C2145 Structural bioinformatics in praxis

Faculty of Science
Autumn 2020
Extent and Intensity
0/1/1. 3 credit(s). Type of Completion: k (colloquium).
Teacher(s)
doc. RNDr. Radka Svobodová, Ph.D. (lecturer)
Guaranteed by
doc. RNDr. Radka Svobodová, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science
Course Enrolment Limitations
The course is offered to students of any study field.
Course objectives
The course is focused on obtaining of practical knowledge in a field of structural bioinformatics.
Basic idea of the subject is to focus on individual steps of biomacromolecular structure analysis, specifically: Finding of structures in databases, their visualization, validation, extraction of biologically important fragments and their characterization. In each step, its realization is described, relevant software tools are showed and applied on selected examples. At the end of the course, the whole process of structure data analysis is shown on two biologically important examples.

At the end of the course, the student will be able to:
Work with databases of structural biomacromolecules.
Work with methods and software tool for analysis of these data.
Perform the whole process of analysis of these data.
Interpret and discuss outputs of individual steps.
Learning outcomes
After finishing of the course, a student will be able to describe methods for realization of individual steps during analysis of structural bioinformatics data. The student will be also able to use software tools, implementing the methods. Last but not least, the student can describe and perform complete workflow for analysis of these data.
Syllabus
  • 1) Biomacromolecular Fragments and Patterns - Pattern Examples 2) Biomacromolecular Fragments and Patterns - Pattern Prediction 3) Structural Bioinformatics Databases of General Use 4) Data Delivery and Visualization of Biomacromolecules 5) Biomacromolecule Structure Validation - Validation Criteria and Validation Reports 6) Ligand Validation - Validation Criteria and Validation Reports 7) Detection and Extraction of Fragments - Creating a Query and Querying of the Database 8) Detection of Channels and Pores - Selection of Starting Point and Properties, Calculation of Tunnels 9) Characterization via Partial Atomic Charges - Approaches for Empirical Charge Calculation and their Mapping to the Structure 10) Channel Characteristics - Geometrical, Physico-chemical and Biochemical Properties 11) Complete Process of Data Extraction and Analysis: Lectin example (Validation, extraction, comparison, charge calculation) 12) Complete Process of Data Extraction and Analysis: Cytochrome P450 example (Database search, detection of channels, channel characterization)
Literature
    recommended literature
  • KOČA, Jaroslav, Radka SVOBODOVÁ VAŘEKOVÁ, Lukáš PRAVDA, Karel BERKA, Stanislav GEIDL, David SEHNAL and Michal OTYEPKA. Structural Bioinformatics Tools for Drug Design: Extraction of Biologically Relevant Information from Structural Databases. Online. 1st ed. Cham: Springer International Publishing, 2016, 144 pp. SpringerBriefs in Biochemistry and Molecular Biology. ISBN 978-3-319-47388-8. Available from: https://dx.doi.org/10.1007/978-3-319-47388-8. URL info
Teaching methods
lectures with practical demonstrations
Assessment methods
Written examination
Language of instruction
Czech
The course is also listed under the following terms autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.
  • Enrolment Statistics (Autumn 2020, recent)
  • Permalink: https://is.muni.cz/course/sci/autumn2020/C2145