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Barbara Herlah

Personal bibliography for the period 2015-2025

2015

1. HERLAH, Barbara. Napovedovanje razgradnje, metabolizma in toksičnosti benzofenona-3 in silico = Prediction of degradation, metabolism and toxicity of benzophenone-3 in silico. Ljubljana: [B. Herlah], 2015. IX, 79 f., tabele, ilustr. http://www.ffa.uni-lj.si/fileadmin/datoteke/Knjiznica/diplome/2015/Herlah_Barbara_dipl_nal_2015.pdf, Repository of the University of Ljubljana – RUL . [COBISS.SI-ID 3922289]

2018

2. HERLAH, Barbara. Sinteza in vrednotenje piperazinskih in piperidinskih derivatov N-fenilpirolamidov kot zaviralcev DNA-giraze B = Synthesis and evaluation of piperazine and piperidine substituted N-phenylpyrrolamides as inhibitors of DNA gyrase B : industrijska farmacija. Ljubljana: [B. Herlah], 2018. XI, 61 f., tabele, graf. prikazi. Repository of the University of Ljubljana – RUL . [COBISS.SI-ID 4533105]

2021

3. PERDIH, Andrej, PAVLIN, Matic, VALJAVEC, Katja, HERLAH, Barbara. All-atom molecular simulations of a type II DNA topoisomerase molecular motor. In: 29th Conference on Intelligent Systems for Molecular Byology and the 20th European Conference on Computational Biology, July 25-30, 2021. [S. l.: s. n.]. 2021, str. [1]. https://www.iscb.org/cms_addon/conferences/ismbeccb2021/posters.php?track=3DSIG&session=C#search. [COBISS.SI-ID 72917251]
4. PAVLIN, Matic, VALJAVEC, Katja, HERLAH, Barbara, PERDIH, Andrej. All-atom simulations of a type II DNA topoisomerase molecular motor. In: PINTAR, Albin (ed.), et al. Zbornik povzetkov = Book of abstracts : Slovenski kemijski dnevi 2021 = 27th Annual Meeting of the Slovenian Chemical Society : 22.-24. september 2021, Portorož, Portorose, Slovenija. Ljubljana: Slovensko kemijsko društvo, 2021. Str. 80. ISBN 978-961-93849-9-2. [COBISS.SI-ID 80449539]
5. JANEŽIČ, Matej, VALJAVEC, Katja, BERGANT LOBODA, Kaja, HERLAH, Barbara, OGRIS, Iza, GOLIČ GRDADOLNIK, Simona, WOLBER, Gerhard, PERDIH, Andrej. Dynophore models applied in the discovery of human DNA topoisomerase ▫$II\alpha$▫ catalytic inhibitor. In: Interfacing chemical biology and drug discovery : 56th International Conference on Medicinal Chemistry : July 7-9, 2021, virtual event : book of abstracts. [S. l.: s. n.], 2021. Str. 114. [COBISS.SI-ID 72936707]
6. 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 ▫$II\alpha$▫. International journal of molecular sciences. 2 Dec. 2021, vol. 22, iss. 24, str. 1-24, ilustr. ISSN 1422-0067. https://www.mdpi.com/1422-0067/22/24/13474, DOI: 10.3390/ijms222413474. [COBISS.SI-ID 89972227]
7. JANEŽIČ, Matej, VALJAVEC, Katja, BERGANT LOBODA, Kaja, HERLAH, Barbara, WOLBER, Gerhard, PERDIH, Andrej. Dynophore-based approach to inhibitor design : development of human DNA topoisomerase IIa catalytic inhibitors. In: Book of abstracts. 2021. Str. 351. https://www.efmc-ismc.org/v2/data/1630081893EFMC-ISMC-BookOfAbstracts-webHD.pdf. [COBISS.SI-ID 75291907]
8. JANEŽIČ, Matej, VALJAVEC, Katja, BERGANT LOBODA, Kaja, HERLAH, Barbara, WOLBER, Gerhard, PERDIH, Andrej. Dynophore-based approach to inhibitor design : development of human DNA topoisomerase IIa catalytic inhibitors. In: Book of abstracts. 2021. Str. 107, ilustr. https://www.efmc-ymcs.org/v2/data/1630930688BookYMCS-Virtual-HD.pdf. [COBISS.SI-ID 77413891]
9. KENDA, Maša, VEGELJ, Jan, HERLAH, Barbara, PERDIH, Andrej, MLADĚNKA, Přemysl, SOLLNER DOLENC, Marija. Evaluation of firefly and renilla luciferase inhibition in reporter-gene assays : a case of Isoflavonoids. International journal of molecular sciences. 2021, vol. 22, no. 13, str. 1-14, ilustr. ISSN 1422-0067. https://www.mdpi.com/1422-0067/22/13/6927, Repository of the University of Ljubljana – RUL , DOI: 10.3390/ijms22136927. [COBISS.SI-ID 72671747]
project: P1-0208; funder: ARRS
project: P1-0012; funder: ARRS
project: CZ.02.1.01/0.0/0.0/16_019/0000841
project: funder: Young researchers
10. PERDIH, Andrej, HERLAH, Barbara. Uporaba molekulskih simulacij pri načrtovanju zdravilnih učinkovin : prispevek na delavnici Računske in statistične metode v kemiji, 19-21 oktober 2021. [COBISS.SI-ID 82916355]

2022

11. HERLAH, Barbara, PAVLIN, Matic, VALJAVEC, Katja, PERDIH, Andrej. All-atom simulations of a type II DNA topoisomerase: Insights into its catalytic cycle. In: Remote BioExcel School on Biomolecular Simulations : 25 March - 1 April 2022 : abstract book. [S. l.]: BioExcel CoE, 2022. Str. 10. [COBISS.SI-ID 103920899]
12. 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 ▫$3CL^{pro}$▫ main protease. Pharmaceuticals. May 2022, vol. 15, iss. 5, [article no.] 539, str. 1-24, ilustr. ISSN 1424-8247. https://www.mdpi.com/1424-8247/15/5/539/htm, DOI: 10.3390/ph15050539. [COBISS.SI-ID 106569987]
13. HERLAH, Barbara, OGRIS, Iza, GOLIČ GRDADOLNIK, Simona, SOSIČ, Izidor, GOBEC, Stanislav, PERDIH, Andrej. Development of 4,6-substituted-1,3,5-triazin-2(1H)-ones as catalytic inhibitors of the human DNA topoisomerase IIΑ. In: Book of abstracts : XXVII National meeting on medicinal chemistry : NPCF14 : 14th Young medicinal chemistsʼ symposium : Nuove prospettive in chimica farmaceutica : Università degli studi di Bari Aldo Moro, September 11-14, 2022. [Bari: Società di Chimica Italiana: Università degli studi di Bari Aldo Moro], 2022. Str. 121, ilustr. [COBISS.SI-ID 123653123]
14. 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 II▫$\alpha$▫. In: PINTAR, Albin (ed.). Slovenski kemijski dnevi 2022 = 28th Annual Meeting of the Slovenian Chemical Society : zbornik povzetkov = book of abstracts : 21.-23. september 2022, Portorož, Portorose, Slovenija. Ljubljana: Slovensko kemijsko društvo, 2022. Str. 170. ISBN 978-961-95922-1-2. [COBISS.SI-ID 125079811]
15. CVIJETIĆ, Ilija N., HERLAH, Barbara, PERDIH, Andrej. Molecular simulations of 1,5-bis(salicylidene) thiocarbohydrazide bound to ATPase domain of human DNA topoisomerase II▫$\alpha$▫. In: MILOVANOVIĆ, Jelena (ed.). Book of abstracts : 8th Conference of Young Chemists of Serbia : 29th October 2022 University of Belgrade, Faculty of Chemistry, [Belgrade]. Belgrade: Serbian Chemical Society: Serbian Young Chemists Club, 2022. Str. 3. ISBN 978-86-7132-080-1. [COBISS.SI-ID 129777923]
16. HERLAH, Barbara, VALJAVEC, Katja, JANEŽIČ, Matej, BERGANT LOBODA, Kaja, OGRIZEK, Mitja, OGRIS, Iza, KOZOROG, Mirijam, ŠTAMPAR, Martina, PODOBNIK, Marjetka, WOLBER, Gerhard, GOLIČ GRDADOLNIK, Simona, ŽEGURA, Bojana, FILIPIČ, Metka, PERDIH, Andrej. Type II DNA topoisomerase revisited : molecular simulations and development of catalytic inhibitors as safer chemotherapeutics. In: 23rd EuroQSAR : 23rd European Symposium on Quantitative Structure-Activity Relationship : Integrative Data-Intensive Approaches to Drug Design : book of abstracts : September 26-30, 2022 Heidelberg, Germany. [S. l.: s. n.], 2022. Str. 151. [COBISS.SI-ID 124118787]

2023

17. PERDIH, Andrej, JANEŽIČ, Matej, OGRIZEK, Mitja, BERGANT LOBODA, Kaja, HERLAH, Barbara, VALJAVEC, Katja, WOLBER, Gerhard. Advancing type II DNA topoisomerase research through QM/MM simulations and development of catalytic inhibitors. In: SCS Fall Meeting 2023 : 24.-25. August 2023, vonRoll Areal, University of Bern. [Bern: Swiss Chemical Society]. 2023, str. [1]. https://fm23.scg.ch/program1/abstracts. [COBISS.SI-ID 162966787]
18. HERLAH, Barbara, JANEŽIČ, Matej, BERGANT LOBODA, Kaja, VALJAVEC, Katja, PERDIH, Andrej. Development of catalytic inhibitors of topoisomerase IIα as chemotherapeutic agents. In: 10th IAPC Meeting : Tenth World Conference on Physico-Chemical Methods in Drug Discovery & Sixth World Conference on ADMET and DMPK : Belgrade, Serbia, September 4-6, 2023 : book of abstracts. [S. l.]: International Association of Physical Chemists, 2023. Str. 19. https://iapchem.org/index.php/iapc-10program/book-of-abstracts. [COBISS.SI-ID 167308291]
19. CVIJETIĆ, Ilija N., HERLAH, Barbara, MARINKOVIC, Aleksandar, PERDIH, Andrej, BJELOGRLIC, Snezana K. Phenotypic discovery of thiocarbohydrazone with anticancer properties and catalytic inhibition of human dna topoisomerase IIα. Pharmaceuticals. 2023, vol. 16, iss. 3, [article no.] 341, str. 1-19, ilustr. ISSN 1424-8247. https://www.mdpi.com/1424-8247/16/3/341. [COBISS.SI-ID 149391875]
20. HERLAH, Barbara, OGRIS, Iza, GOLIČ GRDADOLNIK, Simona, SOSIČ, Izidor, GOBEC, Stanislav, PERDIH, Andrej. Simulation-based optimization of 4,6-substituted-1,3,5-triazin-2(1H)-ones as catalytic inhibitors of the human DNA Topoisomerase IIΑ. In: Abstracts book : Lisbon 2023, at the edge of Europe and Science. [S. l.]: [s. n.], 2023. Str. 88. https://annualmeeting.eufeps.org/programme.html. [COBISS.SI-ID 156434691]
21. HERLAH, Barbara, OGRIS, Iza, GOLIČ GRDADOLNIK, Simona, GOBEC, Stanislav, SOSIČ, Izidor, PERDIH, Andrej. Structure-based optimization of 4,6-substituted-1,3,5-triazin2(1H)-ones as catalytic inhibitors of human DNA topoisomerase IIα. In: PINTAR, Albin (ed.). Slovenski kemijski dnevi 2023 = 29th Annual Meeting of the Slovenian Chemical Society : zbornik povzetkov = book of abstracts : 13.-15. september 2023, Portorož, Portorose, Slovenija. Ljubljana: Slovensko kemijsko društvo, 2023. Str. 118. ISBN 978-961-95922-2-9. https://www.conftool.org/scs-annual-meeting-2023/index.php?page=browseSessions&form_session=47#paperID119, https://www.conftool.org/scs-annual-meeting-2023/index.php/Herlah-Structure-based_optimization_of_4%2C6-substituted-1%2C3%2C5-triazin-2-119.pdf?page=downloadPaper&filename=Herlah-Structure-based_optimization_of_4%2C6-substituted-1%2C3%2C5-triazin-2-119.pdf&form_id=119. [COBISS.SI-ID 167932931]
22. 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, vol. 21, str. 3746-3759, ilustr. ISSN 2001-0370. https://www.sciencedirect.com/science/article/pii/S2001037023002593, Repository of the University of Ljubljana – RUL , DOI: 10.1016/j.csbj.2023.07.019. [COBISS.SI-ID 160446211]

2024

23. HERLAH, Barbara. Dinamični model DNA topoizomeraze tipa II ter in silico načrtovanje novih katalitičnih zaviralcev kot potencialnih kemoterapevtikov = Dynamical model of a type II DNA topoisomerase and in silico design of novel catalytic inhibitors as potential chemotherapeutics : doktorska disertacija. Ljubljana: [B. Herlah], 2024. V, 207 str., ilustr. [COBISS.SI-ID 214908931]
project: Raziskave, predstavljene v tem doktorskem delu, so bile izvedene v okviru ARIS temeljnega raziskovalnega projekta J1-4402 Dinamični model molekulskega stroja DNA topoizomeraze tipa II in razvoj katalitičnih inhibitorjev, ter raziskovalnega programa P1-0012 Molekulske simulacije, bioinformatika in načrtovanje zdravilnih učinkovin in v okviru programa Mladih raziskovalcev na Kemijskem inštitutu v Ljubljani.
24. HERLAH, Barbara, JANEŽIČ, Matej, OGRIS, Iza, GOLIČ GRDADOLNIK, Simona, KOLOŠA, Katja, ŽABKAR, Sonja, ŽEGURA, Bojana, PERDIH, Andrej. Dynophore-derived discovery of nature-inspired substituted 3-(imidazol-2-yl) morpholines targeting topoisomerase IIα. In: PINTAR, Albin (ed.). Slovenski kemijski dnevi 2024 : zbornik povzetkov = book of abstracts : 30 let = 30 years : 18.-20. september 2024, Bernardin, Portorož. Elektronska izd. Ljubljana: Slovensko kemijsko društvo, 2024. Str. 82. ISBN 978-961-95922-3-6. https://skd2024.chem-soc.si/wp-content/uploads/2024/08/SKD-2024-Zbornik-povzetkov_compressed.pdf. [COBISS.SI-ID 210759427]
25. OGRIS, Iza, ZUPANČIČ, Barbara, HERLAH, Barbara, PERDIH, Andrej, MERZEL, Franci, GOLIČ GRDADOLNIK, Simona. Exploring the impact of MurD conformational dynamics on ligand P21 binding with NMR and MD simulations. In: ANDERLUH, Gregor (ed.), CRNKOVIĆ, Ana (ed.). 3rd MOSBRI Scientific Conference : 10th - 13th June 2024, Ljubljana, Slovenia : programme & abstracts. Ljubljana: National Institute of Chemistry, 2024. Str. 130. ISBN 978-961-6104-94-4. https://www.mosbri.eu/events/conferences/ljubljana-2024/programme-ljubljana/. [COBISS.SI-ID 199722755]
26. 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. Jun. 2024, vol. 269, pt. 2, [article no.] 131991, str. 1-17, ilustr. ISSN 1879-0003. https://www.sciencedirect.com/science/article/pii/S014181302402796X, Repository of the University of Ljubljana – RUL , DOI: 10.1016/j.ijbiomac.2024.131991. [COBISS.SI-ID 195700995]
27. 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. In: 24th EuroQSAR : September 22-26, 2024, Barcelona, Spain : book of abstracts. [S. l.: s. n.], 2024. Str. 195. [COBISS.SI-ID 212602371]
28. 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. Jun. 2024, vol. 175, [article no.] 116676, str. 1-18, ilustr. ISSN 1950-6007. https://doi.org/10.1016/j.biopha.2024.116676, DiRROS - Digital repository of Slovenian research organizations, Repository of the University of Ljubljana – RUL , DOI: 10.1016/j.biopha.2024.116676. [COBISS.SI-ID 196316419]
29. 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. Dec. 2024, vol. 23, str. 2995-3018, ilustr. ISSN 2001-0370. https://www.sciencedirect.com/science/article/pii/S2001037024002344, Repository of the University of Ljubljana – RUL , DOI: 10.1016/j.csbj.2024.06.037. [COBISS.SI-ID 200950531]
project: This work was supported by the Slovenian Research and Innovation Agency (ARIS) through research projects J1-4402 (A.P.) and J1-4400 (S.G.G.) and research programs P1-0012, P1-0010 and P1-0208 as well as a young researcher funding to B.H.
30. PERDIH, Andrej, PAVLIN, Matic, VALJAVEC, Katja, HERLAH, Barbara, JANEŽIČ, Matej. Understanding and inhibiting type IIA DNA topoisomerases : the interplay of molecular simulations and ligand design. In: Topoisomerases in biology and medicine : program and abstract book : Miami, Florida July 15-18 2024. [S. l.: s. n.], 2024. Str. 82. https://case.fiu.edu/news-events/topoisomerases-in-biology-and-medicine-conference. [COBISS.SI-ID 214534147]
31. HERLAH, Barbara, PAVLIN, Matic, PERDIH, Andrej. Unveiling the interdomain dynamics of type II DNA topoisomerase through all-atom simulations : implications for understanding its catalytic cycle. In: KRAJNC, Alen (ed.), GOBEC, Martina (ed.). Brunching with soft- and research skills at UL FFA: unlocking your full potential : 1st UL FFA Graduate Student Research Symposium : book of abstracts : University of Ljubljana, Faculty of Pharmacy, April 2024. Online ed. Ljubljana: Faculty of Pharmacy, 2024. Str. 15, ilustr. ISBN 978-961-6378-97-0. https://www.ffa.uni-lj.si/docs/default-source/e-knjige/brunching-with-soft-and-research-skills-at-ul-ffa.pdf?sfvrsn=2. [COBISS.SI-ID 198852611]

2025

32. STEVANOVIĆ, Kristina, HERLAH, Barbara, PAVLIN, Matic, PERDIH, Andrej. After T–segment passage : type IIA DNA topoisomerase catalytic cycle studied by all atom simulations. In: ChemBioParis2025 : approaching biology through chemistry : ICBS & ECBS joint meeting : PARIS 2025 : Sorbonne Université, October 6-9, 2025 : abstract book. Paris: Société Chimique de France, 2025. Str. 208. [COBISS.SI-ID 253411075]
33. 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. Oct. 2025, vol. 327, pt. 1, [article no.] 147216, str. 1-17, ilustr. ISSN 1879-0003. https://www.sciencedirect.com/science/article/pii/S0141813025077736, DiRROS - Digital repository of Slovenian research organizations, Repository of the University of Ljubljana – RUL , DOI: 10.1016/j.ijbiomac.2025.147216. [COBISS.SI-ID 249271555]
34. HERLAH, Barbara. Dinamični model DNA-topoizomeraze tipa II ter in silico načrtovanje novih katalitičnih zaviralcev kot potencialnih kemoterapevtikov = Dynamical model of type II DNA topoisomerase and in silico design of novel catalytic inhibitors as potential chemotherapeutics. In: PLEVNIK, Miha (ed.). 55. Krkine nagrade : 35. simpozij : zbornik povzetkov = 55th Krka prizes : 35th Symposium : book of abstracts : [Novo mesto, 17. oktober 2025]. Novo mesto: Krka, 2025. Str. 72. https://www.krkinenagrade.si/media/store/55-KN/633903-2025-KN-Krka-prizes-Book-of-abstracts-SI-EN.pdf, https://www.krkinenagrade.si/o-krkinih-nagradah/krkine-nagrade-po-letih/2025/. [COBISS.SI-ID 254318339]
35. JANEŽIČ, Matej, HERLAH, Barbara, VALJAVEC, Katja, WOLBER, Gerhard, PERDIH, Andrej. Harnessing the power of dynamic pharmacophores in the discovery of catalytic inhibitors of human topoisomerase IIα. In: Conformational Design in Drug Discovery 2025 : Monday 3rd March 2025 : AstraZeneca, Cambridge, UK : handbook. [S. l.: s. n.], 2025. Str. 44. [COBISS.SI-ID 230472963]
36. HOJAN, Ana. Molekulske simulacije triazinonskih inhibitorjev človeške DNA topoizomeraze IIα : zaključna naloga = Molecular simulations of triazinone inhibitors of human dna topoisomerase IIα. Koper: [A. Hojan], 2025. 1 spletni vir (1 datoteka PDF (XI, 56 str., [4] str. pril.)), ilustr. Repository of University of Primorska - RUP. [COBISS.SI-ID 244661507]
37. HERLAH, Barbara, PERDIH, Andrej. Računalniški mikroskop : raziskovanje skrivnosti atomskih svetov z molekulskimi simulacijami. Alternator : misliti znanost. 24. 4. 2025, št. 7, str. [1-6], ilustr. ISSN 2712-3510. https://www.alternator.science/sl/daljse/racunalniski-mikroskop-raziskovanje-skrivnosti-atomskih-svetov-z-molekulskimi-simulacijami/, DOI: 10.3986/alternator.2025.07. [COBISS.SI-ID 236004611]
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A source of bibliographic data: shared data base COBISS.SI/COBIB.SI, 11. 7. 2026