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Last update: Spiwok Vojtěch prof. Ing. Ph.D. (09.11.2012)
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Last update: Spiwok Vojtěch prof. 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. |
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Last update: Spiwok Vojtěch prof. 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) |
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Last update: Spiwok Vojtěch prof. Ing. Ph.D. (05.03.2013)
http://web.vscht.cz/spiwokv/struktbio/ |
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Last update: Spiwok Vojtěch prof. 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
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Last update: Spiwok Vojtěch prof. 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 |