1. Martin Šimon, Špela Mikec, Nicholas M. Morton, Santosh S. Atanur, Janez Konc, Simon Horvat, Tanja Kunej. Genome-wide screening for genetic variants in polyadenylation signal (PAS) sites in mouse selection lines for fatness and leanness. Mamm. Genome, 2023, 34, 12-31. Full Text
  2. Janez Konc, Dušanka Janežič. Protein Binding Sites for Drug Design. Biophys. Rev., 2022, 14, 1413–1421. Open Access
  3. Anja Pavlin, Anže Lovše, Gregor Bajc, Jan Otoničar, Amela Kujović, Živa Lengar, Ion Gutierrez Aguirre, Rok Kostanjšek, Janez Konc, Nadine Fornelos, Matej Butala. A small bacteriophage protein determines the hierarchy over co-residential jumbo phage in Bacillus thuringiensis serovar israelensis. Commun. Biol., 2022, 5, 1286. Open Access
  4. Janez Konc, Dušanka Janežič. 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. J. Chem. Inf. Model., 2022, 62, 5821-5829. Full Text
  5. Janez Konc, Samo Lešnik, Blaž Škrlj, Matej Sova, Matic Proj, Damijan Knez, Stanislav Gobec, Dušanka Janežič. ProBiS-Dock: A Hybrid Multitemplate Homology Flexible Docking Algorithm Enabled by Protein Binding Site Comparison. J. Chem. Inf. Model., 2022, 62, 1573-1584. Full Text
  6. Špela Mikec, Martin Šimon, Nicholas M. Morton, Santosh S. Atanur, Janez Konc, Peter Dovč, Simon Horvat, Tanja Kunej. Genetic variants of the hypoxia-inducible factor 3 alpha subunit (Hif3a) gene in the Fat and Lean mouse selection lines. Mol. Biol. Rep., 2022 doi: 10.1007/s11033-022-07309-0
  7. Matic Proj, Steven De Jonghe, Tom Van Loy, Marko Jukič, Anže Meden, Luka Ciber, Črtomir Podlipnik, Uroš Grošelj, Janez Konc, Dominique Schols, Stanislav Gobec. A Set of Experimentally Validated Decoys for the Human CC Chemokine Receptor 7 (CCR7) Obtained by Virtual Screening. Front. Pharmacol., 2022, 13: 855653 Open Access
  8. Kristjan Reba, Matej Guid, Kati Rozman, Dušanka Janežič, Janez Konc. Exact Maximum Clique Algorithm for Different Graph Types Using Machine Learning. Mathematics, 2022, 10, 97. Open Access
  9. Blaž Škrlj, Jan Kralj, Janez Konc, Marko Robnik Šikonja, Nada Lavrač. Deep Node Ranking for Neuro-symbolic Structural Node Embedding and Classification. Int. J. Intell. Syst., 2022, 37, 914-943. Full Text
  10. Janez Konc, Samo Lešnik, Blaž Škrlj, Dušanka Janežič. ProBiS-Dock Database: A Web Server and Interactive Web Repository of Small Ligand Protein Binding Sites for Drug Design. J. Chem. Inf. Model., 2021, 61, 4097-4107. Full Text
  11. Sebastjan Kralj, Milan Hodošček, Barbara Podobnik, Tanja Kunej, Urban Bren, Dušanka Janežič, Janez Konc. Molecular Dynamics Simulations Reveal Interactions of an IgG1 antibody with selected Fc Receptors. Front. Chem, 2021, 9, 533. Open Access
  12. Katarina Kores, Janez Konc, Urban Bren. Mechanistic Insights into Side Effects of Troglitazone and Rosiglitazone Using a Novel Inverse Molecular Docking Protocol. Pharmaceutics, 2021, 13, 315. Open Access
  13. Blaž Škrlj, Nika Eržen, Nada Lavrač, Tanja Kunej, Janez Konc. CaNDis: A web server for investigation of causal relationships between diseases, drugs, and drug targets. Bioinformatics, 2021, 37, 885-887. Open Access
  14. Samo Lešnik, Milan Hodošček, Barbara Podobnik, Janez Konc. Loop Grafting between Similar Local Environments for Fc-Silent Antibodies. J. Chem. Inf. Model., 2020, 60, 5475–5486. Full Text
  15. Marko Jukic, Janez Konc, Urban Bren, Dusanka Janezic. ProBiS H2O MD Approach for Identification of Conserved Water Sites in Protein Structures for Drug Design. ACS Med. Chem. Lett., 2020, 11, 877-882. Full Text
  16. Jonathan A. Fine, Janez Konc, Ram Samudrala, Gaurav Chopra. CANDOCK: Chemical Atomic Network-based Hierarchical Flexible Docking Algorithm using Generalized Statistical Potentials. J. Chem. Inf. Model., 2020, 60, 1509-1527. Full Text
  17. Damijan Knez, Natalia Colettis, Luca Giacinto Iacovino, Matej Sova, Anja Pišlar, Janez Konc, Samo Lešnik, Josefina Higgs, Fabiola Kamecki, Irene Mangialavori, Ana Dolšak, Simon Žakelj, Jurij Trontelj, Janko Kos, Claudia Binda, Mariel Marder, Stanislav Gobec. Stereoselective Activity of 1-Propargyl-4-Styrylpiperidine-Like Analogues that can Discriminate between Monoamine Oxidase Isoforms A and B. J. Med. Chem., 2020, 63, 1361-1387. Full Text
  18. Samo Lešnik, Janez Konc. In Silico Laboratory: Tools for Similarity-Based Drug Discovery. In: Labrou N. (eds) Targeting Enzymes for Pharmaceutical Development. Methods Mol. Biol., 2020, 2089, pp 1-28. Full Text
  19. Anamarija Habic, John S. Mattick, George Adrian Calin, Rok Krese, Janez Konc, and Tanja Kunej. Genetic Variations of Ultraconserved Elements in the Human Genome. OMICS J. Integr. Biol., 2019, 23, 549-559. Open Access
  20. Janez Konc. Identification of neurological disease targets of natural products by computational screening. Neural Regen. Res., 2019, 14:2075-2076. PDF
  21. Ana Dolšak, Urban Švajger, Samo Lešnik, Janez Konc, Stanislav Gobec, Matej Sova. Selective Toll-like receptor 7 agonists with novel chromeno[3,4-d]imidazol-4(1H)-one and 2-(trifluoromethyl)quinoline/ quinazoline-4-amine scaffolds. Eur. J. Med. Chem., 2019, 179, 109-122. Full Text
  22. Katarina Kores, Samo Lešnik, Urban Bren, Dušanka Janežič, Janez Konc. Discovery of Novel Potential Human Targets of Resveratrol by Inverse Molecular Docking. J. Chem. Inf. Model., 2019, 59, 2467-2478. Full Text
  23. Janez Konc. Binding site comparisons for target-centered drug discovery. Expert Opin. Drug Discov., 2019, 14, 445-454. Full Text . PDF
  24. Veronika Furlan, Janez Konc, Urban Bren. Inverse Molecular Docking as a Novel Approach to Study Anticarcinogenic and Anti-Neuroinflammatory Effects of Curcumin. Molecules, 2018, 23, 3351. Open Access
  25. Blaž Škrlj, Tanja Kunej, Janez Konc. Insights from ion binding site network analysis into evolution and functions of proteins. Mol. Inform., 2018, 37, 1700144. Full Text
  26. Samo Lešnik, Blaž Škrlj, Nika Eržen, Urban Bren, Stanislav Gobec, Janez Konc, Dušanka Janežič. BoBER: web interface to the base of bioisosterically exchangeable replacements. J. Cheminform., 2017, 9:62. Open Access
  27. Marko Jukič, Janez Konc, Stanislav Gobec, Dušanka Janežič. Identification of Conserved Water Sites in Protein Structures for Drug Design. J. Chem. Inf. Model., 2017, 57, 3094-3103. Full Text
  28. Juyong Lee, Janez Konc, Dušanka Janežič, Bernard R. Brooks. Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins. Sci. Rep., 2017, 7:11652. Open Access
  29. Janez Konc, Blaž Škrlj, Nika Eržen, Tanja Kunej, Dušanka Janežič. GenProBiS: web server for mapping of sequence variants to protein binding sites. Nucleic Acids Res., 2017, 45, W253-W259. Open Access
  30. Blaž Škrlj, Janez Konc, Tanja Kunej. Identification of Sequence Variants within Experimentally Validated Protein Interaction Sites Provides New Insights into Molecular Mechanisms of Disease Development. Mol. Inform., 2017, 36, 1700017. Full Text
  31. Janez Konc, Dušanka Janežič. ProBiS tools (algorithm, database, and web servers) for predicting and modeling of biologically interesting proteins. Prog. Biophys. Mol. Biol., 2017, 128, 24-32. Full Text
  32. Kaja Rozman, Samo Lešnik, Boris Brus, Martina Hrast, Matej Sova, Delphine Patin, Helene Barreteau, Janez Konc, Dušanka Janežič, Stanislav Gobec. Discovery of new MurA inhibitors using induced-fit simulation and docking. Bioorg. Med. Chem. Lett., 2017, 27, 944-949. Full Text
  33. Tanja Štular, Samo Lešnik, Kaja Rozman, Julia Schink, Mitja Zdouc, An Ghysels, Feng Liu, Courtney C. Aldrich, V. Joachim Haupt, Sebastian Salentin, Simone Daminelli, Michael Schroeder, Thierry Langer, Stanislav Gobec, Dušanka Janežič, and Janez Konc. Discovery of Mycobacterium tuberculosis InhA Inhibitors by Binding Sites Comparison and Ligands Prediction. J. Med. Chem, 2016, 59, 11069-11078. Full Text
  34. Samo Lešnik, Janez Konc, Dušanka Janežič. Scaffold Hopping and Bioisosteric Replacements Based on Binding Site Alignments. Croat. Chem. Acta, 2016, 89, DOI: 10.5562/cca2993. Open Access
  35. Athira Dilip, Samo Lešnik, Tanja Štular, Dušanka Janežič, Janez Konc. Ligand-based virtual screening interface between PyMOL and LiSiCA. J. Cheminform., 2016, 8:46. Open Access
  36. Izidor Sosič, Martina Gobec, Boris Brus, Damijan Knez, Matej Živec, Janez Konc, Samo Lešnik, Mitja Ogrizek, Aleš Obreza, Dušan Žigon, Dušanka Janežič, Irena Mlinarič-Raščan, Stanislav Gobec. Nonpeptidic Selective Inhibitors of the Chymotrypsin-Like (beta5i) Subunit of the Immunoproteasome. Angew. Chem. Int. Ed., 2016, 55, 5745-5748. Full Text
  37. Mitja Ogrizek, Janez Konc, Urban Bren, Milan Hodošček, Dušanka Janežič. Role of magnesium ions in the reaction mechanism at the interface between Tm1631 protein and its DNA ligand. Chem. Cent. J., 2016, 10:41. Open Access
  38. V. Joachim Haupt, Jesus E. Aguilar Uvalle, Sebastian Salentin, Simone Daminelli, Franziska Leonhardt, Janez Konc, Michael Schroeder. Computational Drug Repositioning by Target Hopping: A Use Case in Chagas Disease. Curr. Pharm. Des., 2016, 22, 3124-3134. Full Text
  39. Janez Konc, Benjamin T. Miller, Tanja Štular, Samo Lešnik, Lee H. Woodcock, Bernard R. Brooks, Dušanka Janežič. ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites. J. Chem. Inf. Model., 2015, 55, 2308-2314. Full Text
  40. Janez Konc, Samo Lešnik, Dušanka Janežič. Modeling enzyme-ligand binding in drug discovery. J. Cheminform., 2015, 7:48. Open Access
  41. Samo Lešnik, Tanja Štular, Boris Brus, Damijan Knez, Stanislav Gobec, Dušanka Janežič, Janez Konc. LiSiCa: A Software for Ligand-based Virtual Screening and its Application for the Discovery of Butyrylcholinesterase Inhibitors. J. Chem. Inf. Model., 2015, 55, 1521-1528. Full Text
  42. Mitja Ogrizek, Samo Turk, Samo Lešnik, Izidor Sosič, Milan Hodošček, Bojana Mirković, Janko Kos, Dušanka Janežič, Stanislav Gobec, Janez Konc. Molecular dynamics to enhance structure-based virtual screening on cathepsin B. J. Comp. Aided Mol. Design, 2015, 29, 707-712. Full Text
  43. Janez Konc, Dušanka Janežič. ProBiS-ligands: a web server for prediction of ligands by examination of protein binding sites. Nucleic Acids Res., 2014, 42, W215-W220. Open Access
  44. Janez Konc, Dušanka Janežič. Binding site comparison in protein function prediction and pharmaceutical discovery. Curr. Opin. Struct. Biol., 2014, 25, 34-39. Full Text
  45. Janez Konc, Milan Hodošček, Mitja Ogrizek, Joanna Trykowska Konc, Dušanka Janežič. Structure-based function prediction of uncharacterized protein using binding sites comparison. PloS Comput. Biol., 2013, 9, e1003341. Open Access
  46. Muhammad Yusuf, Janez Konc, Choi Sy Bing, Joanna Trykowska Konc, Nurul Bahiyah Ahmad Khairudin, Dušanka Janežič, Habibah A Wahab. Structurally conserved binding sites of hemagglutinin as targets for influenza drug and vaccine development J. Chem. Inf. Model., 2013, 53, 2423–2436. Full Text
  47. Matjaz Depolli, Janez Konc, Kati Rozman, Roman Trobec, Dušanka Janežič. Exact parallel maximum clique algorithm for general and protein graphs J. Chem. Inf. Model., 2013, 53, 2217-2228. Full Text
  48. Nejc Carl, Milan Hodošček, Blaž Vehar, Janez Konc, Bernard R. Brooks, Dušanka Janežič. Correlating protein hot spot surface analysis using ProBiS with simulated free energies of protein-protein interfacial residues J. Chem. Inf. Model., 2012, 52, 2541–2549. Full Text
  49. Petra Brozic, Samo Turk, Adegoke O. Adeniji, Janez Konc, Dušanka Janežič, Trevor M. Penning, Teja Lanišnik Rižner, Stanislav Gobec. Selective Inhibitors of Aldo-Keto Reductases Akr1C1 and Akr1C3 Discovered by Virtual Screening of a Fragment Library. J. Med. Chem., 2012, 55, 7417-7424. Full Text
  50. Martina Hrast, Blaž Vehar, Samo Turk, Janez Konc, Stanislav Gobec, Dušanka Janežič. Function of the D-alanine:D-alanine ligase lid loop: a Molecular Modeling and Bioactivity Study. J. Med. Chem., 2012, 55, 6849–6856. Full Text
  51. Janez Konc, Matjaž Depolli, Roman Trobec, Kati Rozman, Dušanka Janežič. Parallel-ProBiS: Fast Parallel Algorithm for Local Structural Comparison of Protein Structures and Binding Sites. J. Comp. Chem., 2012, 33, 2199-2203. Open Access
  52. Janez Konc, Dušanka Janežič. ProBiS - 2012: Web server and web services for detection of structurally similar binding sites in proteins. Nucleic Acids Res., 2012, 40, W214-W221. Open Access
  53. Janez Konc, Tomo Česnik, Joanna Trykowska Konc, Matej Penca, Dušanka Janežič. ProBiS-Database: Precalculated Binding Site Similarities and Local Pairwise Alignments of Pdb Structures J. Chem. Inf. Model., 2012, 52, 604-612. Open Access
  54. Blaž Vehar, Martina Hrast, Andreja Kovač, Janez Konc, Katherine Mariner, Ian Chopra, Alex O'Neill, Dušanka Janežič, Stanislav Gobec. Ellipticines and 9-acridinylamines as inhibitors of d-alanine:d-alanine ligase. Bioorg. Med. Chem., 2011, 19, 5137-5146. Full Text
  55. Staš Bevc, Janez Konc, Jure Stojan, Milan Hodošček, Matej Penca, Matej Praprotnik, Dušanka Janežič. ENZO: a web tool for derivation and evaluation of kinetic models of enzyme catalyzed reactions. PloS One, 2011, 6(7): e22265. Open Access
  56. Janez Konc, Joanna Trykowska Konc, Matej Penca, Dušanka Janežič. Binding-sites prediction assisting protein-protein docking. Acta Chim. Slov., 2011, 58, 396-401. Pdf
  57. Janez Konc, Dušanka Janežič. ProBiS: A web server for detection of structurally similar protein binding sites. Nucleic Acids Res., 2010, 38, W436-W440. Open Access
  58. Nejc Carl, Janez Konc, Blaž Vehar, Dušanka Janežič. Protein-protein binding site prediction by local structural alignment. J. Chem. Inf. Model., 2010, 50, 1906-1913. Full Text
  59. Janez Konc, Dušanka Janežič. ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment. Bioinformatics, 2010, 26, 1160-1168. Open Access
  60. Andreja Kovač, Janez Konc, Blaž Vehar, Julieanne Bostock, Ian Chopra, Dušanka Janežič, Stanislav Gobec. Discovery of new inhibitors of D-alanine:D-alanine ligase by structure-based virtual screening. J. Med. Chem., 2008, 51, 7442-7448. Full Text
  61. Nejc Carl, Janez Konc, Dušanka Janežič. Protein surface conservation in binding sites. J. Chem. Inf. Model., 2008, 48, 1279-1286. Full Text
  62. Janez Konc, Dušanka Janežič. Protein-protein binding-sites prediction by protein surface structure conservation. J. Chem. Inf. Model., 2007, 47, 940-944. Full Text
  63. Janez Konc, Dušanka Janežič. A branch and bound algorithm for matching protein structures. Lect. Notes Comput. Sci., 2007, 4432, 399-406. Full Text
  64. Janez Konc, Dušanka Janežič. An improved branch and bound algorithm for the maximum clique problem. Match Commun. Math. Comput. Chem., 2007, 58, 569-590. Pdf
  65. Janez Mravljak, Janez Konc, Milan Hodošček, Tomaž Šolmajer, Slavko Pečar. Spin-labeled alkylphospholipids in a dipalmitoylphosphatidylcholine bilayer : molecular dynamics simulations. J. Phys. Chem. B, 2006, 110, 25559-25561. Full Text
  66. Janez Konc, Milan Hodošček, Dušanka Janežič. Molecular surface walk. Croat. Chem. Acta, 2006, 79, 237-241. Pdf
  67. Katja Kristan, Katja Krajnc, Janez Konc, Stanislav Gobec, Jure Stojan, Tea Lanišnik Rižner. Phytoestrogens as inibitors of fungal 17ß-hydroxysteroid dehydrogenase. Steroids, 2005, 70, 626-635. Full Text