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. Computer system for advanced studies in molecular design,  new materials and nanotechnology (website)
    Bulgarian National Science Fund, Project DD02-52/10.12.2008
    Leader of the IBPhBME team: Ilza Pajeva
  2. In silico study of effects of bioactive compounds: applications to objects of priority for human health and environment
    Bulgarian National Science Fund, Project DТК02/58
    Project leader: Ilza Pajeva
  3. Integrated in silico models for the prediction of human repeated dose toxicity of cosmetics to optimise safety – COSMOS (website)
    FP7 of EC, Project N266835
    Leader of the IBPhBME team: Ivanka Tsakovska

Past projects

International collaboration

  • Joint Research Centre – European Commission, Ispra, Italy
  • 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


  • 2011 – Ilza Pajeva – Award of Excellence of the Union of the Scientists in Bulgaria for scientists above 35 years of age
  • 2011 – Dessislava Jereva – 2nd Award of the 9th National Young  Scientific Session, organized by the Federation of the Scientific-Engineering Unions in Bulgaria
  • 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

  • Molecular modeling with QSAR – Master Program “Computational Chemistry”, University of Sofia, Faculty of Chemistry, 2002/2003, 2003/2004, 2008/2009, 2009/2010, 2010/2011
  • Computer–Aided Drug Design: Ligand-Based Methods – Master Program “In Silico Drug Design”, University Paris-Diderot – Paris 7, Paris, France, 2011/2012

Selected publications

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