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	Molecular dynamics as a tool to study biological systems SOVOVÁ, Žofie Molecular dynamics simulations are a theoretical method enabling to trace the movement of atoms within a system. The system studied is usually treated on the atomistic level, however its overall properties can be also described satisfactory if several atoms are handled as one particle (coarse-grained molecular dynamics). This thesis presents molecular modeling and (coarse-grained) molecular dynamics as tools for the description of different biologically relevant systems. The coarse-grained force field parameters had to be developed prior to characterization of the thylakoid membrane from cyanobacterium Synechocystis PCC6803. Two different compositions of the membrane were studied in order to reveal differences in their behavior. The PsbI subunit of photosystem II was embedded into the thylakoid membrane and its behavior, both as an isolated protein and as a cluster of several units, was described. The last system examined was the C-type lectin-like domain of NKR-P1, a surface receptor of natural killer cells. Attention was payed to its structural characterization. Detailed record
	Aplication of quantum-chemical methods and molecular-dynamics simulations on real biological systems SOVOVÁ, Žofie Detailed record
	Homology and energetic modeling of proteins in connection with molecular dynamics and vibrational spectroscopy SOVOVÁ, Žofie Detailed record

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