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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.
Last update: Spiwok Vojtěch (14.01.2018)
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Credit will be awarded based on a project done by a pair of students. Credit classification will be based on a test. Last update: Spiwok Vojtěch (14.01.2018)
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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) Last update: Spiwok Vojtěch (14.01.2018)
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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
Last update: Spiwok Vojtěch (14.01.2018)
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http://web.vscht.cz/spiwokv/struktbio/ Last update: Hladíková Jana (13.12.2017)
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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. Last update: Hladíková Jana (13.12.2017)
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Biology, Biochemistry Last update: Spiwok Vojtěch (20.02.2018)
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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 |