Mu.Ta.Lig - COST ACTION CA15135


14 June 2016


General information

Name: Črtomir
Surname: Podlipnik
Cell phone number with international prefix: +386 41 440 198
Country: Slovenia
Affiliation: PhD
Gender: F □ M x
Year of the PhD title: 2003
Personal web page:
Previous COST participation: No x Yes


List of 10 selected publications within last 5 years

1.  ŠENICA, Luka, STOPAR, Karmen, FRIEDRICH, Miha, GROŠELJ, Uroš, PLAVEC, Janez, POČKAJ, Marta, PODLIPNIK, Črtomir, ŠTEFANE, Bogdan, SVETE, Jurij. Synthesis and rotational isomerism of 1-substituted methyl (S)-[5-(2- nitrophenyl)-1H-pyrazole-4-carbonyl]alaninates. Journal of organic chemistry, ISSN 0022-3263, 2016, vol. 81, iss. 1, str. 146-161.
2. PLEŠKO, Sebastian, VOLK, Helena, LUKŠIČ, Miha, PODLIPNIK, Črtomir. In silico study of plant polyphenolsʼ interactions with VP24-ebola virus membrane-associated protein. Acta chimica slovenica, ISSN 1318-0207. [Tiskana izd.], 2015, vol. 62, no. 3, str. 555-564.
3. BONČINA, Matjaž, PODLIPNIK, Črtomir, PIANTANIDA, I., EILMES, Julita, TEULADE-FICHOU, Marie-Paule, VESNAVER, Gorazd, LAH, Jurij. Thermodynamic fingerprints of ligand binding to human telomeric G-quadruplexes. Nucleic acids research, ISSN 0305-1048, 2015, vol. 43, issue 21, str. 10376-1038
4. BENEDIK, Evgen, SKRT, Mihaela, PODLIPNIK, Črtomir, POKLAR ULRIH, Nataša. Binding of flavonoids to Staphylococcal enterotoxin B. Food and chemical toxicology, ISSN 0278-6915, 2014, vol. 74, str. 1-8.
5. TOMAŠIČ, Tihomir, RABBANI, Said Rahnamaye, GOBEC, Martina, MLINARIČ-RAŠČAN, Irena, PODLIPNIK, Črtomir, ERNST, Beat, ANDERLUH, Marko. Branched [alpha]-D-mannopyranosides; a new class of potent FimH antagonists.MedChemComm, ISSN 2040-2503, 2014, vol. 2014, iss. 5, str. 1247-1253
6. SKRT, Mihaela, BENEDIK, Evgen, PODLIPNIK, Črtomir, POKLAR ULRIH, Nataša. Interactions of different polyphenols with bovine serum albumin using fluorescence quenching and molecular docking. Food chemistry, ISSN 0308-8146. [Print ed.], 2012, vol. 135, str. 2418-2424.
7. MARUŠIČ, Jaka, PODLIPNIK, Črtomir, JEVŠEVAR, Simona, KUZMAN, Drago, VESNAVER, Gorazd, LAH, Jurij. Recognition of human tumor necrosis factor [alpha] (TNF-[alpha]) by therapeutic antibody fragment : energetics and structural features. The Journal of biological chemistry, ISSN 0021-9258, 2012, vol. 287, no. 11, str. 8613-8620.
8. CHESHEV, Pavel, MORELLI, Laura, MARCHESI, Marco, PODLIPNIK, Črtomir, BERGSTRÖM, Maria, BERNARDI, Anna. Synthesis and affinity evaluation of a small library of bidentate cholera toxin ligands : towards nonhydrolyzable ganglioside mimics. Chemistry, ISSN 0947-6539. [Print ed.], 2010, vol. 16, no. 6, str. 1951-1967.
9.  PODLIPNIK, Črtomir, TUTINO, Federico, BERNARDI, Anna, SENECI, Pierfausto. DFG-in and DFG-out homology models of TrkB kinase receptor : induced-fit and ensemble docking. Journal of Molecular Graphics & Modelling, ISSN 1093-3263. [Print ed.], 2010, vol. 29, no. 3, str. 309-320.
10. PODLIPNIK, Črtomir, REINA, Jose J. Structure based design of Cholera toxin antagonists. V: GOWDER, Sivakumar Joghi Thatha (ur.). Cholera. Rijeka: InTech, cop. 2012, str. 177-200.




Main skills and expertise (up to 5)

1. Experienced user of Molecular Modeling Programs (Schrodinger Suite, YASARA, Gaussian, Gamess US, ChemAxon, etc.)
2. Computer programming, scripting and manipulation with databases (Fortran, Perl, MySQL/PHP, Python,).
3. Structure based molecular design.
4. Study of intermolecular interactions by experiment and in silico.
5. Teaching and tutoring.


Main equipment/facilities available in the participants’ lab (up to 5)

1.      Computer cluster .
2.      Fully equipped laboratory for study of biomolecular interactions (ITC, DSC, UV-VIS, CD, …).
3.      Licenses for Schrodinger Suite & YASARA

4.      System for augmented reality (collaboration with Prof. P.Peer from faculty of Computer and Information Science, Ljubljana)




Short personal activity proposal for the COST Action CA15135 (max 1000 characters)

I would like to contribute in following activities: Selection of biological targets and assessment of biological data (WG2);  Development of chemical databases (WG3); Development of Computational methods for multiple ligand design and discovery (WG4). All these activities could be integrated in development and design of  user friendly Inverse Docking Web platform. A proteochemometric platform, which will use docking technology to estimate affinity of certain compounds for each of target included in ensemble of  receptors (biological targets). Faculty of Chemistry has completly new facilities therfore we could organize one WG meeting and/or Summer School here in Ljubljana.


Work Group preference: score from 1 (preferred) to 4 (not preferred)

Work Group of the CA15135 COST Action Score
WG1: Development of new chemical entities 3
WG2: Selection of biological targets and assessment of biological data 2
WG3: Development of chemical databases 1
WG4: Development of Computational methods for multiple ligand design and discovery 2