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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.
Last update: Spiwok Vojtěch (09.11.2012)
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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: Spiwok Vojtěch (12.07.2013)
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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: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) Last update: Spiwok Vojtěch (12.07.2013)
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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
Last update: Spiwok Vojtěch (08.11.2012)
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http://web.vscht.cz/spiwokv/struktbio/ Last update: Spiwok Vojtěch (05.03.2013)
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Essential Bioinformatics Last update: Spiwok Vojtěch (27.08.2013)
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| 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 |