Thesis topics
Introduction to the thesis topics offered
The research group offers thesis topics for bachelor's, master's, and dissertation theses, both at the Faculty of Science and the Faculty of Informatics of Masaryk University.
The topics of Bachelor's and Master's theses are listed below on this page. Each topic has a supervisor contact and a link to its listing in the Masaryk University Information System. Some thesis topics are offered at both faculties mentioned above, while others are only offered at one of them.
A part-time job may also be offered to skilled students.
The topics currently offered are listed below. If you are interested in any of them, please do not hesitate to contact the topic supervisor.
Dissertation thesis topics are determined by agreement between the prospective PhD student and the research group leader, based on the prospective student's abilities and research interests and the research direction of the Structural Bioinformatics group. If you are interested in a dissertation topic, don't hesitate to get in touch with the research group leader.
Bachelor's thesis topics
Generalization of the SQE+qp empirical method for calculating partial atomic charges
Supervisor: RNDr. Ondřej Schindler (e-mail, MUNI)
Topic description: Partial atomic charges describe the electron density distribution within a molecule. Calculating them using quantum chemistry methods is computationally demanding. Therefore, empirical methods are being developed that calculate partial atomic charges much faster. The empirical method SQE+qp is suitable for calculating the partial atomic charges of proteins. The disadvantage of this method is its applicability only to proteins without ligands.
The aim of this thesis is to modify the method so that it is also suitable for small organic molecules.
Prerequisites: Knowledge of Python programming and experience with the Linux operating system. Experience in using MetaCentrum computing resources is an advantage.
Link to this topic in the topic list in the IS MUNI:
Validation of cycle conformations of a selected group of ligands
Supervisor: Mgr. Bc. Gabriela Bučeková (e-mail, MUNI)
Consultant: Mgr. Viktoriia Doshchenko (e-mail)
Topic description: One of the most widely used resources that contain 3D structural data of macromolecules and their corresponding small molecules - ligands - is the Protein Data Bank (PDB). The PDB contains structure validation reports that include information not only about their quality. Despite validation, some structures may have minor or major errors, so it is crucial to verify their quality. Ligands can be divided into different groups based on, for example, their function, type or structure.
This thesis aims to verify whether the conformations of the cycles of a selected group of ligands correspond to the most energetically favourable conformation. The second step is to produce a statistical and biological analysis of the ligands.
Prerequisites: Python programming basics.
Link to this topic in the topic list in the IS MUNI: