Bi4999en Structural Biology and Bioinformatics

Přírodovědecká fakulta
podzim 2023
Rozsah
2/0/0. 2 kr. (plus ukončení). Ukončení: zk.
Vyučující
Sérgio Manuel Marques, PhD. (přednášející)
doc. Mgr. David Bednář, Ph.D. (přednášející)
Joan Planas Iglesias (přednášející)
Mgr. Martina Damborska (pomocník), Mgr. Martina Damborská (zástupce)
Mgr. Jana Horáčková (cvičící)
MUDr. Jan Mičan (cvičící)
Garance
prof. Mgr. Jiří Damborský, Dr.
Ústav experimentální biologie – Biologická sekce – Přírodovědecká fakulta
Kontaktní osoba: prof. Mgr. Jiří Damborský, Dr.
Dodavatelské pracoviště: Ústav experimentální biologie – Biologická sekce – Přírodovědecká fakulta
Rozvrh
St 14:00–15:50 B11/333
Předpoklady
During the course all the necessary information will be provided. However, a basic knowledge of chemistry will be very useful.
Omezení zápisu do předmětu
Předmět je nabízen i studentům mimo mateřské obory.
Mateřské obory/plány
Cíle předmětu
Structural biology and bioinformatics are scientific disciplines derived from molecular biology, biochemistry, biophysics and computer sciences. These disciplines focus on the understanding of living organisms at the level of individual macromolecules and their interactions. Bioinformatics is the information technology for obtaining, storing, analyzing and distributing biological data. Structural biology enables determining or predicting structure of macromolecules and investigating structure-function relationships.
Learning outcomes:
- description of macromolecular structure
- download and basic analysis of structure quality and identification of errors
- experimental structural methods and structure prediction in silico - analysis of function, dynamics and stability
- effect of mutation on structure, function, dynamics and stability of macromolecules
Výstupy z učení
On successful completion of the course, the students will be able to:
- understand basic principles of structural bioinformatics and structural biology
- study and analyze structures of macromolecules and experimental methods for their determination
- identify and obtain structures of macromolecules from bioinformatics databases
- identify possible errors in the protein structures
- predict structure of macromolecules and theirs complexes
analyze protein structures to acquire information about their function, dynamics and stability evaluate an effect of mutations on biological function.
Osnova
  • 1. Introduction to the structure of macromolecules – composition, methods for determination, application in biology, visualization.
  • 2. Structure of biomolecules – different levels of structure of proteins and nucleic acids
  • 3. Bioinformatics databases and structure prediction – sequence databases, structural databases, retrieval and evaluation of macromolecular structures
  • 4. Models of structures – structural databases, validation and methods for quality assessment, preparation of models.
  • 5. Stability and dynamics of macromolecules – analysis of molecular dynamics and stability, prediction of stability, databases.
  • 6. Analysis of protein structures – identification of important regions: binding/active sites, aggregation propensity, transport pathways, flexible regions, binding/catalytic amino acids.
  • 7. Protein-ligand complexes – evaluation of complexes, analysis of interactions, druggability, databases, transport of small molecules.
  • 8. Macromolecular complexes and interactions – protein-protein and protein-DNA complexes, analysis of interactions, databases.
  • 9. Engineering of protein structures –effect of mutations on the protein structure, stability and function.
  • 10. Application of structural biology and bioinformatics – biological research, drug design, engineering of biocatalysts.
Literatura
    doporučená literatura
  • GU, Jenny a Philip E. BOURNE. Structural bioinformatics. 2nd ed. Hoboken, N.J.: Wiley-Blackwell, 2009. xxvi, 1035. ISBN 9780470181058. info
  • PETSKO, Gregory A a Dagmar RINGE. Protein structure and function. London: New Science Press, 2004. xxii, 195. ISBN 0-9539181-4-9. info
  • LILJAS, Anders, Lars LILJAS, Miriam-Rose ASH, Göran LINDBLOM, Poul NISSEN a Morten KJELDGAARD. Textbook of structural biology. Second edition. Singapore: World Scientific Publishing, 2016. 599 stran. ISBN 9789813142473. info
  • XIONG, Jin. Essential bioinformatics. 1st pub. Cambridge: Cambridge University Press, 2006. xi, 339. ISBN 0521600820. info
  • Computational structural biology : methods and applications. Edited by Torsten Schwede - Manuel Claude Peitsch. 1st pub. Hackensack, N.J.: World Scientific, 2008. x, 779. ISBN 9789812778772. info
  • CLAVERIE, Jean-Michel a Cedric NOTREDAME. Bioinformatics for dummies. 2nd ed. Hoboken, N.J.: Wiley, 2007. xviii, 436. ISBN 9780470089859. info
Výukové metody
The course will run in the form of lectures (2 h each), once per week.
Metody hodnocení
Multiple-choice test, multiple correct answers possible, 10 correct answers out of 25 are needed to pass the test.
Vyučovací jazyk
Angličtina
Informace učitele
https://smarques.weebly.com/
Další komentáře
Studijní materiály
Předmět je vyučován každoročně.
Předmět je zařazen také v obdobích podzim 2021, podzim 2022.
  • Statistika zápisu (nejnovější)
  • Permalink: https://is.muni.cz/predmet/sci/podzim2023/Bi4999en