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Institute for Advanced Simulation (IAS)

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Dr. Agata Kranjc Pietrucci


I am interested in elucidating molecular mechanisms of diseases in silico by focusing not only on the structure and function of a single protein involved in a disease, but also on its interactions with its molecular network partners. I am interested in drug design taking into account all the information of the spatial and temporal organization of the multiprotein complexes. Finally, I am interested in studying how different ligands/drugs and mutations  impact  the structure and function of the target protein and of its molecular network, in order to achieve 1) a complete understanding of all the factors at play in pathology-related processes at the molecular scale, and 2) a detailed explanation and interpretation of experiments from the structural, thermodynamic and kinetic viewpoints.

Professional career

IAS-5/INM-9 Computational Biomedicine
Forschungszentrum Jülich, Jülich, Germany
2018Research fellow
National Institut for blood transfusion (INTS)
Dynamics of Structures and Interactions of Macromolecules in Biology, Paris, France
2009-2012Postdoctoral researcher
Pharmaceutical Biochemistry group, University of Geneva, Switzerland
2009-2010External research collaborator
Biopharmaceutical company AC Immune SA Lausanne, Switzerland



2009Ph.D. in Structural and Functional Genomics
International School for Advanced Studies (SISSA/ISAS), Trieste, Italy
2004M.Sc. in Pharmacy
University of Ljubljana, Slovenia

University Teaching Responsabilities

2009Co-supervision of master thesis student Michela Candotti (postdoc)
International School for Advanced Studies, Trieste, Italy

Co-supervisor of master thesis student Michela Snider (postdoc)
University of Geneva, Pharmaceutical Biochemistry group, Geneva, Switzerland

Thesis: Molecular modelling for pathway-based drug design: the chronic myeloid leukaemia case study (Mentors: Dr. Agata Kranjc Pietrucci, Prof. Dr. Leonardo Scapozza)

2010Teaching molecular modelling course at master level (postdoc)
University of Geneva, Pharmaceutical Biochemistry group, Geneva, Switzerland

Co-supervisor of master thesis student Jérémie Nayak (postdoc)
University of Geneva, Pharmaceutical Biochemistry group, Geneva, Switzerland

Thesis: How chronic myeloid leukaemia inhibitors and Abl partner protein CrkII influence the open conformation of Abl  (Mentors: Dr. Agata Kranjc Pietrucci, Prof. Dr. Leonardo Scapozza)


  1. N. Hanna, S. Kicka, G. Chiriano, C. Harrison, H. Ouertatani Sakouhi, V. Trofimov, A. Kranjc, J. Nitschke, M. Pagni, P. Cosson, H. Hilbi, L. Scapozza, and T. Soldati; Identification of novel anti-mycobacterium and anti-Legionella compounds with potential distinctive structural scaffold from an HD-PBL using phenotypic screens in amoebae host models, Frontiers in Microbiology: Antimicrobials, Resistance and Chemotherapy, submitted October 2019.
  2. L. Slepikas, G. Chiriano, R. Perozzo, S. Tardy, A. Kranjc, O. Patthey-Vuadens, H. Ouertatani-Sakouhi, S. Kicka, C. F. Harrison, T. Scrignari, K. Perron, H. Hilbi, T. Soldati, P. Cosson, E. Tarasevicius, L. Scapozza; In silico driven design and synthesis of rhodanine derivatives as novel antibacterials targeting the enoyl reductase InhA, J Med Chem 59 (2016) 10917 – 10928.
  3. F. Pietrucci, A. V. Vargiu, A. Kranjc; HIV-1 protease dimerization dynamics reveals a transient druggable binding pocket at the interface, Scientific Reports, 5 (2015) article number 18555.
  4. C.F. Harrison, G. Chiriano, I. Finsel, C. Manske, C. Hoffmann, B. Steiner, A. Kranjc, O. Patthey-Vuadens, S. Kicka, V. Trofimov, H. Ouertatani-Sakouhi, T. Soldati, L. Scapozza, H. Hilbi; Amoebae-based screening reveals a novel family of compounds restricting intracellular Legionella pneumophila, ACS Infectious Diseases, 1 (2015) 327-338 (Editor’s choice).
  5. C.F. Harrison, S. Kicka, A. Kranjc, I. Finsel, G. Chiriano, H. Ouertatani-Sakouhi, T. Soldati, L. Scapozza, H. Hilbi; Adrenergic antagonists restrict replication of Legionella, Microbiology 161 (2015) 1392-1406.
  6. D. Latawiec, F. Herrera, A. Bek, V. Losasso, M. Candotti, F. Benetti, E. Carlino,A. Kranjc, M. Lazzarino, S. Gustincich, P. Carloni, G. Legname; Modulation of alpha-synuclein aggregation by dopamine analogs, PLoS ONE, 5 (2010) e9234.
  7. A. Kranjc, S. Bongarzone, G. Rossetti, X. Biarnés, A. Cavalli, M. L. Bolognesi, M. Roberti, G. Legname, P. Carloni; Docking ligands on protein surfaces. The case study of prion protein, J. Chem. Theory Comput., 5 (2009) 2565-2573.
  8. A. Kranjc, F. W. Grillo, J. Rievaj, A. Boccaccio, F. Pietrucci, P. Carloni, A. Menini, C. Anselmi; Regulation of bestrophins by Ca 2+ : a theoretical and experimental study, PLoS ONE, 4 (2009) e46722009.
  9. V. Campana, L. Zentilin, I. Mirabile, A. Kranjc, P. Casanova, M. Giacca, S.B. Prusiner, G. Legname and C. Zurzolo; Antibody fragments for immunotherapy of prion diseases, Biochem. J., 418 (2009) 507-515.
  10. K. Galesa, U. Bren, A. Kranjc and J. Mavri; Carcinogenicity of Acrylamide: A Computational Study, J. Arg. Food Chem, 56 (2008) 8720-8727.
  11. A. Kranjc, C. Anselmi, P. Carloni and F. E. Blaney; Structural Models of Human Big Conductance Calcium- and Voltage-gated Potassium Channels, Comp. Phys. Comm., 177 (2007) 21-26.
  12. A. Kranjc, J. Mavri; Guanine Alkylation by Ethylene Oxide: Calculation of Chemical Reactivity, J. Phys. Chem. A, 110 (2006) 5740-5744.


Laboratoire de Biochimie Théorique
Institut de Biologie Physico-Chimique
13 Rue Pierre et Marie Curie
75005 Paris
IAS-5 / INM-9
Computational Biomedicine
Forschungszentrum Jülich
52428 Jülich


Phone: +49 (0)246161 8940