Bi4999en Structural Biology and Bioinformatics

Faculty of Science
autumn 2021
Extent and Intensity
2/0/0. 2 credit(s) (plus extra credits for completion). Type of Completion: zk (examination).
Teacher(s)
Sérgio Manuel Marques, PhD. (lecturer)
doc. Mgr. David Bednář, Ph.D. (lecturer)
Joan Planas Iglesias (lecturer)
Mgr. Martina Damborska (assistant), Mgr. Martina Damborská (deputy)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: prof. Mgr. Jiří Damborský, Dr.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Tue 12:00–13:50 C13/332
Prerequisites
During the course all the necessary information will be provided. However, a basic knowledge of chemistry is welcome.
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
Course objectives
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
Learning outcomes
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.
Syllabus
  • 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.
Literature
    recommended literature
  • GU, Jenny and Philip E. BOURNE. Structural bioinformatics. 2nd ed. Hoboken, N.J.: Wiley-Blackwell, 2009, xxvi, 1035. ISBN 9780470181058. info
  • PETSKO, Gregory A and 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 and 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 and Cedric NOTREDAME. Bioinformatics for dummies. 2nd ed. Hoboken, N.J.: Wiley, 2007, xviii, 436. ISBN 9780470089859. info
Teaching methods
Lectures. The course will run in a condensed format as a block.
Dates: 13-17 December 2021
Location: building B11/room 333
Monday: 12:00-15:50
Tuesday: 12:00-15:50
Wednesday: 10:00-13:50
Thursday: 12:00-15:50
Friday: 8:00-11:50
Assessment methods
Multiple-choice test, multiple correct answers possible, 10 correct answers out of 25 needed to pass the test.
Language of instruction
English
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
Teacher's information
https://smarques.weebly.com/
The course is also listed under the following terms Autumn 2022, Autumn 2023, Autumn 2024.
  • Enrolment Statistics (autumn 2021, recent)
  • Permalink: https://is.muni.cz/course/sci/autumn2021/Bi4999en