Thesis (Selection of subject)

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Molecular Dynamics and Clustering Techniques in the Study of Intrinsically Disordered Proteins and their Post-Translational Modifications

Thesis title in Czech:	Studium vnitřně neuspořádaných proteinů a jejich post-translačních modifikací pomocí metod molekulové dynamiky a klastrovacích technik
Thesis title in English:	Molecular Dynamics and Clustering Techniques in the Study of Intrinsically Disordered Proteins and their Post-Translational Modifications
Key words:	chemický posun, NMR, neuspořádaný protein
English key words:	chemical shift, NMR, disordered protein
Academic year of topic announcement:	2019/2020
Thesis type:	dissertation
Thesis language:	angličtina
Department:	Department of Biophysics and Physical Chemistry (16-16110)
Supervisor:	Mgr. Jana Pavlíková Přecechtělová, Ph.D.
Author:	hidden - assigned and confirmed by the Study Dept.
Date of registration:	16.03.2020
Date of assignment:	16.03.2020
Confirmed by Study dept. on:	01.04.2020
Date and time of defence:	31.01.2025 09:00
Date of electronic submission:	31.10.2024
Date of submission of printed version:	08.12.2024
Date of proceeded defence:	31.01.2025
Opponents:	prof. Mgr. Lubomír Rulíšek, DSc.
	Alex Holehouse, Ph.D.

Preliminary scope of work in English

Design of quantum mechanics-based protocols for the calculation and prediction of NMR chemical shifts in disordered proteins involved in the molecular mechanisms of neurodegenerative diseases. Optimization of the protocols towards applications in the structure characterization of disordered proteins by experimental NMR spectroscopy. Implementation of software tools and scripting frameworks facilitating database-driven NMR calculations. Application of the designed approaches to example intrinsically disordered proteins and comparison with fast semiempirical predictions.