Odseki

1. Dekleva Dominik, Voronov Alexey, Janet Jon Paul, Ekborg Albin, Borišek Jure, Rambaher Martina H., Loeffler Hannes H. Synthesizability via reward engineering: expanding generative molecular design into synthetic space. Chemical Science. 2026, 17, 10015-10028. Full text 

2. Borišek Jure, Aupič Jana, Magistrato Alessandra. Monovalent ions aid catalysis of two-metal-ion dependent RNA editors. Coordination Chemistry Reviews. 2026, 557, 1-12. Full text 

3. Cresca Sofia, Borišek Jure, Magistrato Alessandra, Križaj Igor. Current status of molecular dynamics simulations of membrane permeabilization by antimicrobial peptides and pore-forming proteins : a review. Journal of Chemical Information and Modeling. 2026, 66, 1982–2005. Full text 

4. Hubman Anže, Merzel Franci. A variational method for efficient estimation of diffusion and free-energy profiles along collective variables. Journal of Chemical Physics. 2026, 164, 174108. Full text

5. Srnko Marija, Šolinc Gašper, Crnković Ana, Merzel Franci, Jordan Michael, Wallace E. Jayne, Podobnik Marjetka, Anderluh Gregor. High-throughput human histone detection by an engineered actinoporin nanopore. ACS Sensors. 2026, 11, 2016–2029. Full text

6. Marojević Andrijana, Pavčnik Tjaša, Lužanin Olivera, Grdadolnik Jože, Pirnat Klemen, Ponrouch Alexandre, Dominko Robert, Bitenc Jan. Influence of salt concentration on the electrochemical performance of magnesium hexafluoroisopropoxy aluminate electrolyte. Batteries & Supercaps. 2026, 9, e202500497. Full text

7. Mohamed E. A. Abdelmonaem. Antimicrobial Copper Coatings: Mechanisms, Applications, Challenges, and AI-Driven Advancements. Copper - Properties, Metallurgy and Application. 2026. Full text

8. Slejko Ema, Coste Amaury, Potisk Tilen, Zavadlav Julija, Praprotnik Matej. Achieving all-atom molecular dynamics accuracy from the Poisson-Boltzmann method through machine learning. Journal of Chemical Physics. 2026, 164, 054107. Full text

9. Lah Maša, Potisk Tilen, Praprotnik Matej. Open-boundary molecular dynamics of red blood cell suspensions. Journal of Chemical Physics. 2026, 164, 104107. Full text

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 

13. Vračko Marjan, Mora Lagares Liadys. Clustering of bisphenols based on toxicity predictions for key aquatic species : Daphnia magna, Pimephales promelas, and Oryzias latipes. Ecotoxicology and Environmental Safety. 2025, 295, 118149. Full text 

14. Saçan Türker Melek, Tuğcu Gülçin, Fjodorova Natalja Stanislavovna, Venko Katja, Usmanov Durbek, Rasulev Bakhtiyor, Sağ Erdem Safiye, Novič Marjana. In silico study of the solubility of fullerene derivatives in chlorobenzene. Results in Chemistry. 2025, 18, 102754. Full text

15. Bajželj Benjamin, Novič Marjana, Drgan Viktor. Utilizing molecular descriptor importance to enhance endpoint predictions.Toxics. 2025, 13, 383. Full text

16. Zorman Maša, Minovski Nikola, Anderluh Marko, Gobec Stanislav, Hrast Rambaher Martina. Boj proti bakterijski odpornosti : ali so bakterijske topoizomeraze tipa II še zanimive tarče?. Farmacevtski vestnik : strokovno glasilo slovenske farmacije. 2025, 76, 10-21. Full text

17. Ogris Iza, Zupančič Barbara, Sosič Izidor, Merzel Franci, Golič Grdadolnik Simona. Mechanistic insight into the dynamics of Mur ligase through a comprehensive timescale-specific approach. Communications Chemistry. 2025, 8, 285. Full text

18. Šolinc Gašper, Srnko Marija, Merzel Franci, Crnković Ana, Kozorog Mirijam, Podobnik Marjetka, Anderluh Gregor. Cryo-EM structures of a protein pore reveal a cluster of cholesterol molecules and diverse roles of membrane lipids. Nature Communications. 2025, 16, 2972. Full text

19. Venianakis Themistoklis, Goričan Tjaša, Papamokos Georgios, Golič Grdadolnik Simona, Siskosa Michael G., Gerothanassis Ioannis P. Are the pKₐ values of free fatty acids in aqueous solution abnormally high? An NMR and computational perspective. Chemical Communications. 2025, 61, 19890-19893. Full text

20. Kuzikov Maria, Morasso Stefano, Reinshagen Jeanette, Wolf Markus, Monaco Vittoria, Cozzolino Flora, Golič Grdadolnik Simona, Šket Primož, Plavec Janez, Iaconis Daniela, et al. Thiol-reactive or redox-active : revising a repurposing screen led to a new invalidation pipeline and identified a true noncovalent inhibitor against papain-like protease from SARS-CoV-2. ACS Pharmacology & Translational Science. 2025, 8, 66–77. Full text

21. Goričan Tjaša, Golič Grdadolnik Simona. Insights into the allosteric regulation of human Hsp90 revealed by NMR spectroscopy. Biomolecules. 2025, 15, 37. Full text

22. Mohaček-Grošev Vlasta, Grdadolnik Jože. Hyaluronic acid dipeptide gels studied by raman spectroscopy. Crystals. 2025, 15, 559. Full text

23. Paoletti Francesca, Goričan Tjaša, Cassetta Alberto, Grdadolnik Jože, Toporash Mykola, Lamba Doriano, Golič Grdadolnik Simona, Covaceuszach Sonia. Unveiling the solvent effect : DMSO interaction with human nerve growth factor and its implications for drug discovery. Molecules. 2025, 30, 3030. Full text

24. Križman Mitja, Zekič Jure, Šket Primož, Anžlovar Alojz, Zupančič Barbara, Grdadolnik Jože. A novel glucosamine-based cannabidiol complex based on intermolecular bonding with improved water solubility. Molecules. 2025, 30, 3179. Full text

25. Ntarakas Nikolaos, Lah Maša, Svenšek Daniel, Potisk Tilen, Praprotnik Matej. Dissipative particle dynamics models of encapsulated microbubbles and nanoscale gas vesicles for biomedical ultrasound simulations. ACS Applied Nano Materials. 2025, 8, 16053-16070. Full text

26. Lah Maša, Ntarakas Nikolaos, Potisk Tilen, Papež Petra, Praprotnik Matej. Open-boundary molecular dynamics of ultrasound using supramolecular water models. Journal of Chemical Physics. 2025, 162, 024103. Full text

27. Aupič Polona, Potisk Tilen, Svenšek Daniel, Skačej Gregor. External field-induced caloric effects in liquid crystals from molecular simulation. Journal of Chemical Physics. 2025, 163, 044902. Full text

28. Hirci Jernej, Škufca Sandra, Kunej Tanja, Janežič Dušanka, Konc Janez. Identification of potential human targets for epigallocatechin gallate through a novel protein binding site screening approach. Journal of Molecular Modeling. 2025, 31, 189. Full text

29. Lešnik Samo, Konc Janez, Vodopivec Seravalli Tina, Čamernik Katja, Potokar Urška Karolina, Legiša  Matic. Small-molecule inhibitors of 6-phosphofructo-1-kinase simultaneously suppress lactate and superoxide generation in cancer cells. PloS One. 2025, 20, e0321998. Full text

30. Amaro Rommie E., Åqvist Johan, Bahar Ivet, Battistini Federica, Bellaiche Adam, Beltran Daniel, Biggin Philip C., Bonomi Massimiliano, Praprotnik Matej, et al. The need to implement FAIR principles in biomolecular simulations. Nature Methods. 2025, 22, 641–645. Full text

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

11. Kokot Maja, Hrast Rambaher Martina, Feng Lipeng, Mitchenall Lesley A., Lawson David M., Maxwell Anthony, Parish Tanya, Minovski Nikola, Anderluh Marko. Structural aspects of Mycobacterium tuberculosis DNA gyrase targeted by novel bacterial topoisomerase inhibitors. ACS Medicinal Chemistry Letters. 2024, 15, 2164-2170. Full text

12. Kokot Maja, Minovski Nikola. Dynamic profiling and binding affinity prediction of NBTI antibacterials against DNA gyrase enzyme by multidimensional machine learning and molecular dynamics simulations. ACS Omega. 2024, 9, 18278–18295. Full text

13. Borišek Jure, Aupič Jana, Magistrato Alessandra. Third metal ion dictates the catalytic activity of the two-metal-ion pre-ribosomal RNA-processing machinery. Angewandte Chemie : International Edition. 2024, 63, e202405819. Full text

14. Sluga Janja, Tomašič Tihomir, Anderluh Marko, Hrast Rambaher Martina, Bajc Gregor, Sevšek Alen, Martin Nathaniel I., Pieters Roland J., Novič Marjana, Venko Katja. Targeting N-acetylglucosaminidase in Staphylococcus aureus with iminosugar inhibitors. Antibiotics. 2024, 13, 751. Full text

15. Zorman Maša, Kokot Maja, Zdov Irena, Šenerović Lidija, Mandic Mina, Zidar Nace, Cotman Andrej Emanuel, Durcik Martina, Peterlin-Mašič Lucija, Minovski Nikola, Anderluh Marko, Hrast Rambaher Martina. Enhancing antibacterial efficacy : combining novel bacterial topoisomerase inhibitors with efflux pump inhibitors and other agents against gram-negative bacteria. Antibiotics. 2024, 13, 1081. Full text

16. Zorman Maša, Hrast Rambaher Martina, Kokot Maja, Minovski Nikola, Anderluh Marko. The overview of development of novel bacterial topoisomerase inhibitors effective against multidrug-resistant bacteria in an academic environment : from early hits to in vivo active antibacterials. European Journal of Pharmaceutical Sciences. 2024, 192, 106632. Full text

17. Drgan Viktor, Venko Katja, Sluga Janja, Novič Marjana. Merging counter-propagation and back-propagation algorithms : overcoming the limitations of counter-propagation neural network models. International Journal of Molecular Sciences. 2024, 25, 4156. Full text

18. Ljubič Martin, D'ercole Claudia, Waheed Yossma, De Marco Ario, Borišek Jure, De March Matteo. Computational study of the HLTF ATPase remodeling domain suggests its activity on dsDNA and implications in damage tolerance. Journal of Structural Biology. 2024, 216, 108149. Full text

19. Mora Lagares Liadys, Perez Castillo Yunierkis, Novič Marjana. Exploring the dynamics of the ABCB1 membrane transporter P-glycoprotein in the presence of ATP and active/non-active compounds through molecular dynamics simulations. Toxicology. 2024, 502, 153732. Full text 

20. Adamovsky Ondrej, Groh Ksenia J, Białk-Bielińska, Anna, Escher, Beate I., Beaudouin Rémy, Mora Lagares Liadys, Tollefsen Knut-Erik, Fenske Martina, Mulkiewicz Ewa, Štern Alja, Eleršek Tina, Vračko Marjan, Žegura Bojana, et al. Exploring BPA alternatives – environmental levels and toxicity review. Environment International. 2024, 189, 108728. Full text

21. Tariq Farina, Ahrens Lutz, Alygizakis Nikiforos A., Audouze Karine, Benfenati Emilio, Carvalho Pedro, Chelcea Ioana, Karakitsios Spyros P., Karakoltzidis Achilleas, Kumar Vikas, Mora Lagares Liadys, et al. Computational tools to facilitate early warning of new emerging risk chemicals. Toxics. 2024, 12, 736. Full text 

22. Dernovšek Jaka, Zajec Živa, Poje Goran, Urbančič Dunja, Goričan Tjaša, Golič Grdadolnik Simona, Mlinarič-Raščan Irena, Cotman Andrej Emanuel, Zidar Nace, Tomašič Tihomir, et al. Exploration and optimisation of structure-activity relationships of new triazole-based C-terminal Hsp90 inhibitors towards in vivo anticancer potency. Biomedicine & Pharmacotherapy. 2024, 177, 116941. Full text

23. Dernovšek Jaka, Urbančič Dunja, Zajec Živa, Sturtzel Caterina, Goričan Tjaša, Golič Grdadolnik Simona, Skok Žiga, Ilaš Janez, Zidar Nace, Tomašič Tihomir, et al. First dual inhibitors of human topoisomerase IIα and Hsp90 C-terminal domain inhibit the growth of Ewing sarcoma in vitro and in vivo. Bioorganic Chemistry. 2024, 153, 107850. Full text

24. Mohaček-Grošev Vlasta, Škrabić Marko, Gebavi Hrvoje, Blažek Bregović Vesna, Marić Ivan, Amendola Vincenzo, Grdadolnik Jože. Binding of glutamic acid to silver and gold nanoparticles investigated by surface-enhanced Raman spectroscopy. Biosensors. 2024, 14, 522. Full text

25. Drinčić Ana, Noč Luka, Merzel Franci, Jerman Ivan. Future Parabolic Trough Collector Absorber Coating Development and Service Lifetime Estimation. Coatings. 2024, 14, 1111. Full text

26. Kavčič, Luka, Kežar, Andreja, Koritnik, Neža, Tušek-Žnidarič, Magda, Klobučar, Tajda, Vičič, Žiga, Merzel, Franci, Holden, Ellie, Benesch, Justin L. P., Podobnik, Marjetka. From structural polymorphism to structural metamorphosis of the coat protein of flexuous filamentous potato virus Y. Communications Chemistry. 2024, 7, 14. Full text

27. Dernovšek Jaka, Goričan Tjaša, Gedgaudas Marius, Zajec Živa, Urbančič Dunja, Jug Ana, Skok Žiga, Golič Grdadolnik Simona, Ilaš Janez, Zidar Nace, Tomašič Tihomir, Et Al. Hiding in plain sight : Optimizing topoisomerase IIα inhibitors into Hsp90β selective binders. European Journal of Medicinal Chemistry. 2024, 280, 116934. Full text

28. Kaplunov Julius, Zupančič Barbara, Nikonov Anatolij. Asymptotic analysis of the axisymmetric problem for the transverse compression of a thin elastic disk in the case of mixed boundary conditions along its faces. Izvestiâ Saratovskogo universiteta : Novaâ seriâ. Seriâ Matematika, mehanika, informatika. 2024, 24, 57–62. Full text

29. Diamantis Dimitrios A., Tsiailanis Antonios D., Papaemmanouil Christina, Nika Maria-Christina, Kanaki Zoi, Golič Grdadolnik Simona, Babič Andrej, Tzakos Eleftherios Paraskevas, Fournier Isabelle, Salzet Michel, Kushwah, Prem Prakash, Thomaidis Nikolaos S., Rampias Theodoros, Shankar Eswar, Karakurt Serdar, Gupta Sanjay Kumar, Tzakos Andreas G. Development of a novel apigenin prodrug programmed for alkaline-phosphatase instructed self-inhibition to combat cancer. Journal of Biomolecular Structure & Dynamics. 2024, 42, 8638-8659. Full text

30. Zajec Živa, Dernovšek Jaka, Cingl Jernej, Ogris Iza, Gedgaudas Marius, Zubriené Asta, Mitrović Ana, Golič Grdadolnik Simona, Gobec Martina, Tomašič Tihomir. New class of Hsp90 C-terminal domain inhibitors with anti-tumor properties against triple-negative breast cancer. Journal of Medicinal Chemistry. 2024, 67, 12984-13018. Full text

31. Alzaidi Ahmed S. M., Kaplunov Julius, Zupančič Barbara, Nikonov Anatolij. Transverse compression of a thin inhomogeneous elastic layer. Mathematics. 2024, 12, 2502. Full text

32. Georgiou Nikitas, Karta Danai, Cheilari Antigoni, Merzel Franci, Tzeli Demeter, Vassiliou Stamatia, Mavromoustakos Thomas Michael. Synthesis of thiazolidin-4-ones derivatives, evaluation of conformation in solution, theoretical isomerization reaction paths and discovery of potential biological targets. Molecules. 2024, 29, 2458. Full text

33. Venianakis Themistoklis, Parisis Nikolaos, Christou Atalanti, Goulas Vlasios, Nikoloudakis Nikolaos, Botsaris George, Goričan Tjaša, Golič Grdadolnik Simona, Tzakos Andreas G., Gerothanassis Ioannis P. Phytochemical analysis and biological evaluation of carob leaf (Ceratonia siliqua L.) crude extracts using NMR and mass spectroscopic techniques. Molecules. 2024, 29, 5273. Full text

34. Dernovšek Jaka, Gradišek Nina, Zajec Živa, Urbančič Dunja, Cingl Jernej, Goričan Tjaša, Golič Grdadolnik Simona, Tomašič Tihomir. Discovery of new Hsp90–Cdc37 protein–protein interaction inhibitors : in silico screening and optimization of anticancer activity. RSC Advances. 2024, 14, 28347–28375. Full text 

35. Adamek Maksimiljan, Kavčič Anja, Debeljak Marta, Šala Martin, Grdadolnik Jože, Vogel-Mikuš Katarina, Kroflič Ana. Toxicity of nitrophenolic pollutant 4-nitroguaiacol to terrestrial plants and comparison with its non-nitro analogue guaiacol (2-methoxyphenol). Scientific Reports. 2024, 14, 2198. Full text

36. Alzaidi Ahmed S. M., Kaplunov Julius, Nikonov Anatolij, Zupančič Barbara. Transverse compression of a thin elastic disc. Zeitschrift für angewandte Mathematik und Physik. 2024, 75, 116. Full text

37. Prislan Rok, Kržič Urša, Svenšek Daniel. Quantifying sound colour of musical instruments – precise harmonic timbre coordinates of like instruments. Acta Acustica. 2024, 8, 8. Full text

38. Jug Matevž, Potisk Tilen, Svenšek Daniel, Praprotnik Matej. Learning macroscopic equations of motion from dissipative particle dynamics simulations of fluids. Computer Methods in Applied Mechanics and Engineering. 2024, 432, 117379. Full text

39. Šimon Martin, Mikec Špela, Atanur Santosh S., Konc Janez, Morton Nicholas M., Horvat Simon, Kunej Tanja. Whole genome sequencing of mouse lines divergently selected for fatness (FLI) and leanness (FHI) revealed several genetic variants as candidates for novel obesity genes. Genes & Genomics. 2024, 46, 557-575. Full text

40. Coste Amaury, Slejko Ema, Zavadlav Julija, Praprotnik Matej. Developing an implicit solvation machine learning model for molecular simulations of ionic media. Journal of Chemical Theory and Computation. 2024, 20, 411–420. Full text

41. Rozman Kati, Ghysels An, Zavalnij Bogdan, Kunej Tanja, Bren Urban, Janežič Dušanka, Konc Janez. Enhanced molecular docking : novel algorithm for identifying highest weight k-cliques in weighted general and protein-ligand graphs. Journal of Molecular Structure. 2024, 1304, 137639. Full text

42. Kralj Sebastjan, Jukič Marko, Bahun Miha, Kranjc Luka, Kolarič Anja, Hodošček Milan, Poklar Ulrih Nataša, Bren Urban. Identification of triazolopyrimidinyl scaffold SARS-CoV-2 papain-like protease (PLpro) inhibitor. Pharmaceutics. 2024, 16, 169. Full text

43. Svenšek Daniel, Sočan Jaka, Praprotnik Matej. Density–nematic coupling in isotropic solution of DNA : multiscale model. Macromolecular Rapid Communications. 2024, 45, 2400382. Full text

44. Draškovič-Bračun Aljaž, Potisk Tilen, Svenšek Daniel. Modeling ultrasonic metafluids : the significance of discrete oscillators. Physical Review E. 2024, 109, 014604. Full text

45. Rozman Kati, Ghysels An, Janežič Dušanka, Konc Janez. An exact algorithm to find a maximum weight clique in a weighted undirected graph. Scientific Reports. 2024, 14, 9118. Full text

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 La_0.987Ti_1.627Nb_3.307O₁₃ by Synchrotron and Neutron Powder Diffraction and DFT Calculations. Crystals.  2023, 13, 439. Full Text

10. Kokot Maja, Novak Doroteja, Zdovc Irena, Anderluh Marko, Hrast Rambaher Martina, Minovski, Nikola. Exploring alternative pathways to target bacterial type II topoisomerases using NBTI antibacterials : beyond halogen-bonding interactions. Antibiotics. 2023, 12, 930. Full text

11. Stanojević Mark, Vračko Marjan, Sollner Dolenc Marija. Development of in silico classification models for binding affinity to the glucocorticoid receptor. Chemosphere. 2023, 336, 139147. Full text

12. Soler Miguel A., Minovski Nikola, Rocchia Walter, Fortuna Sara. Replica-exchange optimization of antibody fragments. Computational Biology and Chemistry. 2023, 103, 107819. Full text

13. Kokot Maja, Weiss Matjaž, Zdovc Irena, Šenerović Lidija, Radakovic Natasa, Anderluh Marko, Minovski Nikola, Hrast Rambaher Martina. Amide containing NBTI antibacterials with reduced hERG inhibition, retained antimicrobial activity against gram-positive bacteria and in vivo efficacy. European Journal of Medicinal Chemistry. 2023, 250, 115160. Full text

14. Venko Katja, Žerovnik Eva. Protein Condensates and Protein Aggregatesb : In Vitro, in the Cell, and In Silico. Frontiers in Bioscience. 2023, 28, 183. Full text

15. Toropova Alla P., Toropov Andrey A., Fjodorova Natalja. QSPR and Nano-QSPR : Which One is Common? : The Case of Fullerenes Solubility. Inorganics. 2023, 11, 344. Full text

16. Toropova Alla P., Toropov Andrey A., Fjodorova Natalja. In silico simulation of impacts of metal nano-oxides on cell viability in THP-1 cells based on the correlation weights of the fragments of molecular structures and codes of experimental conditions represented by means of quasi-SMILES. International Journal of Molecular Sciences. 2023, 24, 2058. Full text

17. Fjodorova Natalja, Novič Marjana, Venko Katja, Rasulev Bakhtiyor, Saçan Türker Melek, Tuğcu Gülçin, Sağ Erdem Safiye, Toropova Alla P., Toropov Andrey A. Cheminformatics and machine learning approaches to assess aquatic toxicity profiles of fullerene derivatives. International Journal of Molecular Sciences. 2023, 24, 14160. Full text

18. Mora Lagares Liadys, Vračko Marjan. Ecotoxicological evaluation of bisphenol A and alternatives : a comprehensive in silico modelling approach. Journal of Xenobiotics. 2023, 13, 719-739. Full text 

19. Aupič Jana, Borišek Jure, Fica Sebastian M., Galej Wojciech P., Magistrato Alessandra. Monovalent metal ion binding promotes the first transesterification reaction in the spliceosome. Nature Communications. 2023, 14, 8482. Full text

20. Tušar Marjan, Kakar Muhammad Rafiq, Poulikakos Lily D., Pasquini Emiliano, Baliello Andrea, Pasetto Marco, Porot Laurent, Wang Di, Falchetto Augusto Cannone, Dalmazzo Davide, et al. RILEM TC 279 WMR round robin study on waste polyethylene modified bituminous binders : advantages and challenges. Road Materials and Pavement Design. 2023, 24, 311-339. Full text

21. Stanojević Mark, Sollner Dolenc Marija, Vračko Marjan. Predictive models for compound binding to androgen and estrogen receptors based on counter-propagation artificial neural networks. Toxics. 2023, 11, 486. Full text

22. Novič Marjana. Quantitative structure activity/toxicity relationship through neural networks for drug discovery or regulatory use. Current Topics in Medicinal Chemistry. 2023, 23, 2792-2804. Full text 

23. Borišek Jure, Aupič Jana, Magistrato Alessandra. Establishing the catalytic and regulatory mechanism of RNA-based machineries. Wiley Interdisciplinary Reviews. Computational Molecular Science. 2023, 13, e1643. Full text 

24. Novak Urban, Žerovnik Eva, Taler-Verčič Ajda, Tušek-Žnidarič Magda, Zupančič Barbara, Grdadolnik Jože. Amyloid formation of Stefin B protein studied by infrared spectroscopy. Frontiers in Bioscience. 2023, 28, 46. Full text

25. Zupančič Barbara Ugwoke Chiedozie Kenneth, Abdelmonaem Mohamed Elwy, Alibegović Armin, Cvetko Erika, Grdadolnik Jože, Šerbec Anja, Umek Nejc. Exploration of macromolecular phenotype of human skeletal muscle in diabetes using infrared spectroscopy. Frontiers in Endocrinology. 2023, 14, 1308373. Full text

26. Naneh Omar, Kozorog Mirijam, Merzel Franci, Gilbert Robert J., Anderluh Gregor. Surface plasmon resonance and microscale thermophoresis approaches for determining the affinity of perforin for calcium ions. Frontiers in Immunology. 2023, 14, 1181020. Full text

27. Jeran Marko, Romolo Anna, Spasovski Vesna, Hočevar Matej, Novak Urban, Štukelj Roman, Šuštar Vid, Kisovec Matic, Bedina Zavec Apolonija, Kogej Ksenija, Iglič Aleš, Trebše Polonca, Kralj-Iglič Veronika. Small cellular particles from European spruce needle homogenate. International Journal of Molecular Sciences. 2023, 24, 4349. Full text

28. Sever Marko, Merzel Franci. Collective domain motion facilitates water transport in SGLT1. International Journal of Molecular Sciences. 2023, 24, 10528. Full text 

29. Papež Petra, Merzel Franci, Praprotnik Matej. Sub-THz acoustic excitation of protein motion. Journal of Chemical Physics. 2023, 159, 135101. Full text 

30. Hubman Anže, Merzel Franci. Determination of thermal conductivities in liquids by identifying heat transport in nonequilibrium MD simulations. Journal of Molecular Liquids. 2023, 370, 120916. Full text

31. Papež Petra, Merzel Franci, Praprotnik Matej. Rotational dynamics of a protein under shear flow studied by the Eckart frame formalism. Journal of Physical Chemistry B. 2023, 127, 7231-7243. Full text

32. Sever Marko, Merzel Franci. Influence of SGLT1 sugar uptake inhibitors on water transport. Molecules. 2023, 28, 5295. Full text

33. Hubman Anže, Volavšek Janez, Urbič Tomaž, Zabukovec Logar Nataša, Merzel Franci. Water–aluminum interaction as driving force of linde type A aluminophosphate hydration. Nanomaterials. 2023, 13, 2387. Full text

34. Giacomazzi Luigi, Shcheblanov, Nikita S. Povarnitsyn, Mikhail E. Li, Yanbo, Mavrič Andraž, Zupančič Barbara, Grdadolnik Jože, Pasquarello Alfredo. Infrared spectra in amorphous alumina : a combined ab initio and experimental study. Physical Review Materials. 2023, 7, 045604. Full text

35. Paoletti Francesca, Covaceuszach Sonia, Cassetta Alberto, Calabrese Antonio N., Novak Urban, Konarev Peter, Grdadolnik Jože, Lamba Doriano, Golič Grdadolnik Simona. Distinct conformational changes occur within the intrinsically unstructured pro-domain of pro-Nerve Growth Factor in the presence of ATP and Mg2+. Protein Science. 2023, 32, e4563. Full text 

36. Zupančič Barbara, Grdadolnik Jože. Water–hydrogen-bond network and hydrophobic effect. V: Marek J. Wójcik (ur.), Ozaki Yukihiro (ur.). Spectroscopy and computation of hydrogen-bonded systems. Weinheim: Wiley-VCH, 2023. 435-478. Full text

37. Potisk Tilen, Remškar Maja, Pirker Luka, Filipič Gregor, Mihelič Igor, Ješelnik Marjan, Čoko Urban, Ravnik Miha. Single-layer and double-layer filtration materials based on polyvinylidene fluoride-co-hexafluoropropylene nanofibers coated on melamine microfibers. ACS Applied Nano Materials. 2023, 6, 15807-15819. Full text

38. Potisk Tilen, Sablić Jurij, Svenšek Daniel, Sanz-De Diego Elena, Teran Francisco J., Praprotnik Matej. Analyte-driven clustering of bio-conjugated magnetic nanoparticles. Advanced Theory and Simulations. 2023, 6, 2200796. Full text

39. Lisgarten David R., Palmer Rex Alfred, Cooper Jon, Naylor Claire E., Talbert Rosemary C., Howlin Brendan J., Lisgarten John N., Konc Janez, Najmudin Shabir, Lobley Carina M. C. Ultra-high resolution X-ray structure of orthorhombic bovine pancreatic Ribonuclease A at 100K. BMC Chemistry. 2023, 17, 91. Full text 

40. Šimon Martin, Mikec Špela, Morton Nicholas M., Atanur Santosh S., Konc Janez, Horvat Simon, Kunej Tanja. Genome-wide screening for genetic variants in polyadenylation signal (PAS) sites in mouse selection lines for fatness and leanness. Mammalian Genome. 2023, 34, 12-31. Full text

41. Turk Janez, Svenšek Daniel. Thermoelasticity of injection-molded parts. Polymers. 2023, 15, 2841. Full text

42. Hladnik Jurij, Svenšek Daniel, Jerman Boris, Supej Matej. Mass point versus whole-body modelling of skiers for performance evaluation in alpine skiing. Scandinavian Journal of Medicine & Science in Sports. 2023, 33, 943-953. Full text

43. Ent Florian Van Der, Skagseth Susann, Lund Bjarte A., Sočan Jaka, Griese Julia J., Brandsdal Bjørn Olav, Åqvist Johan. Computational design of the temperature optimum of an enzyme reaction. Science Advances. 2023, 9, eadi0963. Full text

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. Kokot Maja, Weiss Matjaž, Zdovc Irena, Anderluh Marko, Hrast Rambaher Martina, Minovski Nikola. Diminishing hERG inhibitory activity of aminopiperidine-naphthyridine linked NBTI antibacterials by structural and physicochemical optimizations. Bioorganic Chemistry. 2022, 128, 106087. Full text

12. Fjodorova Natalja Stanislavovna, Novič Marjana, Venko Katja, Drgan Viktor, Rasulev Bakhtiyor, Saçan Türker Melek, Sağ Erdem Safiye, Tuğcu Gülçin, Toropova Alla P., Toropov Andrey A. How fullerene derivatives (FDs) act on therapeutically important targets associated with diabetic diseases. Computational and Structural Biotechnology Journal. 2022, 20, 913-924. Full text

13. Spînu Nicoleta, Cronin Mark T. D., Lao Junpeng, Bal-Price Anna, Campia Ivana, Enoch Steven J., Madden Judith C., Mora Lagares Liadys, Novič Marjana, Pamies David, Scholz Stefan, Villeneuve Daniel L., Worth Andrew P. Probabilistic modelling of developmental neurotoxicity based on a simplified adverse outcome pathway network. Computational Toxicology. 2022, 21, 100206. Full text

14. Tušar Marjan, Ravnikar Turk Mojca, Ržek Lidija. A triangular representation of the volumetric properties of asphalt mixtures. Construction & Building materials. 2022, 314, 125496. Full text

15. Mora Lagares Liadys, Perez Castillo Yunierkis, Minovski Nikola, Novič Marjana. Structure–function relationships in the human P-Glycoprotein (ABCB1) : insights from molecular dynamics simulations. International Journal of Molecular Sciences. 2022, 23, 362. Full text

16. Ržek Lidija, Tušar Marjan, Slemenik Perše Lidija. Modelling rheological characteristics of rejuvenated aged bitumen. International Journal of Pavement Engineering. 2022, 23, 1282-1294. Full text

17. Poulikakos Lily D., Pasquini Emiliano, Tušar Marjan, Hernando David, Wang Di, Mikhailenko Peter, Pasetto Marco, Baliello Andrea, Falchetto Augusto Cannone, Miljković Miomir, Oreškovič Marko, et al. RILEM interlaboratory study on the mechanical properties of asphalt mixtures modified with polyethylene waste. Journal of Cleaner Production. 2022, 375, 134124. Full text

18. Sukač Sergij, Čenčevoj Volodimir, Fjodorova Natalja Stanislavovna, Čenčeva Olga, Baharev Volodimir, Korcovoj Olena, Ševčenko Volodimir, Petrenko Ivan. Applying a neural network method to search for optimal air ionization conditions. Journal of Enterprise Technologies. 2022, 6, 27–34. Full text

19. Toropova Alla P., Toropov Andrey A., Fjodorova Natalja Stanislavovna. Quasi-SMILES for predicting toxicity of Nano-mixtures to Daphnia Magna. NanoImpact. 2022, 28, 100427. Full text

20. Wang Di, Baliello Andrea, Poulikakos Lily D., Vasconcelos Kamilla, Kakar Muhammad Rafiq, Giancontieri Gaspare, Pasquini Emiliano, Porot Laurent, Tušar Marjan, Riccardi Chiara, et al. Rheological properties of asphalt binder modified with waste polyethylene: an interlaboratory research from the RILEM TC WMR. Resources, Conservation and Recycling. 2022, 186, 106564. Full text

21. Vračko Marjan, Stanojević Mark, Sollner Dolenc Marija. Comparison of predictions of developmental toxicity for compounds of solvent data set. SAR and QSAR in Environmental Research. 2022, 33, 35-48. Full text

22. Pirc Katja, Clifton Luke A., Yilmaz Neval, Saltalamacchia Andrea, Mally Mojca, Snoj Tina, Žnidaršič Nada, Srnko Marija, Borišek Jure, Podobnik Marjetka, Derganc Jure, Anderluh Gregor, et al. An oomycete NLP cytolysin forms transient small pores in lipid membranes. Science Advances. 2022, 8, eabj9406. Full text

23. Caballero Alfonso Ana Yisel, Mora Lagares Liadys, Novič Marjana, Benfenati Emilio, Kumar Kruthiventi Anil, Chayawan Chayawan. Exploration of structural requirements for azole chemicals towards human aromatase CYP19A1 activity : classification modeling, structure-activity relationships and read-across study. Toxicology in Vitro. 2022, 81, 105332. Full text

24. Prašnikar Eva, Borišek Jure, Perdih Andrej. Celična senescenca : nova terapevtska tarča pri zdravljenju s starostjo povezanih boleznih. Farmacevtski vestnik: strokovno glasilo slovenske farmacije. 2022, 73, 40-53. Full text

25. Mora Lagares Liadys, Novič Marjana. Recent advances on P-glycoprotein (ABCB1) transporter modelling with in silico methods. International Journal of Molecular Sciences. 2022, 23, 14804. Full text

26. Kokot Maja, Anderluh Marko, Hrast Rambaher Martina, Minovski Nikola. The structural features of novel bacterial topoisomerase inhibitors that define their activity on topoisomerase IV. Journal of Medicinal Chemistry. 2022, 65, 6431–6440. Full text

27. Koritnik Neža, Gerdol Marco, Šolinc Gašper, Švigelj Tomaž, Caserman Simon, Merzel Franci, Holden Ellie, Benesch Justin L. P., Trenti Francesco, Guella Graziano, Pallavicini Alberto, Modica Maria Vittoria, Podobnik Marjetka, Anderluh Gregor. Expansion and neofunctionalization of actinoporin-like genes in Mediterranean mussel (Mytilus galloprovincialis). Genome Biology and Evolution. 2022, 14, evac151. Full text

28. Covaceuszach Sonia, Peche Leticia Yamila, Konarev Petr Valerjevič, Grdadolnik Jože, Cattaneo Antonino, Lamba Doriano. Untangling the conformational plasticity of V66M human proBDNF polymorphism as a modifier of psychiatric disorder susceptibility. International Journal of Molecular Sciences. 2022, 23, 6596. Full text

29. Zupančič Barbara, Umek Nejc, Ugwoke Chiedozie Kenneth, Cvetko Erika, Horvat Simon, Grdadolnik Jože. Application of FTIR spectroscopy to detect changes in skeletal muscle composition due to obesity with insulin resistance and STZ-induced diabetes. International Journal of Molecular Sciences. 2022, 23, 12498. Full text

30. Grdadolnik Matic, Marušič Arne K., Jenko Monika, Snoj Luka, Mozer Alenka, Dolinar Drago, Novak Urban. The application of vibrational spectroscopy in the analysis of ultra-high molecular weight polyethylene for knee and hip prosthetics. International Journal of Natural Sciences : Current and Future Research Trends. 2022, 14, 92-108. Full text

31. Pavlin Anja, Lovše Anže, Bajc Gregor, Otoničar Jan, Kujović Amela, Lengar Živa, Gutiérrez-Aguirre Ion, Kostanjšek Rok, Konc Janez, Fornelos Nadine, Butala Matej. A small bacteriophage protein determines the hierarchy over co-residential jumbo phage in Bacillus thuringiensis serovar israelensis. Communications Biology. 2022, 5, 1286. Full text

32. Konc Janez, Janežič Dušanka. ProBiS-Fold approach for annotation of human structures from the alphafold database with no corresponding structure in the PDB to discover new druggable binding sites. Journal of Chemical Information and Modeling. 2022, 62, 5821-5829. Full text

33. Proj Matic, De Jonghe Steven, Van Loy Tom, Jukič Marko, Meden Anže, Ciber Luka, Podlipnik Črtomir, Grošelj Uroš, Konc Janez, Schols Dominique, Gobec Stanislav. A set of experimentally validated decoys for the human CC chemokine receptor 7 (CCR7) obtained by virtual screening. Frontiers in Pharmacology. 2022, 13, 855653. Full text 

34. Škrlj Blaž, Kralj Jan, Konc Janez, Robnik Šikonja Marko, Lavrač Nada. Deep node ranking for neuro-symbolic structural node embedding and classification. International Journal of Intelligent Systems. 2022, 37, 914-943. Full text

35. Konc Janez, Lešnik Samo, Škrlj Blaž, Sova Matej, Proj Matic, Knez Damijan, Gobec Stanislav, Janežič Dušanka. ProBiS-Dock : a hybrid multitemplate homology flexible docking algorithm enabled by protein binding site comparison. Journal of Chemical Information and Modeling. 2022, 62, 1573-1584. Full text

36. Vlachas Pantelis R., Zavadlav Julija, Praprotnik Matej, Koumoutsakos Petros. Accelerated simulations of molecular systems through learning of effective dynamics. Journal of Chemical Theory and Computation. 2022, 18, 538–549. Full text

37. Papež Petra, Praprotnik Matej. Dissipative particle dynamics simulation of ultrasound propagation through liquid water. Journal of Chemical Theory and Computation. 2022, 18, 1227–1240. Full text

38. Reba Kristjan, Guid Matej, Rozman Kati, Janežič Dušanka, Konc Janez. Exact maximum clique algorithm for different graph types using machine learning. Mathematics. 2022, 10, 97. Full text

39. Mikec Špela, Šimon Martin, Morton Nicholas M., Atanur Santosh S., Konc Janez, Dovč Peter, Horvat Simon, Kunej Tanja. Genetic variants of the hypoxia-inducible factor 3 alpha subunit (Hif3a) gene in the Fat and Lean mouse selection lines. Molecular Biology Reports. 2022, 49, 4619-4631. Full text

40. Draškovič-Bračun Aljaž, Potisk Tilen, Praprotnik Matej, Svenšek Daniel. Suspension of discrete microscopic oscillators as a model of an ultrasonic metafluid. Physical Review B. 2022, 105, 224317. Full text

41. Papež Petra, Urbič Tomaž. Simple two-dimensional models of alcohols. Physical review E. 2022, 105, 054608. Full text

42. Konc Janez, Janežič Dušanka. Protein binding sites for drug design. Biophysical Reviews. 2022, 14, 1413–1421. Full text

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

11. Borišek Jure, Magistrato Alessandra. An expanded two−Zn2+−ion motif orchestrates pre-mRNA maturation in the 3ʹ-end processing endonuclease machinery. ACS Catalysis. 2021, 11, 4319-4326. Full text

12. Kokot Maja, Weiss Matjaž, Zdovc Irena, Hrast Rambaher Martina, Anderluh Marko, Minovski Nikola. Structurally optimized potent dual-targeting NBTI antibacterials with an enhanced bifurcated halogen-bonding propensity. ACS Medicinal Chemistry Letters. 2021, 12, 1478-1485. Full text

13. Kolarič Anja, Kokot Maja, Hrast Rambaher Martina, Weiss Matjaž, Zdovc Irena, Trontelj Jurij, Žakelj Simon, Anderluh Marko, Minovski Nikola. A fine-tuned lipophilicity/hydrophilicity ratio governs antibacterial potency and selectivity of bifurcated halogen bond-forming NBTIs. Antibiotics. 2021, 10, 862. Full text

14. Stanojević Mark, Vračko Marjan, Sollner Dolenc Marija. Computational evaluation of endocrine activity of biocidal active substances. Chemosphere. 2021, 267, 129284. Full text

15. Vračko Marjan, Basak Subhash C., Sen Dwaipayan, Nandy Ashesh. Clustering of Zika viruses originating from different geographical regions using computational sequence descriptors. Current Computer-Aided Drug Design. 2021, 17, 314-322. Full text

16. Vračko Marjan, Basak Subhash C., Dey Tathagata, Nandy Ashesh. Cluster analysis of coronavirus sequences using computational sequence descriptors : with applications to SARS, MERS and SARS-CoV-2 (CoVID-19). Current Computer-Aided Drug Design. 2021, 17, 936-945. Full text

17. Venko Katja, Novič Marjana, Stoka Veronika, Žerovnik Eva. Prediction of transmembrane regions, cholesterol and ganglioside binding sites in amyloid-forming proteins indicate potential for amyloid pore formation. Frontiers in Molecular Neuroscience. 2021, 14, 619496. Full text

18. Ravnikar Turk Mojca, Ržek Lidija, Tušar Marjan. Karakterizacija s polimeri modificiranih bitumnov z reološkimi preiskavami. Gradbeni vestnik: glasilo Zveze društev gradbenih inženirjev in tehnikov Slovenije. 2021, 70, 42-50. Full text

19. Drgan Viktor, Bajželj Benjamin. Application of supervised SOM algorithms in predicting the hepatotoxic potential of drugs. International Journal of Molecular Sciences. 2021, 22, 4443. Full text

20. Spinello Angelo, Borišek Jure, Malcovati Luca, Magistrato Alessandra. Investigating the molecular mechanism of H3B-8800 : a splicing modulator inducing preferential lethality in spliceosome-mutant cancers. International Journal of Molecular Sciences. 2021, 22, 1222. Full text

21. Spinello Angelo, Saltalamacchia Andrea, Borišek Jure, Magistrato Alessandra. Allosteric cross-talk among Spikeʼs receptor-binding domain mutations of the SARS-CoV-2 South African variant triggers an effective hijacking of human cell receptor. Journal of Physical Chemistry Letters. 2021, 12, 5987-5993. Full text

22. Borišek Jure, Spinello Angelo, Magistrato Alessandra. Molecular basis of SARS-CoV-2 Nsp1-induced immune translational shutdown as revealed by all-atom simulations. Journal of Physical Chemistry Letters. 2021, 12, 11745–11750. Full text

23. Kolarič Anja, Germe Thomas, Hrast Rambaher Martina, Stevenson Clare E. M., Lawson David M., Burton Nicolas P., Vörös Judit, Maxwell Anthony, Minovski Nikola, Anderluh Marko. Potent DNA gyrase inhibitors bind asymmetrically to their target using symmetrical bifurcated halogen bonds. Nature Communications. 2021, 12, 150. Full text

24. Pirc Katja, Hodnik Vesna, Snoj Tina, Lenarčič Tea, Caserman Simon, Podobnik Marjetka, Kotar Anita, Plavec Janez, Borišek Jure, Brus Boris, Sosič Izidor, Gobec Stanislav, Anderluh Gregor, et al. Nep1-like proteins as a target for plant pathogen control. PLOS Pathogens. 2021, 17, e1009477. Full text 

25. Borišek Jure, Casalino Lorenzo, Saltalamacchia Andrea, Mays Suzanne G., Malcovati Luca, Magistrato Alessandra. Atomic-level mechanism of pre-mRNA splicing in health and disease. Accounts of Chemical Research. 2021, 54, 144-154. Full text

26. Spinello Angelo, Borišek Jure, Pavlin Matic, Janoš Pavel, Magistrato Alessandra. Computing metal-binding proteins for therapeutic benefit. ChemMedChem. 2021, 16, 2034-2049. Full text 

27. Bitenc Jan, Scafuri Antonio, Pirnat Klemen, Lozinšek Matic, Jerman Ivan, Grdadolnik Jože, Fraisse Bernard, Berthelot Romain, Stievano Lorenzo, Dominko Robert. Electrochemical performance and mechanism of calcium metal-organic battery. Batteries & Supercaps. 2021, 4, 214-220. Full text

28. Ogris Iza, Zelenko Urška, Sosič Izidor, Gobec Martina, Skubic Cene, Ivanov Marija, Soković Marina, Kocjan Darko, Rozman Damjana, Golič Grdadolnik Simona. Pyridylethanol(phenylethyl)amines are non-azole, highly selective Candida albicans Sterol 14alpha-demethylase inhibitors. Bioorganic Chemistry. 2021, 106, 104472. Full text

29. Petri László, Ábrányi-Balogh Péter, Imre Tímea, Pálfy Gyula, Perczel András, Knez Damijan, Hrast Martina, Gobec Martina, Sosič Izidor, Golič Grdadolnik Simona, Gobec Stanislav, Ogris Iza, et al. Assessment of tractable cysteines by covalent fragments screenings. ChemBioChem. 2021, 22, 743-753. Full text

30. Badasyan Artem, Tonoyan Sh. A., Valant Matjaž, Grdadolnik Jože. Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins. Communications Chemistry. 2021, 4, 57. Full text

31. Paoletti Francesca, Merzel Franci, Cassetta Alberto, Ogris Iza, Covaceuszach Sonia, Grdadolnik Jože, Lamba Doriano, Golič Grdadolnik Simona. Endogenous modulators of neurotrophin signaling : landscape of the transient ATP-NGF interactions. Computational and Structural Biotechnology Journal. 2021, 19, 2938-2949. Full text

32. Potisek Mateja, Likar Matevž, Vogel-Mikuš Katarina, Arčon Iztok, Grdadolnik Jože, Regvar Marjana. 1,8-dihydroxy naphthalene (DHN) - melanin confers tolerance to cadmium in isolates of melanised dark septate endophytes. Ecotoxicology and Environmental Safety. 2021, 222, 112493. Full text

33. Zupančič Barbara, Prokop Yulia, Nikonov Anatolij. FEM analysis of dispersive elastic waves in three-layered composite plates with high contrast properties. Finite Elements in Analysis and Design. 2021, 193, 103553. Full text

34. Badasyan Artem, Valant Matjaž, Grdadolnik Jože, Uversky Vladimir N. The finite size effects and two-state paradigm of protein folding. International Journal of Molecular Sciences. 2021, 22, 2184. Full text

35. Toplak Žan, Merzel Franci, Pardo A. Luis, Peterlin-Mašič Lucija, Tomašič Tihomir. Molecular dynamics-derived pharmacophore model explaining the nonselective aspect of KV10.1 pore blockers. International Journal of Molecular Sciences. 2021, 22, 8999. Full text

36. Zupančič Barbara, Grdadolnik Jože. Solute-induced changes in the water H-bond network of different alcohol-aqueous systems. Journal of Molecular Liquids. 2021, 341, 117349. Full text

37. Novak Urban, Grdadolnik Jože. Infrared spectra of hydrogen bond network in lamellar perfluorocarboxylic acid monohydrates. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy. 2021, 253, 119551. Full text

38. Soumelidou Evangelia, Golič Grdadolnik Simona, Mavromoustakos Thomas Michael. Drug incorporation in the drug delivery system of micelles. Supramolecules in Drug Discovery and Drug Delivery: Methods and Protocols. New York: Humana Press, 2021, 2207, 99-108. Full text

39. Papadopoulou Ermioni, Zavadlav Julija, Podgornik Rudolf, Praprotnik Matej, Koumoutsakos Petros. Tuning the dielectric response of water in nanoconfinement through surface wettability. ACS Nano. 2021, 15, 20311–20318. Full text

40. Škrlj Blaž, Eržen Nika, Lavrač Nada, Kunej Tanja, Konc Janez. CaNDis: a web server for investigation of causal relationships between diseases, drugs, and drug targets. Bioinformatics. 2021, 37, 885-887. Full text

41. Kralj Sebastjan, Hodošček Milan, Podobnik Barbara, Kunej Tanja, Bren Urban, Janežič Dušanka, Konc Janez. Molecular dynamics simulations reveal interactions of an IgG1 antibody with selected Fc receptors. Frontiers in Chemistry. 2021, 9, 705931. Full text

42. Giannos Thomas, Lešnik Samo, Bren Urban, Hodošček Milan, Domratcheva Tatiana, Bondar Ana-Nicoleta. CHARMM force-field parameters for morphine, heroin, and oliceridine, and conformational dynamics of opioid drugs. Journal of Chemical Information and Modeling. 2021, 61, 3964-3977. Full text

43. Konc Janez, Lešnik Samo, Škrlj Blaž, Janežič Dušanka. ProBiS-Dock database : a web server and interactive web repository of small ligand-protein binding sites for drug design. Journal of Chemical Information and Modeling. 2021, 61, 4097-4107. Full text

44. Slejko Ema, Hribar-Lee Barbara. The effect of macromolecular crowders on dielecric constant of aqueous electrolyte solutions. Journal of Molecular Liquids. 2021, 336, 116295. Full text

45. Kores Katarina, Konc Janez, Bren Urban. Mechanistic insights into side effects of troglitazone and rosiglitazone using a novel inverse molecular docking protocol. Pharmaceutics. 2021, 13, 315. Full text 

46. López Núria, Del Debbio Luigi, Baaden Marc, Praprotnik Matej, Grigori Laura, Simões Catarina, Bogaerts Serge, Berberich Florian, Lippert Thomas, Ignatius Janne, Lavocat Philippe, Pineda Oriol, Grazia Giuffreda Maria, Girona Sergi, Kranzlmüller Dieter, Resch Michael M., Scipione Gabriella, Schulthess Thomas. Lessons learned from urgent computing in Europe : tackling the COVID-19 pandemic. Proceedings of the National Academy of Sciences of the United States of America. 2021, 118, e2024891118. Full text

47. Cortes-Huerto Robinson, Praprotnik Matej, Kremer Kurt, Delle Site Luigi. From adaptive resolution to molecular dynamics of open systems. European Physical Journal B. 2021, 94, 189. Full text

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

11. Borišek Jure, Magistrato Alessandra. All-atom simulations decrypt the molecular terms of RNA catalysis in the exon-ligation step of the spliceosome. ACS Catalysis. 2020, 10, 5328-5334. Full text

12. Kroezen Blijke S., Conti Gabriele, Girardi Benedetta, Cramer Jonathan, Jiang Xiaohua, Rabbani Said, Müller Jennifer, Kokot Maja, Luisoni Enrico, Ricklin Daniel, Schwardt Oliver, Ernst Beat. A potent mimetic of the Siglec-8 ligand 6ʹ-sulfo-sialyl Lewisx. ChemMedChem. 2020, 15, 1706-1719. Full text

13. Ržek Lidija, Ravnikar Turk Mojca, Tušar Marjan. Increasing the rate of reclaimed asphalt in asphalt mixture by using alternative rejuvenator produced by tire pyrolysis. Construction & Building Materials. 2020, 232, 117177. Full text

14. Sluga Janja, Venko Katja, Drgan Viktor, Novič Marjana. QSPR models for prediction of aqueous solubility: exploring the potency of Randić-type indices. Croatica Chemica Acta. 2020, 93, 311-319. Full text

15. Mora Lagares Liadys, Minovski Nikola, Caballero Alfonso Ana Yisel, Benfenati Emilio, Wellens Sara, Culot Maxime, Gosselet Fabien, Novič Marjana. Homology modeling of the human P-glycoprotein (ABCB1) and insights into ligand binding through molecular docking studies. International Journal of Molecular Sciences. 2020, 21, 4058. Full text

16. Borišek Jure, Saltalamacchia Andrea, Spinello Angelo, Magistrato Alessandra. Exploiting cryo-EM structural information and all-atom simulations to decrypt the molecular mechanism of splicing modulators. Journal of Chemical Information and Modeling. 2020, 60, 2510-2521. Full text 

17. Kolarič Anja, Anderluh Marko, Minovski Nikola. Two-decades of successful SAR-grounded stories of the novel bacterial topoisomerase inhibitors (NBTIs). Journal of Medicinal Chemistry. 2020, 63, 5664-5674. Full text 

18. Mardirossian Mario, Sola Riccardo, Beckert Bertrand, Valencic Erica, Collis Dominic W. P., Borišek Jure, Armas Federica, Di Stasi Adriana, Buchmann Jan, Syroegin Egor A., Polikanov Yury S., Magistrato Alessandra, Hilpert Kai, Wilson Daniel N., Scocchi Marco. Peptide inhibitors of bacterial protein synthesis with broad spectrum and SbmA-independent bactericidal activity against clinical pathogens. Journal of Medicinal Chemistry. 2020, 63, 9590-9602. Full text

19. Saltalamacchia Andrea, Casalino Lorenzo, Borišek Jure, Batista Victor S., Rivalta Ivan, Magistrato Alessandra. Decrypting the information exchange pathways across the spliceosome machinery. Journal of the American Chemical Society: JACS. 2020, 142, 8403-8411. Full text

20. Bajželj Benjamin, Drgan Viktor. Hepatotoxicity modeling using counter-propagation artificial neural networks : handling an imbalanced classification problem. Molecules. 2020, 25, 481. Full text

21. Fjodorova Natalja Stanislavovna, Novič Marjana, Venko Katja, Rasulev Bakhtiyor. A comprehensive cheminformatics analysis of structural features affecting the binding activity of fullerene derivatives. Nanomaterials. 2020, 10, 90. Full text

22. Basak Subhash C., Vračko Marjan. Parsimony principle and its proper use/ application in computer-assisted drug design and QSAR. Current Computer-Aided Drug Design. 2020, 16, 103495. Full text

23. Merzel Franci, Avbelj Franc. Why do water molecules around small hydrophobic solutes form stronger hydrogen bonds than in the bulk?. Biochimica et Biophysica Acta (G). General Subjects. 2020, 1864, 129537. Full text

24. Vižintin Alen, Bitenc Jan, Kopač Lautar Anja, Grdadolnik Jože, Randon-Vitanova Anna, Pirnat Klemen. Redox mechanisms in Li and Mg batteries containing poly(phenanthrene quinone)/graphene cathodes using operando ATR-IR spectroscopy. ChemSusChem. 2020, 13, 2328-2336. Full text

25. Ivanov Marija, Kannan Abhilash, Stojković Dejan, Glamočlija Jasmina, Golič Grdadolnik Simona, Sanglard Dominique, Soković Marina. Revealing the astragalin mode of anticandidal action. EXCLI journal. 2020, 19, 1436-1445. Full text

26. Dudas Balint, Merzel Franci, Jang Hyunbum, Nussinov Ruth, Perahia David, Balog Erika. Nucleotide-specific autoinhibition of full-length K-Ras4B identified by extensive conformational sampling. Frontiers in Molecular Biosciences. 2020, 7, 145. Full text

27. Androutsou Maria-Eleni, Nteli Agathi, Gkika Areti, Avloniti Maria, Dagkonaki Anastasia, Probert Lesley, Tselios Theodore V., Golič Grdadolnik Simona. Characterization of asparagine deamidation in immunodominant myelin oligodendrocyte glycoprotein peptide potential immunotherapy for the treatment of multiple sclerosis. International Journal of Molecular Sciences. 2020, 21, 7566. Full text

28. Papaemmanouil Christina, Chatziathanasiadou Maria V., Chatzigiannis Christos M., Chontzopoulou Eleni, Mavromoustakos Thomas Michael, Golič Grdadolnik Simona, Tzakos Andreas G. Unveiling the interaction profile of rosmarinic acid and its bioactive substructures with serum albumin. Journal of Enzyme Inhibition and Medicinal Chemistry. 2020, 35, 786-804. Full text

29. Tan Pan, Huang Juan, Mamontov Eugene, Sakai Victoria Garcia, Merzel Franci, Liu Zhuo, Ye Yiyang, Liang Hong. Decoupling between translation and rotation of water in the proximity of a protein molecule. Physical Chemistry Chemical Physics. 2020, 22, 18132-18140. Full text

30. Önder Özgün Can, Utroša Petra, Caserman Simon, Podobnik Marjetka, Tušek-Žnidarič Magda, Grdadolnik Jože, Kovačič Sebastijan, Žagar Ema, Pahovnik David. Emulsion-templated synthetic polypeptide scaffolds prepared by ring-opening polymerization of N-carboxyanhydrides. Polymer Chemistry. 2020, 11, 4260-4270. Full text

31. Kramberger Bine, Ogrinc Nives, Potočnik Doris, Grdadolnik Jože. The multi-disciplinary study of early Copper Age lamps from Zgornje Radvanje (NE Slovenia). Quaternary International. 2020, 569-570, 102-119. Full text

32. Jukič Marko, Konc Janez, Janežič Dušanka, Bren Urban. ProBiS H2O MD approach for identification of conserved water sites in protein structures for drug design. ACS Medicinal Chemistry Letters. 2020, 11, 877-882. Full text

33. Fine Jonathan, Konc Janez, Samudrala Ram, Chopra Gaurav. CANDOCK: Chemical atomic network-based hierarchical flexible docking algorithm using generalized statistical potentials. Journal of Chemical information and Modeling. 2020, 60, 1509-1527. Full text

34. Wolf Alexander, Dragelj Jovan, Wonneberg Juliane, Stellmacher Johannes, Balke Jens, Woelke L. Anna, Hodošček Milan, Knapp W. Ernst, Alexiev Ulrike. The redox-coupled proton-channel opening in cytochrome c oxidase. Chemical Science. 2020, 11, 3804-3811. Full text

35. Lešnik Samo, Hodošček Milan, Bren Urban, Stein Christoph, Bondar Ana-Nicoleta. Potential energy function for fentanyl-based opioid pain killers. Journal of Chemical Information and Modeling. 2020, 60, 3566-3576. Full text

36. Lešnik Samo, Hodošček Milan, Podobnik Barbara, Konc Janez. Loop grafting between similar local environments for Fc-silent antibodies. Journal of Chemical Information and Modeling. 2020, 60, 5475-5486. Full text

37. Thaler S., Praprotnik Matej, Zavadlav Julija. Back-mapping augmented adaptive resolution simulation. Journal of Chemical Physics. 2020, 153, 164118. Full text

38. Knez Damijan, Colettis Natalia, Iacovino Luca G., Sova Matej, Pišlar Anja, Konc Janez, Lešnik Samo, Higgs Josefina, Kamecki Fabiola, Mangialavori Irene, Dolšak Ana, Žakelj Simon, Trontelj Jurij, Kos Janko, Binda Claudia, Marder Mariel Nora, Gobec Stanislav. Stereoselective activity of 1-propargyl-4-styrylpiperidine-like analogues that can discriminate between monoamine oxidase isoforms A and B. Journal of Medicinal Chemistry. 2020, 63, 1361-1387. Full text

39. Delle Site Luigi, Praprotnik Matej, Bell John B., Klein Rupert. Particle-continuum coupling and its scaling regimes: Theory and applications. Advanced Theory and Simulations. 2020, 3, 1900232. Full text

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

9. Borišek Jure, Saltalamacchia Andrea, Gallì Anna, Palermo Giulia, Molteni Elisabetta, Malcovati Luca, Magistrato Alessandra. Disclosing the impact of carcinogenic SF3b mutations on Pre-mRNA recognition via all-atom simulations. Biomolecules. 2019, 9, 633. Full text

10. Minovski Nikola, Saçan Türker Melek, Merve Eminoğlu Elif, Sağ Erdem Safiye, Novič Marjana. Revisiting fish toxicity of active pharmaceutical ingredients: mechanistic insights from integrated ligand-/structure-based assessments on acetylcholinesterase. Ecotoxicology and Environmental Safety. 2019, 170, 548-558. Full text

11. Sizochenko Natalia, Syzochenko Michael, Fjodorova Natalja Stanislavovna, Rasulev Bakhtiyor, Leszczynski Jerzy. Evaluating genotoxicity of metal oxide nanoparticles: application of advanced supervised and unsupervised machine learning techniques. Ecotoxicology and Environmental Safety. 2019, 185, 109733. Full text

12. Kolarič Anja, Novak Doroteja, Weiss Matjaž, Hrast Rambaher Martina, Zdovc Irena, Anderluh Marko, Minovski Nikola. Cyclohexyl amide-based novel bacterial topoisomerase inhibitors with prospective GyrA-binding fragments. Future Medicinal Chemistry. 2019, 11, 935-945. Full text

13. Venko Katja, Novič Marjana. An in silico approach for assessment of the membrane transporter activities of phenols: a case study based on computational models of transport activity for the transporter bilitranslocase. Molecules. 2019, 24, 837. Full text

14. Mora Lagares Liadys, Minovski Nikola, Novič Marjana. Multiclass classifier for P-glycoprotein substrates, inhibitors, and non-active compounds. Molecules. 2019, 24, 2006. Full text

15. Lenarčič Tea, Pirc Katja, Hodnik Vesna, Albert Isabell, Borišek Jure, Magistrato Alessandra, Nürnberger Thorsten, Podobnik Marjetka, Anderlu, Gregor. Molecular basis for functional diversity among microbial Nep1-like proteins. PLOS Pathogens. 2019, 15, e1007951. Full text

16. Basak Subhash C., Majumdar Subhabrata, Nandy Ashesh, Roy Proyasha, Dutta Tathagata, Vračko Marjan, Bhattacharjee Apurba K. Computer-assisted and data driven approaches for surveillance, drug discovery, and vaccine design for the Zika virus. Pharmaceuticals. 2019, 12, 157. Full text 

17. Bitenc Jan, Vižintin Alen, Grdadolnik Jože, Dominko Robert. Tracking electrochemical reactions inside organic electrodes by operando IR spectroscopy. Energy Storage Materials. 2019, 21, 347-353. Full text

18. Noč Luka, Šest Ervin, Kapun Gregor, Ruiz-Zepeda Francisco, Binyamin Yaniv, Merzel Franci, Jerman Ivan. High-solar-absorptance CSP coating characterization and reliability testing with isothermal and cyclic loads for service-life prediction. Energy & Environmental Science. 2019, 12, 1679-1694. Full text

19. Hrast Martina, Rožman Kaja, Ogris Iza, Škedelj Veronika, Patin Delphine, Sova Matej, Barreteau Hélène, Gobec Stanislav, Golič Grdadolnik Simona, Zega Anamarija. Evaluation of the published kinase inhibitor set to identify multiple inhibitors of bacterial ATP-dependent mur ligases. Journal of Enzyme Inhibition and Medicinal Chemistry. 2019, 34, 1010-1017. Full text

20. Kežar Andreja, Kavčič Luka, Pólak Martin, Nováček Jiři, Gutiérrez-Aguirre Ion, Tušek-Žnidarič Magda, Coll Rius Anna, Stare Katja, Gruden Kristina, Ravnikar Maja, Pahovnik David, Žagar Ema, Merzel Franci, Anderluh Gregor, Podobnik Marjetka. Structural basis for the multitasking nature of the potato virus Y coat protein. Science Advances. 2019, 5, eaaw3808. Full text

21. Noč Luka, Ruiz-Zepeda Francisco, Merzel Franci, Jerman Ivan. High-temperature ʺion baseballʺ for enhancing concentrated solar power efficiency. Solar Energy Materials and Solar Cells. 2019, 200, 109974. Full text

22. Popadić Aleksandar, Svenšek Daniel, Podgornik Rudolf, Praprotnik Matej. Density-nematic coupling in isotropic linear polymers: acoustic and osmotic birefringence. Advanced Theory and Simulations. 2019, 2, 1900019. Full text 

23. Dolšak Ana, Švajger Urban, Lešnik Samo, Konc Janez, Gobec Stanislav, Sova Matej. SelectiveToll-like receptor 7 agonists with novel chromeno[3,4-d]imidazol-4(1H)-one and 2-(trifluoromethyl)/ Quinoline/ quinazoline-4-amine scaffolds. European Journal of Medicinal Chemistry. 2019, 179, 109-122. Full text

24. Kores Katarina, Lešnik Samo, Bren Urban, Janežič Dušanka, Konc Janez. Discovery of novel potential human targets of resveratrol by inverse molecular docking. Journal of Chemical Information and Modeling. 2019, 59, 2467-2478.Full text

25. Konc Janez. Binding site comparisons for target-centered drug discovery. Expert Opinion on Drug Discovery. 2019, 14, 445-454. Full text

26. Zavadlav Julija, Marrink Siewert J., Praprotnik Matej. SWINGER : a clustering algorithm for concurrent coupling of atomistic and supramolecular liquids. Interface Focus. 2019, 9, 20180075. Full text

27. Konc Janez. Identification of neurological disease targets of natural products by computational screening. Neural Regeneration Research. 2019, 14, 2075-2076. Full text