Publications

  1. Jonathan A. Fine, Janez Konc, Ram Samudrala, Gaurav Chopra. CANDOCK: Chemical atomic network based hierarchical flexible docking algorithm using generalized statistical potentials. bioRxiv, 2018, doi: doi.org/10.1101/442897
  2. Blaž Škrlj, Tanja Kunej, Janez Konc. Insights from ion binding site network analysis into evolution and functions of proteins. Mol. Inform., 2018, doi: 10.1002/minf.201700144
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. Janez Konc, Samo Lešnik, Dušanka Janežič. Modeling enzyme-ligand binding in drug discovery. J. Cheminform., 2015, 7:48. Open Access
  18. 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
  19. 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
  20. 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
  21. Janez Konc, Dušanka Janežič. Binding site comparison in protein function prediction and pharmaceutical discovery. Curr. Opin. Struct. Biol., 2014, 25, 34-39. Full Text
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. 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
  29. 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
  30. 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
  31. 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
  32. 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
  33. Janez Konc, Joanna Trykowska Konc, Matej Penca, Dušanka Janežič. Binding-sites prediction assisting protein-protein docking. Acta Chim. Slov., 2011, 58, 396-401. Pdf
  34. 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
  35. 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
  36. 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
  37. 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
  38. Nejc Carl, Janez Konc, Dušanka Janežič. Protein surface conservation in binding sites. J. Chem. Inf. Model., 2008, 48, 1279-1286. Full Text
  39. Janez Konc, Dušanka Janežič. Protein-protein binding-sites prediction by protein surface structure conservation. J. Chem. Inf. Model., 2007, 47, 940-944. Full Text
  40. Janez Konc, Dušanka Janežič. A branch and bound algorithm for matching protein structures. Lect. Notes Comput. Sci., 2007, 4432, 399-406. Full Text
  41. 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
  42. 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
  43. Janez Konc, Milan Hodošček, Dušanka Janežič. Molecular surface walk. Croat. Chem. Acta, 2006, 79, 237-241. Pdf
  44. 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