Departments

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

2. 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. 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

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

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

4. 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

5. 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

6. 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. 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

2. 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

3. 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

4. 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 

5. 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

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

7. 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

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

9. 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. 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

2. 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

3. 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 

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

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

6. 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

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

8. 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

9. 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. 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

2. 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

3. 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 

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

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

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

1. 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

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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 

8. 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

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

1. 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 

2. 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

3. 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

4. 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

5. 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

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

7. 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

8. 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. 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 

2. 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

3. 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

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

5. 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

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