Barbara Zdrazil

Data Science & Computational Molecular Design

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People

From left to right:
Sonali Vaidya, Alzbeta Tuerkova, Barbara Zdrazil, Danilo Dokic, Yordan Yordanov
Barbara Zdrazil, PI

I did a PhD in Pharmaceutical Chemistry at the University of Vienna concentrating on QSAR and similarity-based descriptors with a focus on the multidrug efflux pump P-glycoprotein (supervisor: Gerhard F. Ecker). During this time I was lucky to spend some fantastic months in Barcelona to explore the work on similarity further together with Jordi Mestres. Later on, I moved to the lab of Hans-Dieter Höltje at the Heinrich-Heine University in Düsseldorf in order to conduct my first postdoctoral studies. These were mainly structure-based, with a focus on molecular dynamics simulations for the exploration of novel therapies for actinic keratosis based on the target DNA Polymerase alpha. Later I was recruited back to the University of Vienna, where I further applied all my skills in computational molecular design, especially in the framework of the FWF-funded special research focus SFB35 (“Transmembrane Transporters in Health and Disease”) . I was also involved in the projects Open PHACTS and eTOX which was quite inspiring since it allowed me to step into the worlds of large data integration and in silico toxicology predictions. During 2012-2016, most of my papers dealt with data integration and data annotation, including biomedical ontologies. I discovered that Open PHACTS and ChEMBL are great data sources and further used them for machine learning applications and predictive toxicology. In 2016, I also started to explore data that is incorporated in the corpus of Medicinal Chemistry literature in a time-wise manner. Together with Rajarshi Guha we recently published a paper on time-trends in scaffold popularity in the Journal of Medicinal Chemistry which also made it to Derek Lowe’s blog. Trying to unit all my skills in data science and computational molecular design, I am since 2017 leading a research group at the Department of Pharmaceutical Chemistry in Vienna. My current FWF project “Elucidating hepatic OATP ligand interactions and selectivity”, allows me to apply both ligand- and structure based modelling techniques, as well as integrative data mining. Experimental validation in this project is done by Gergely Szakacs (Medical University of Vienna) and Csilla Ozvegy-Laczka (Hungarian Academy of Sciences). I am also involved in the H2020 project EU-ToxRisk where I am currently applying machine learning techniques for in silico toxicology predictions and leading a task force on read across tool development.

📃Curriculum Vitae
📞+43-1-4277-55113
📧barbara.zdrazil@univie.ac.at
Alzbeta Tuerkova, PhD student
Alzbeta Tuerkova is a PhD student supervised by Dr. Barbara Zdrazil at the University of Vienna. In 2015, Alžběta graduated in bachelor study program Cheminformatics and Bioinformatics. Her bachelor thesis was focused on the calculations of atomic charges in proteins by means of Quantum Mechanics. Within her master study in Biomolecular Chemistry (2015-2017), she switched to the mesoscale (bio)physics of peptide-membrane interactions. Her primary focus was to identify optimal peptide properties for their pore-forming activity by means of multiscale coarse-grained simulations with enhanced sampling. In August 2017, Alžběta started her PhD on exploring ligand interactions with hepatic Organic Anion Transporting Polypeptides (OATPs). Following a holistic in silico approach, linking data mining approaches with structure-based modeling, Alžběta seeks to unravel molecular determinants for explaining selectivity switches among the three hepatic OATPs. Her special research interest is also to treat protein flexibility in structure-based modelling by applying elastic network normal mode analysis.
📃Curriculum Vitae
📧alzbeta.tuerkova@univie.ac.at
Danilo Dokic, Master student

Danilo Đokić is a student in the program “Drug Discovery and Development” at the University of Vienna. Since March 2020, he is working on his Master’s thesis performing Data Science approaches to study the current COVID-19 pandemics (by also making comparisons to SARS-CoV and MERS-CoV). Danilo obtained his  MSc  in Pharmacy  in  January  2018,  at the Department of Pharmacy,  Faculty  of  Medicine, University of Niš. His research work focused on the consequences of anticancer therapy on cognitive functions in patients with malignant tumor and resulted in the Master’s thesis on the topic: Effects of Chemotherapy and Hormone Therapy on the Cognitive Function in Cancer Patients: Potential Risks. The interests in immunology and pharmacology led Danilo to the internship at the Bandung Institute of Technology in Indonesia during August 2017 where he worked on the project of the immunomodulatory effect of the extract from Marchantia Paleacea. During the summer semester 2019 at the University of Vienna, he was a part of a team that was working on the case study related to development of the Novel STS Inhibitor for the treatment of breast cancer.

Yordan Yordanov, Master student
Mert Basaran, Master student

Alumni

  • Rosa Friesacher, student assistant (October 2018 – February 2019)
  • Bola Khalil, internship student (August 2019)
  • Danilo Dokic, internship student (October/November 2019)
  • Helene Hönigsperger, internship student (November/December 2019)
  • Yordan Yordanov, internship student (August/September 2020)
  • Sonali Vaidya, internship student (August/September 2020)
  • Mert Basaran, internship student (November/December 2020)


Contact

Mag. Dr. Barbara Zdrazil, Priv. Doz.
Department of Pharmaceutical Chemistry
University of Vienna
Althanstraße 14 (UZA II)
1090 Vienna, Austria
Room 2D 551

📞+43-1-4277-55116
📧barbara.zdrazil@univie.ac.at
BZdrazil

Meet us

RSC-CICAG Open Chemical Sciences conference, Session: Open  Data for Chemistry, November 9-13, virtual meeting

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