Bioinformatics Research:
Protein Folding, Docking and Prediction of Biological Activity

Center for Advanced Bioinformatics Research
 South-West University "Neofit Rilski", Blagoevgrad

About the project

By performing in silico (computerized) experiments we aim:

  • modeling and optimizing of the structure of mu-, delta- and kappa- opioid receptors, cannabinoid receptors and neurotensin receptors;
  • determining the structure of the ligand-receptor complex and the minimum free energy of binding in certain structures of receptor and ligand, and studing the method of connection in order to offer modifications to ligands;
  • prediction of biological activity;
  • development of a mathematical model for predicting the biological activity by using the results of molecular docking of new ligands and the results of in vitro tests;
  • studying the applicability of cloud structures and server virtualization tasks in protein folding, docking and the prediction of biological activity.

Methods and models to achieve the objectives:

  • "hydrophobic-hydrophilic" model;
  • method of homology modeling;
  • solving the problem of protein folding by using the following three types of combinatorial algorithms: heuristic, combinatorial-optimizational, and approximational;
  • determining the binding mode of the ligand and the receptor using geometrical and energetic methods;
  • application of ligand-based and structure-based approaches, in which: molecular analysis of the fields of protein homology modeling, docking and virtual screening of bioactive compounds, the determination and analysis of protein-ligand interactions for the 3d structure of the target biomacromolecule.

Key results:

  • modeling and optimization of the 3d structure of the study receptors - opioid, cannabinoid, and neurotensin;
  • development of a mathematical model describing the relationship between the parameters and the results of the docking of particular biological importance of in vitro assays to predict biological activity of the compounds;
  • determination of the quantitative relationship between the biological activity of a series of compounds and their physico-chemical properties.
About the project
About bioinformatics
Objectives