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Course, academic year 2024/2025
  
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Advanced structural bioinformatics - AP143005
Title: Advanced structural bioinformatics
Guaranteed by: Department of Informatics and Chemistry (143)
Faculty: Faculty of Chemical Technology
Actual: from 2022
Semester: both
Points: 0
E-Credits: 0
Examination process:
Hours per week, examination: 3/0, other [HT]
Capacity: winter:unlimited / unknown (unknown)
summer:unknown / unknown (unknown)
Min. number of students: unlimited
State of the course: taught
Language: English
Teaching methods: full-time
Teaching methods: full-time
Level:  
Note: course is intended for doctoral students only
can be fulfilled in the future
you can enroll for the course in winter and in summer semester
Guarantor: Lankaš Filip doc. Ing. Ph.D.
Interchangeability : P143005
Annotation -
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.
Last update: Pátková Vlasta (08.06.2018)
Aim of the course -

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

Last update: Pátková Vlasta (08.06.2018)
Course completion requirements -

Oral exam

Last update: Pátková Vlasta (08.06.2018)
Literature -

B: N. Haspel, F. Jagodzinsky, K. Molloy (eds.), Algorithms and Methods in Structural Bioinformatics, Springer 2022

B: S. Neidle and M. Sanderson, Principles of Nucleic Acid Structure, 2nd ed., Academic Press 2021

R: Z. Gaspari (ed.), Structural Bioinformatics Methods and Protocols, Springer 2020

Last update: Lankaš Filip (15.11.2022)
Syllabus -

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

Last update: Kubová Petra (17.06.2018)
Learning resources -

Online course materials

Last update: Pátková Vlasta (08.06.2018)
Registration requirements -

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

Last update: Pátková Vlasta (08.06.2018)
 
VŠCHT Praha