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Lecturer(s)
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Krepl Miroslav, RNDr.
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Berka Karel, prof. RNDr. Ph.D.
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Course content
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Description of biomacromolecules, Structural hierarchy, proteins, nucleic acids Structure determination (X-Ray, NMR, EM, etc.) Structure file formats PDB database NDB database Other structural databases (CATH, SCOP, Drugbank) Vizualization of structure, structural alignment Structure prediction, CASP Function prediction Ligand docking Challenges of structural bioinformatics - membrane proteins, nucleic acids, protein-protein interactions prediction
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Learning activities and teaching methods
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Monologic Lecture(Interpretation, Training), Training in job and motor Skils
- Preparation for the Exam
- 60 hours per semester
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Learning outcomes
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Structural bioinformatics is a part of bioinformatics, which is related to the analysis and prediction of the three-dimensional structure of biomacromolecules for the analysis of their function.
ability to define fundamental concepts, describe fubdamental approaches applied to structural bioinformatics of proteins
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Prerequisites
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unspecified
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Assessment methods and criteria
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Oral exam, Analysis of Activities ( Technical works)
Structural bioinformatical analysis of model system, discussion on a given topic (2 questions)
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Recommended literature
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Burley, S. K. et al. Updated resources for exploring experimentally-determined PDB structures and Computed Structure Models at the RCSB Protein Data Bank. Nucleic Acids Research, 53(D1), D564?D574. 2025.
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Gáspári, Z. (2020). Structural Bioinformatics: Methods and Protocols. Methods in Molecular Biology, vol. 2112.
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Gu, J. & Bourne, P. E. (2009). Structural Bioinformatics (2nd ed.).
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Jumper, J., Evans, R., Pritzel, A. et al. Highly accurate protein structure prediction with AlphaFold. Nature, 596, 583?589. 2022.
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Kagaya, Y., Liu, B. & Kihara, D. Computational approaches for RNA structure prediction and design. Cell Reports Physical Science, 7(2), 103097. 2026.
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Leach AR. (2001). Molecular Modelling - Principles and Applications (2 edition). Pearson Education.
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Orengo CA., Jones DT., Thornton JM. (Eds.). (2003). Bioinformatics - Genes, Proteins and Computers.
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Voet D. & Voet JG. (2004). Biochemistry (3rd edition).
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