ProBiS Plugin ProBiS H2O ProBiS H2O MD ProBiS-Dock Algorithm Maximum Clique Algorithm LiSiCA Maximum Weight Clique Algorithm

Publications

  1. Kati Rozman, An Ghysels, Dušanka Janežič, Janez Konc. An exact algorithm to find a maximum weight clique in a weighted undirected graph. Sci. Rep., 2024, 14, 9118. Open Access

  2. Martin Šimon, Špela Mikec, Santosh S. Atanur, Janez Konc, Nicholas M. Morton, Simon Horvat, Tanja Kunej. 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 Genom., 2024, doi: 10.1007/s13258-024-01507-9. Open Access

  3. Kati Rozman, An Ghysels, Bogdan Zavalnij, Tanja Kunej, Urban Bren, Dušanka Janežič, Janez Konc. Enhanced Molecular Docking: Novel Algorithm for Identifying Highest Weight k-Cliques in Weighted General and Protein-Ligand Graphs. J. Mol. Struct., 2024, 1304, 137639. Open Access

  4. David R. Lisgarten, Rex A. Palmer, Jon B. Cooper, Claire E. Naylor, Rosemary C. Talbert, Brendan J. Howlin, John N. Lisgarten, Janez Konc, Shabir Najmudin, Carina M. C. Lobley. Ultra-High Resolution X-ray Structure of Orthorhombic Bovine Pancreatic Ribonuclease A at 100K. BMC Chem., 2023, 17, 91. Open Access

  5. 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

  6. Janez Konc, Dušanka Janežič. Protein Binding Sites for Drug Design. Biophys. Rev., 2022, 14, 1413–1421. Open Access

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. Janez Konc. Identification of neurological disease targets of natural products by computational screening. Neural Regen. Res., 2019, 14:2075-2076. PDF

  25. 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

  26. 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

  27. Janez Konc. Binding site comparisons for target-centered drug discovery. Expert Opin. Drug Discov., 2019, 14, 445-454. Full Text . PDF

  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

  34. 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

  35. 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

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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

  42. 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

  43. 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

  44. Janez Konc, Samo Lešnik, Dušanka Janežič. Modeling enzyme-ligand binding in drug discovery. J. Cheminform., 2015, 7:48. Open Access

  45. 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

  46. 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

  47. 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

  48. Janez Konc, Dušanka Janežič. Binding site comparison in protein function prediction and pharmaceutical discovery. Curr. Opin. Struct. Biol., 2014, 25, 34-39. Full Text

  49. 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

  50. 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

  51. 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

  52. 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

  53. 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

  54. 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

  55. 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

  56. 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

  57. 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

  58. 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

  59. 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

  60. Janez Konc, Joanna Trykowska Konc, Matej Penca, Dušanka Janežič. Binding-sites prediction assisting protein-protein docking. Acta Chim. Slov., 2011, 58, 396-401. Pdf

  61. 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

  62. 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

  63. 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

  64. 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

  65. Nejc Carl, Janez Konc, Dušanka Janežič. Protein surface conservation in binding sites. J. Chem. Inf. Model., 2008, 48, 1279-1286. Full Text

  66. Janez Konc, Dušanka Janežič. Protein-protein binding-sites prediction by protein surface structure conservation. J. Chem. Inf. Model., 2007, 47, 940-944. Full Text

  67. Janez Konc, Dušanka Janežič. A branch and bound algorithm for matching protein structures. Lect. Notes Comput. Sci., 2007, 4432, 399-406. Full Text

  68. 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

  69. 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

  70. Janez Konc, Milan Hodošček, Dušanka Janežič. Molecular surface walk. Croat. Chem. Acta, 2006, 79, 237-241. Pdf

  71. 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