SubjectsSubjects(version: 853)
Course, academic year 2019/2020
  
Structural Bioinformatics - M143013
Title: Strukturní bioinformatika
Guaranteed by: Department of Informatics and Chemistry (143)
Actual: from 2019
Semester: summer
Points: summer s.:3
E-Credits: summer s.:3
Examination process: summer s.:
Hours per week, examination: summer s.:2/0 Ex [hours/week]
Capacity: unknown / unknown (unknown)
Min. number of students: unlimited
Language: Czech
Teaching methods: full-time
Level:  
For type:  
Note: course can be enrolled in outside the study plan
enabled for web enrollment
Guarantor: Vondrášek Jiří RNDr. CSc.
Lankaš Filip doc.Ing. Ph.D.
Examination dates   Schedule   
Annotation -
Last update: Svozil Daniel doc. Mgr. Ph.D. (26.01.2018)
The course introduces structural bioinformatics – a multifields discipline which utilizes biomolecular structural data obtained by a range of experimental methods – X-Ray, NMR and electron microscopy. High numbers of structures in structural databases (ca. 130 000 structures in total) allow the application of computational and statistical methods to extract principles which control the folding process. These principles are used in structure prediction methods or as a basis for structural modelling in combination with physico-chemical rules. Students will get knowledge of basic principles used in structural bioinformatics, statistical methods, and available tools for structural analysis and prediction.
Aim of the course -
Last update: Svozil Daniel doc. Mgr. Ph.D. (26.01.2018)

Students will know:

Basic principles of structure classification as well as physico-chemical principles determining spatial structures of proteins, DNA and RNA.

Priciples and algorithms used for prediction of physico-chemical properties of biomolecules based on primary sequence knowledge.

Background and principles of algorithms used for secondary structure prediction of proteins and RNA, coparison of their accuracy.

Practical application of methods for tertiary structure prediction of biomolecules including homology modelling, threading, and ab initio methods.

Orientation in primary resources of data (structural databases) as well as in knowledge-based databases.

Description of intermolecular complexes, their statistical foundation and computational methods for intermolecular docking.

Literature -
Last update: Svozil Daniel doc. Mgr. Ph.D. (04.11.2018)

R: Sokol A., Ab initio predikce struktury membránových proteinů, PřF UK, Bc. thesis, 2016, https://is.cuni.cz/webapps/zzp/detail/143778/

R: Filippi M., Predikce sekundární struktury proteinu pomocí hlubokých neuronových sítí, MFF UK, dipl. thesis, 2017, https://dspace.cuni.cz/handle/20.500.11956/90584

R: Havrila M., Struktura a dynamika RNA, dipl. thesis, MU Brno, 2012, https://is.muni.cz/th/bj1ru/

R: Klímová M., Predikce sekundární struktury RNA sekvencí, dipl. thesis, VUT Brno, 2015, https://www.vutbr.cz/studenti/zav-prace?zp_id=84425

R: Jenny Gu, Phylip Bourne: Structural Bioinformatics, Wiley-Blackwell 2009

A: Thomas Hamelryck,‎ Kanti Mardia,‎ Jesper Ferkinghoff-Borg: Bayesian Methods in Structural Bioinformatics (Statistics for Biology and Health), Springer 2012

A: Stephen Neidle: Principles of Nucleic Acid Structure, Elsevier 2008

A: Andrew D. Bates,‎ Anthony Maxwell, M. Zvelebil, J. Baum: Understanding Bioinformatics, Oxford University Press 2007

A: Christina Marshall: Structural Bioinformatics Handbook, Syrawood Publishing House 2016

Learning resources -
Last update: Svozil Daniel doc. Mgr. Ph.D. (26.01.2018)

Online course materials at http://bioinfo.uochb.cas.cz/teaching.html

Training courses: https://www.ebi.ac.uk/training/events/2017/structural-bioinformatics-1

SIB training portal: https://edu.isb-sib.ch

Bioinformatics tutorials: http://beckerinfo.net/bioinformatics/bioinformatics-tutorials-2/

Syllabus -
Last update: Svozil Daniel doc. Mgr. Ph.D. (26.01.2018)

1. Proteins - basic characteristics, structural building blocks

2. Protein Databases - structure and knowledge based

3. Prediction of biomolecular properties based on their sequences

4. Secondary structure prediction of proteins, utilization and methods

5. Protein folding – principles, experimental methods, protein code

6. Tertiary structure prediction of proteins - homology modelling

7. Tertiary sructure prediction of proteins - threading

8. Tertiary structure prediction of proteins – ab initio methods

9. Methods used for prediction and analysis of protein protein interactions

10. Proteins - a case study

11. DNA structure and its quantitative description

12. Basic characteristics of RNA structural motifs

13. Structural databases of nucleic acids

14. Nucleic acids – a case study

Registration requirements -
Last update: Svozil Daniel doc. Mgr. Ph.D. (26.01.2018)

Molecular Biology/Genetics, Biochemistry, Physical Chemistry, Molecular modelling

Course completion requirements -
Last update: Svozil Daniel doc. Mgr. Ph.D. (26.01.2018)

The exam consists of written and oral parts.

Teaching methods
Activity Credits Hours
Účast na přednáškách 1 28
Příprava na přednášky, semináře, laboratoře, exkurzi nebo praxi 1 28
Příprava na zkoušku a její absolvování 1 28
3 / 3 84 / 84
Coursework assessment
Form Significance
Examination test 50
Oral examination 50

 
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