Syllabus
Sylabus * Lecture topics:
1. Molecular foundations of disease, biomolecular targets, drug design and discovery (ML)
2. Structure and dynamics of biomolecular targets (proteins, nucleic acids) (VV)
3. Structural biology methods (X-ray crystallography, NMR, cryo-EM, AlphaFold) (VV)
4. Hands-on Session: PDB database (VV, ML)
5. Biologically active compounds, properties, noncovalent and covalent interactions (JF)
6. Hands-on Session: visualisation of proteins and ligands - PyMol (JF, ML)
7. Virtual screening, docking, scoring (JF)
8. Hands-on Session: Docking - AceDock (JF, ML)
9. Molecular mechanics and dynamics, binding free energy calculations (ML)
10. Ligand-based drug design - QSAR, ADMET, databases (ML)
Annotation
One-semester practical course in English aims at obtaining an overview and hands-on experience in using computational methods for modern drug design. It is desirable that the attendees have previous knowledge of structure and function of biomolecules, general chemistry and use of computers for scientific work. Aimed at Master students of 1st or 2nd year (potentially 3rd year Bachelor students) and PhD students including medical faculties. The topics covered in the course:
1. Discovery of new biologically active compounds
2. Structure, dynamics and interactions in biomolecule-ligand complexes
3. Biologically active compounds, their properties and interactions
4. Docking, molecular mechanics and dynamics, scoring
5. Ligand-based drug design