SubjectsSubjects(version: 850)
Course, academic year 2019/2020
  
Advanced structural bioinformatics - P143005
Title in English: Pokročilá strukturní bioinformatika
Guaranteed by: Department of Informatics and Chemistry (143)
Actual: from 2019
Semester: winter
Points: winter s.:0
E-Credits: winter s.:0
Examination process: winter s.:
Hours per week, examination: winter s.:3/0 other [hours/week]
Capacity: unlimited / unknown (unknown)
Min. number of students: unlimited
Language: Czech
Teaching methods: full-time
Level:  
For type: doctoral
Guarantor: Vondrášek Jiří RNDr. CSc.
Spiwok Vojtěch doc. Ing. Ph.D.
Lankaš Filip doc.Ing. Ph.D.
Is interchangeable with: AP143005
Annotation -
Last update: Svozil Daniel doc. Mgr. Ph.D. (23.05.2018)
The course covers selected advanced topics in structural bioinformatics. We first focus on protein-protein and protein-DNA interactions. We introduce methods to calculate Gibbs free energy associated with these interactions, as well as docking algorithms, software tools and web interfaces. We then explain computational proteomics, protein interaction networks, induced fit, and ab initio methods for protein and peptide design. The section devoted to nucleic acids deals with sequence-dependent structural features of DNA, as well as RNA secondary and tertiary structure modelling. Finally, integrative structural bioinformatics combining experimental and theoretical approaches is exposed. Case studies will present selected problems based on current journal literature.
Aim of the course -
Last update: Svozil Daniel doc. Mgr. Ph.D. (23.05.2018)

Students will know:

  • They will learn advanced approaches to biomolecular interactions and their networks
  • They will obtain an overview of protein and peptide design, and of induced fit prediction
  • They will get the basics about DNA sequence-dependent features and RNA structural modelling
  • They will be acquainted with applications of structural bioinformatics in contemporary science

Literature -
Last update: Svozil Daniel doc. Mgr. Ph.D. (23.05.2018)

R: F. J. Burkowski, Structural bioinformatics, an algorithmic approach. CRC Press 2009

D: J. Gu and P. E. Bourne, eds., Structural bioinformatics, 2nd ed. Wiley-Blackwell 2009

Learning resources -
Last update: Svozil Daniel doc. Mgr. Ph.D. (23.05.2018)

Online course materials

Syllabus -
Last update: Svozil Daniel doc. Mgr. Ph.D. (16.06.2018)

1. Protein-protein and protein-nucleic acid interactions

2. Gibbs free energy calculation methods for biomolecular interactions

3. Docking algorithms for protein-protein and protein-DNA interactions

4. Software, servers and web interfaces for predicting biomolecular interactions

5. Protein Structure Initiative and computational proteomics

6. Interactome and protein interaction networks

7. Prediction of induced fit

8. Protein design and peptide docking using ab initio methods

9. Sequence dependent structural properties of DNA and their functional role

10. RNA secondary structure prediction

11. Modeling of 3D RNA structure

12. Integrative structural bioinformatics – combining experimental data and computational methods

13. – 14. Case studies

Registration requirements -
Last update: Svozil Daniel doc. Mgr. Ph.D. (23.05.2018)

Mathematics, physical chemistry, algorithms and programming, and biochemistry or molecular biology at the level of basic university courses

Course completion requirements -
Last update: Svozil Daniel doc. Mgr. Ph.D. (23.05.2018)

Oral exam

 
VŠCHT Praha