KFC/MOM Molecular Modelling

Lecturer: Michal Otyepka
Lecture: 2 hours/week
Credits: 3
Winter semester
Form of course completion: colloquium

The lecture is focused on empirical methods and non-empirical are concerned marginally.   

• Mmolecular coordinates ans topology
• Principles of molecular mechanics, harmonic approximation, torzional terms, noncovalent interaction and  its description by empirical potencial, parc. charges, RESP, Ewald summ., vdW interaction, LJ potencial, cutoff, parametrization
• Common force fields and their limitations  (AMBER, CHARMM, OPLS-AA etc.)
• United atoms, coarse grained models, CGFF-MARTINI
• Classical molecular dynamics, PBC, thermostat, barostat, conditions, simulation protocols, analysis – evolution RMSD, Rg; essencial dynamics
• Water models, explicit and implicit (PB, GB)
• Enzyme and RNA catalysis, definition of catalytic effect, sources of catalysis, RNA and DNA enzymes, hybrid methods QM/MM
• Drug design, drug tests and evaluation, CADD, molecular docking, scoring function, COMFA
• Protein and NA folding
• Examples