SubjectsSubjects(version: 853)
Course, academic year 2019/2020
  
Structural Bioinformatics seminar - M320022
Title: Seminář strukturní bioinformatiky
Guaranteed by: Department of Biochemistry and Microbiology (320)
Actual: from 2019
Semester: winter
Points: winter s.:2
E-Credits: winter s.:2
Examination process: winter s.:
Hours per week, examination: winter s.:0/2 MC [hours/week]
Capacity: unknown / unknown (unknown)
Min. number of students: unlimited
Language: Czech
Teaching methods: full-time
Level:  
For type: Master's (post-Bachelor)
Guarantor: Spiwok Vojtěch doc. Ing. Ph.D.
Interchangeability : N320086
Annotation -
Last update: Spiwok Vojtěch doc. Ing. Ph.D. (14.01.2018)
The subject gives practical training in computational methods for prediction of structures of proteins, their application in modeling 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: Hladíková Jana (13.12.2017)

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. (14.01.2018)

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: Hess B., van der Spoel D., Lindahl E. GROMACS user manual, Version 2018. The GROMACS development teams at the Royal Institute of Technology and Uppsala University, Sweden (http://www.gromacs.org/, 14.1.2018, without ISBN)

Learning resources -
Last update: Hladíková Jana (13.12.2017)

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

Syllabus -
Last update: Spiwok Vojtěch doc. Ing. Ph.D. (14.01.2018)

1. Cloud computing - installation of a virtual machine

2. Cloud computing - administration and use of the virtual machine

3. 3D structures of G protein-coupled receptors

4. Homology modeling - prediction of the structure of histamine H2 receptor based on H1 receptor

5. Homology modeling - prediction of the structure of histamine H2 receptor based on other receptors

6. Application of a homology models - docking of known ligands

7. Application of a homology models - preparation for virtual screening

8. Application of a homology models - virtual screening

9. Application of a homology models - analysis of the results of virtual screening

10. Application of a homology models - dynamics of histamine H2 receptor

11. Application of a homology models - dynamics of histamine H2 receptor with a ligand

12. Dynamics of histamine H2 receptor - acceleration by metadynamics

13. Dynamics of histamine H2 receptor - acceleration by parallel tempering

14. Evaluation of student projects

Registration requirements -
Last update: Spiwok Vojtěch doc. Ing. Ph.D. (20.02.2018)

Biology, Biochemistry

Course completion requirements -
Last update: Spiwok Vojtěch doc. Ing. Ph.D. (14.01.2018)

Credit will be awarded based on a project done by a pair of students. Credit classification will be based on a test.

Teaching methods
Activity Credits Hours
Konzultace s vyučujícími 0,5 14
Práce na individuálním projektu 0,5 14
Účast na seminářích 1 28
2 / 2 56 / 56
Coursework assessment
Form Significance
Report from individual projects 20
Examination test 80

 
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