallographic study of the N-dialkyl O-arylcarbamate warhead. European Journal of Medicinal Chemistry. 2023, 247, 115048. Full text
9. Stare Katarina, Stare Jernej, Škapin Srečo D., Spreitzer Matjaž, Meden Anton. Structure Determination and Analysis of the Ceramic Material La0.987Ti1.627Nb3.307O13 by Synchrotron and Neutron Powder Diffraction and DFT Calculations. Crystals. 2023, 13, 439. Full Text
2022
1. Ogrizek Mitja, Janežič Matej, Valjavec Katja, Perdih Andrej. Catalytic Mechanism of ATP Hydrolysis in the ATPase Domain of Human DNA Topoisomerase IIα. Journal of Chemical Information and Modeling. 2022, 62, 3869-3909. Full text
2. Prah Alja, Pregeljc Domen, Stare Jernej, Mavri Janez. Brunner syndrome caused by point mutation explained by multiscale simulation of enzyme reaction. Scientific Reports. 2022, 12, 21889. Full text
3. 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, 15, 539. Full text
4. 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, 23, 1910. Full text
5. 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 Journal. 2022, 20, 1254-1263. Full text
6. Prah Alja, Gavranić Tanja, Sollner Dolenc Marija, Perdih Andrej, Mavri Janez. Computational Insights into β-Carboline Inhibition of Monoamine Oxidase A. Molecules. 2022, 27, 6711. Full text
7. 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, 40, 1671-1691. Full text
8. Prašnikar Eva, Perdih Andrej, Borišek Jure. What a Difference an Amino Acid Makes: An All-Atom Simulation Study of Nonameric Peptides in Inhibitory HLA-E/NKG2A/CD94 Immune Complexes. Frontiers in Pharmacology. 2022, 13, 925427. Full text
9. Reberc Maja, Mazaj Matjaž, Stare Jernej, Počkaj Marta, Mali Gregor, Li Xiao, Filinchuk Yaroslav, Černý Radovan, Meden Anton. Trinuclear magnesium imidazolate borohydride complex. Inorganic Chemistry. 2022, 61, 12708-12718. Full text
10. Novak Urban, Golobič Amalija, Klačnik Natalija, Mohaček-Grošev Vlasta, Stare Jernej, Grdadolnik Jože. Strong hydrogen bonds in acetylenedicarboxylic acid dihydrate. International Journal of Molecular Sciences. 2022, 23, 6164. Full text
11. Prašnikar Eva, Borišek Jure, Perdih Andrej. Celična senescenca : nova terapevtska tarča pri zdravljenju s starostjo povezanih boleznih. Farmacevtski vestnik. 2022, 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, 22, 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. Physical Chemistry Chemical Physics. 2021, 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, 61, 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, 34, e4275. Full text
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, 22, 6670. Full text
6. Stevanović Strahinja, Marjanović Djordje S., Trailović Sasa M., Zdravković Nemanja, Perdih Andrej, Nikolić Katarina. 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 methods. Acta Chimica Slovenica. 2021, 68, 426–432. 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, 22, 6927. Full text
9. Prašnikar Eva, Borišek Jure, Perdih Andrej. Senescent cells as promising targets to tackle age-related diseases. Aging Research Reviews. 2021, 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, 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 IIα. Journal of Chemical Information and Modeling. 2020, 60, 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 A. Physical Chemistry Chemical Physics. 2020, 13, 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, 99, 103828. Full text
4. Kump J. Karson, Miao Lei , Mady A.S. 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, 63, 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 Biology. 2020, 3, 178. 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 Research. 2020, 37, 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 study. International Journal of Molecular Sciences. 2020, 21, 6151. 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. Molecules. 2020, 25, 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. Physical Chemistry Chemical Physics. 2020, 22, 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 computations. ACS Catalysis. 2019, 9, 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 IIα. European Journal of Medicinal Chemistry. 2019, 175, 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 Reports. 2019, 9, 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. Molecules. 2019, 24, 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 protein. International Journal of Molecular Sciences. 2019, 20, 4172. 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. Chemico-Biological Interactions. 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 dihydrate. Spectrochimica Acta. Part A, Molecular and Biomolecular spectroscopy. 2019, 218, 1-8. Full text
8. Valjavec Katja, Perdih Andrej. Razvoj zdravilnih učinkovin in metode računalniško podprtega načrtovanja. Proteus. 2019, 81, 350-358. Full text