QSAR and Molecular Modelling

Head of Department

Prof. Ilza Pajeva, DSc.

  • Email: pajevabiomed.bas.bg
  • Phone: (359 2) 9793605
  • Fax: (359 2) 8723787
  • Address: “Acad. G. Bonchev” Str., Block 105, Room 206
    Sofia 1113, Bulgaria


Main research topics

Studies are based on QSAR (quantitative structure-activity relationships) and molecular modeling approaches for characterizing the relationship between the structure of chemical compounds and their biological effect. The models use integral and local two-dimensional (2D) and / or three-dimensional (3D) structural features; the effect may be medicinal (therapeutic), toxic etc.

Depending on the information available on the 3D structure of the target biomacromolecule, ligand-based and structure-based approaches are used including: pharmacophore modeling, molecular fields analysis, homology modeling of proteins, docking and virtual screening of bioactive compounds, identification and analysis of protein-lignad interactions, formation of chemical categories using different chemometrical methods. The applications are in the field of rational drug design and evaluation of toxic effects of chemicals on human health and environment. Subject matter is highly interdisciplinary and integrates knowledge from scientific fields such as medicine, pharmacology, physics, chemistry, methods of structural analysis, mathematical and engineering methods (mathematical statistics, pattern recognition, experimental design, programming, software development etc.

Research projects

Current projects

  1. New approach based on intercriteria data analysis for decision support in in silico research of complex biomolecular systems
    Bulgarian National Science Fund, Project DN 17/6, 2017-2020
    Project leader: Prof. Tania Pencheva
  2. Interaction of natural products with drug metabolizing enzymes
    Bulgarian National Science Fund, Project DNTS /France 01/1, 2017-2019
    Project leader: Prof. Tania Pencheva
  3. Challenging organic syntheses inspired by nature – from natural products chemistry to drug discovery
    EU Framework Programme Horizon 2020, COST Action CM1407, 2015-2019
    Project leader for the IBPhBME team: Corr. Memb. Prof. Ilza Pajeva
  4. Programme for Co-funding of COST Action СМ1407
    Bulgarian National Science Fund, Project DCOST 01/11, 2016-2018
    Project leader: Corr. Memb. Prof. Ilza Pajeva
  5. Modulation of metabolic syndrome with natural compounds: combining in silico and in vivo methods for research of the potential role of the nuclear receptor PPARγ
    Bulgarian National Science Fund, Project DM01/1/2016, 2016-2018
    Project leader: Dr Merilin Al Sharif

Past projects

International collaboration

  • Joint Research Centre – European Commission, Ispra, Italy
  • Department of Chemistry and Technology of Drugs, Sapienza University of Rome, Italy
  • School of Pharmacy and Chemistry, Liverpool John Moores University, Liverpool, UK
  • University of Bonn, Bonn, Germany
  • INSERM U.973 – MTI, University Paris-Diderot – Paris 7, Paris, France
  • Institute of Pharmacological Sciences, Pharmaceutical Faculty, University of Siena, Italy


  • 2017 – Antonia Diukendjieva-Todorova – “Ivan Evstratiev Geshov” Youngest Researchers Award of the Bulgarian Academy of Sciences
  • 2015 – Best Poster Award at the 1st Meeting of COST Action CM1407, Rome, Italy – collective award
  • 2015 – Merilin Al Sharif – Best Oral Presentation Award from Teva Czech Industries at 2-nd International Conference on Natural Products Utilization, Plovdiv, Bulgaria
  • 2014 –Best Poster Award at the 16th Congress of the European Neuroendocrine Association, Sofia, Bulgaria – collective award
  • 2011 – Ilza Pajeva – Award of Excellence of the Union of the Scientists in Bulgaria for scientists above 35 years of age
  • 2011 – 2nd Award of the 9th National Young Scientific Session, organized by the Federation of the Scientific-Engineering Unions in Bulgaria – collective award
  • 2006 – Tania Pencheva – Award of the Union of the Scientists in Bulgaria for young scientist’s achievements in the area of medicinal/biological sciences
  • 2004 – Ivanka Tsakovska – Award “Evrika” for achievements in science issued by Evrika Foundation and Higher Accreditation Commission
  • 2003 – Ivanka Tsakovska – National Award “Marin Drinov” for young scientists (up to 35 years of age) issued by Bulgarian Academy of Sciences for scientific contributions
  • 2002 – Ivanka Tsakovska – Award of the National Science Fund, Ministry of Education and Science, Bulgaria for the best junior project (grant MU-I-8/98) in the competition “Young Scientists”
  • 1999 – Ilza Pajeva – 2nd Award of the National Science Fund – Bulgaria for essential research results in 5th Competition Session 1995-1998 (grant L-518)

Lecture courses

  • Computer–Aided Drug Design: Ligand-Based Methods – Master Program “Bio- and Medical Informatics”, University of Sofia, 2014-2017
  • Intelligent Systems – Master Program “Computer Systems and Technologies”, University “Prof. Dr Asen Zlatarov”, Burgas, 2014-2017
  • Molecular modeling with QSAR – Master Program “Computational Chemistry”, University of Sofia, Faculty of Chemistry, 2002-2004, 2008-2017
  • Computer–Aided Drug Design: Ligand-Based Methods – Master Program “In Silico Drug Design”, University Paris-Diderot – Paris 7, Paris, France, 2011/2012

Selected publications

Last update: 25 February 2018

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