Bi9410 Structural Biology

Faculty of Science
Autumn 2020
Extent and Intensity
2/0/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: zk (examination).
Taught partially online.
Mgr. David Bednář, Ph.D. (lecturer)
Sérgio Manuel Marques, PhD. (lecturer)
prof. Mgr. Jiří Damborský, Dr. (lecturer)
Mgr. Martina Damborská (assistant)
Mgr. Ondřej Vávra (lecturer)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology - Biology Section - Faculty of Science
Contact Person: Mgr. David Bednář, Ph.D.
Supplier department: Department of Experimental Biology - Biology Section - Faculty of Science
Wed 14:00–15:50 Pouze distančně
Knowledge on the level of basic lectures of biochemistry or molecular biology.
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 successful completion of the course, students will be able to:
describe structures of biomolecules and experimental methods for their determination
obtain structures of biomoleculs from suitable databases
identify possible errors in the protein structure
predict a structure of biomolecules and theirs complexes
analyze protein structures to acquire information about their function, dynamics and stability
evaluate an effect of mutation on a protein function
Learning outcomes
- description of macromolecular structure and characterization of individual interactions
- download and basic analysis of structure quality and errors identification
- experimental structural methods and structure prediction in silico
- analysis of function, dynamics and stability
- effect of mutation on structure, function, dynamics and stability of macromolecule
  • Structural biology is a scientific discipline derived from molecular biology, biochemistry and biophysics. It focuses on the molecular structure of biomacromolecules, especially proteins and nucleic acids which are essential components of all living organisms. Structural biology enables us to determine a structure of biomacromolecules and to investigate its relationship to the biological role of the molecules.
  • Within this course, the following topic will be addressed:
  • 1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
  • 2. Databases of experimental structures – retrieval and evaluation of macromolecular structures; selected structural databases.
  • 3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
  • 4. Stability and dynamics of macromolecules – analysis of molecular dynamics and stability; databases.
  • 5. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, binding/catalytic amino acids.
  • 6. Prediction of structure of macromolecular complexes.
  • 7. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
  • 8. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
  • 9. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
  • 10. Modification of protein structure – evaluation of the effect of mutation on protein structure and function.
  • 11. Application of structural biology – biological research, drug design and development, design of biocatalyst.
  • Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
  • Textbook Of Structural Biology, A. Liljas, L. Liljas, J. Piskur, G. Lindblom, P. Nissen, M. Kjeldgaard, World Scientific Publishing Company, 2009
  • Structural Bioinformatics, J. Gu &P. E. Bourne, Wiley-Blackwell, 2009
  • Protein Stucture and Function, G. A. Petsko & D. Ringe, New Science Press, 2004
Teaching methods
Assessment methods
multiple choice test, 9 correct answers out of 25 are needed to pass
Language of instruction
Follow-Up Courses
Further comments (probably available only in Czech)
Study Materials
The course is taught annually.
General note: Předmět se doporučuje zapsat v 1. nebo 3. semestru.
Listed among pre-requisites of other courses
The course is also listed under the following terms Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019.
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