Bi9410c Structural Biology - practice

Faculty of Science
Autumn 2020
Extent and Intensity
0/2/0. 2 credit(s) (fasci plus compl plus > 4). Type of Completion: z (credit).
Teacher(s)
doc. Mgr. David Bednář, Ph.D. (seminar tutor)
Mgr. Jan Dvorský, Ph.D. (seminar tutor)
Mgr. Ondřej Vávra, Ph.D. (assistant)
Mgr. Martina Damborská (assistant)
prof. Mgr. Jiří Damborský, Dr. (seminar tutor)
Guaranteed by
prof. Mgr. Jiří Damborský, Dr.
Department of Experimental Biology – Biology Section – Faculty of Science
Contact Person: doc. Mgr. David Bednář, Ph.D.
Supplier department: Department of Experimental Biology – Biology Section – Faculty of Science
Timetable
Thu 12:00–13:50 prace doma
Prerequisites
NOW( Bi9410 Structural Biology )
Knowledge on the level of basic lectures of biochemistry or molecular biology.
Course Enrolment Limitations
The course is offered to students of any study field.
The capacity limit for the course is 24 student(s).
Current registration and enrolment status: enrolled: 0/24, only registered: 0/24, only registered with preference (fields directly associated with the programme): 0/24
Course objectives
The aim of the course is learning students how to operate selected freely available web servers, programs and databases applicable to the study of structure, dynamics and function of proteins.
Learning outcomes
On successful completion of the course, students will be able to:
operate selected freely available web servers, programs and databases applicable to the study of structure, dynamics and function of biomacromolecules, interaction of proteins with proteins, nucleic acids and small organic molecules.
visualize structure of biomolecules
identify functionally relevant regions of proteins
predict a structure of proteins and theirs complexes
evaluate an effect of mutation on a protein functi
Syllabus
  • 1. Structure of biomacromolecules – composition, methods for determination, application in biology, visualization.
  • 2. Databases of experimental structures – deposition, retrieval and evaluation of structures of macromolecules; selected structural databases.
  • 3. Models of structures – databases of models, methods for model quality evaluation, preparation of models.
  • 4. Prediction of structure of macromolecular complexes.
  • 5. Dynamics of macromolecules – analysis of molecular dynamics and its databases.
  • 6. Protein-protein complexes – evaluation of complex, analysis of interactions; databases.
  • 7. Protein-DNA complexes – evaluation of complex, analysis of interactions; databases.
  • 8. Protein-ligand complexes – evaluation of complex, analysis of interactions; databases.
  • 9. Analysis of protein structure – identification of important regions: binding/active sites, transport pathways, flexible regions, catalytic amino acids.
  • 10. Modification of protein structure – evaluation of effect of mutation on protein structure and function.
  • 11. Application of structural biology – biological research, drug design and development, design of biocatalyst.
Literature
  • 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
  • Computational Structural Biology: Methods and Applications, T. Schwede & M. C. Peitsch, World Scientific Publishing Company, 2008
Teaching methods
individual practice in computer lab
Assessment methods
written practical test, 11 exercises awarded 100 points in total, 70 pints are needed to pass.
Language of instruction
Czech
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.
Teacher's information
http://loschmidt.chemi.muni.cz/sbiol
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, autumn 2021, Autumn 2022, Autumn 2023.
  • Enrolment Statistics (Autumn 2020, recent)
  • Permalink: https://is.muni.cz/course/sci/autumn2020/Bi9410c