SubjectsSubjects(version: 854)
Course, academic year 2019/2020
  
Structural Bioinformatics - N320086
Title: Strukturní bioinformatika
Guaranteed by: Department of Biochemistry and Microbiology (320)
Actual: from 2013
Semester: winter
Points: winter s.:3
E-Credits: winter s.:3
Examination process: winter s.:
Hours per week, examination: winter s.:2/0 Ex [hours/week]
Capacity: unlimited / unknown (unknown)
Min. number of students: unlimited
Language: Czech
Teaching methods: full-time
Level:  
For type:  
Guarantor: Spiwok Vojtěch doc. Ing. Ph.D.
Annotation -
Last update: Spiwok Vojtěch doc. Ing. Ph.D. (09.11.2012)
The subject gives practical training in computational methods for prediction of structures of proteins, their complexes with small-molecule ligands and for simulation of their dynamics. The subject follows introduction to bioinformatics and structural biology and develops practical skills based on these subjects. These skills will help students in further praxis in biochemical and pharmaceutical research and development.
Aim of the course -
Last update: Spiwok Vojtěch doc. Ing. Ph.D. (12.07.2013)

Students will be able to:

Predict protein structures at different level of homology proteins with known 3D structure, predict structures of protein-ligand complexes and strengths of interactions, simulate protein dynamics including systems containing non-standard residues and modifications, application of enhanced sampling methods.

Literature -
Last update: Spiwok Vojtěch doc. Ing. Ph.D. (12.07.2013)

R:Eswar N., Eramian D., Webb B., Shen M.Y., Sali A.: Protein structure modeling with MODELLER. Methods Mol. Biol. 426, 145-159, 2008 (http://salilab.org/pdf/Eswar_MethodsMolBiol_2008.pdf, 8.11.2012, ISSN: 1064-3745)

R:Yuriev E., Agostino M., Ramsland P.A.: Challenges and advances in computational docking: 2009 in review. J. Mol. Recognit. 24, 149-164 (2011), ISSN: 1099-1352.

R:Berk Hess, David van der Spoel, and Erik Lindahl. GROMACS user manual, Version 4.5.4. The GROMACS development teams at the Royal Institute of Technology and Uppsala University, Sweden (http://www.gromacs.org/@api/deki/files/152/=manual-4.5.4.pdf, 8.1.2012, without ISBN)

Learning resources -
Last update: Spiwok Vojtěch doc. Ing. Ph.D. (05.03.2013)

http://web.vscht.cz/spiwokv/struktbio/

Syllabus -
Last update: Spiwok Vojtěch doc. Ing. Ph.D. (08.11.2012)

1. Structure of proteins and other biomolecules, structure description

2. Use of programs in UNIX environment, secure shell

3. Prediction of protein structures - homology modelling

4. Prediction of protein structures - advanced topics

5. Protein-ligand docking

6. Virtual screening of ligands

7. Protein-protein docking

8. Simulation of molecular dynamics of proteins

9. Force field customization

10. Simulation of molecular dynamics of nucleic acids and saccharides

11. Biassing - metadynamics

12. Biassing - paralel tempering

13. Simulation of protein folding

14. Other methods of structural bioinformatics

Registration requirements -
Last update: Spiwok Vojtěch doc. Ing. Ph.D. (27.08.2013)

Essential Bioinformatics

Teaching methods
Activity Credits Hours
Konzultace s vyučujícími 0,3 7
Obhajoba individuálního projektu 0,2 5
Účast na přednáškách 1 28
Příprava na přednášky, semináře, laboratoře, exkurzi nebo praxi 1 28
Práce na individuálním projektu 0,5 14
3 / 3 82 / 84
Coursework assessment
Form Significance
Regular attendance 30
Report from individual projects 30
Oral examination 40

 
VŠCHT Praha