Bi4999en Structural Biology and Bioinformatics

Faculty of Science
Autumn 2023
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)
Mgr. Jana Horáčková (seminar tutor)
MUDr. Jan Mičan (seminar tutor)
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
Wed 14:00–15:50 B11/333
Prerequisites
During the course all the necessary information will be provided. However, a basic knowledge of chemistry will be very useful.
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
On the successful completion of the course, the students will be able to: understand the basic principles of structural bioinformatics and structural biology; describe the main experimental methods for obtaining the structures of macromolecules (proteins or nucleic acids) and their complexes; identify and obtain macromolecular structures from bioinformatics databases; identify possible errors in the protein structures; predict the structures of macromolecules and their complexes; analyze protein structures and acquire information about their function, dynamics, and stability; evaluate the effects of mutations on the structure and biological function.
Learning outcomes
- Description of macromolecular structures
- Download and assess the quality of a structure and identify errors
- Describe experimental methods for structure determination and in silico predictions
- Analysis of function, dynamics, and stability
- Evaluate the effect of mutations on the structure, function, dynamics, and stability of macromolecules
Syllabus
  • Structural biology and bioinformatics are scientific disciplines derived from molecular biology, biochemistry, biophysics, and computer sciences. These disciplines focus on understanding living organisms at the level of individual macromolecules (proteins, nucleic acids, etc.) and their interactions. Bioinformatics is the information technology for obtaining, storing, distributing, and analyzing biological data. Structural biology enables the determination or prediction of the structures of macromolecules and the investigation of structure-function relationships.
  • During this course, the following topics will be covered.
  • 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
    not specified
  • https://drive.google.com/open?id=1epUiScKAFNAUa2GA2S8oAM8aa7etCeYC&usp=drive_fs
Teaching methods
The course will run in the form of lectures (2 h each), once per week.
Assessment methods
Multiple-choice test, multiple correct answers possible, 10 correct answers out of 25 are needed to pass the test.
Language of instruction
English
Follow-Up Courses
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
Teacher's information
https://smarques.weebly.com/

NOTE: This theoretical course now has a related practice available in English: "Bi9410cen - Structural Biology - practice". Interested students are highly encouraged to enroll in this practical course to develop their skills and knowledge further.
The course is also listed under the following terms autumn 2021, Autumn 2022, Autumn 2024.
  • Enrolment Statistics (Autumn 2023, recent)
  • Permalink: https://is.muni.cz/course/sci/autumn2023/Bi4999en