Content (Syllabus outline)
Lectures:
-introduction to molecular modelling (molecular data formats, conformational analysis, geometrical optimisation, visualisation of molecules)
-creation and analysis of chemical libraries (calculation of physico-chemical properties, molecular descriptors, library filtering, diversity)
-computational methods for determination and analysis of protein structures (amino acid sequence alignment and analysis, homology modelling, calculation of solvent accessible surface area)
-interactions between target and small molecule (types and strength of interactions, analysis of target–small molecule binding interactions)
-molecular docking (identification of potential binding sites, small molecule binding mode prediction, protein–protein and peptide–protein docking)
-molecular dynamics simulations (MD simulations of water-soluble proteins, MD simulations of membrane proteins, MD simulations of target–ligand complexes, binding free energy calculations)
-virtual screening (structure- and ligand-based virtual screening)
-pharmacophore-based modelling (structure- and ligand-based pharmacophore modelling, structure-activity relationship analysis, dynophores)
-quantitative structure-activity relationship (QSAR)
-hit and lead optimization strategies, principles of rational drug design (optimisation of affinity, optimisation of physico-chemical properties, optimisation of ADMET properties)
-use of artificial intelligence in drug design
Seminars: Presentation of novel concepts/modelling tools/software packages for molecular modelling (presentation of scientific publications, presentation of new software based on the use of trial version). Presentation of selected case studies.
Tutorials: Practical exercises in the computer study hall complement the theoretical content of the course with practical case studies and the use of various tools and software packages for molecular modelling.
Prerequisites
Prerequisites for admittance to final exam:
- presence at at least 80% of practicals,
- seminar presentation.