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Obnovit | RAW

Structural Bioinformatics

Lecture Excercise/laboratory
2019, Summer Semester
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Credits 3
Hours per week 2 / 0 / 0
Examination Ex
Study Language Czech
Level []
Guarantor doc. Ing. Vojtěch Spiwok, Ph.D.

Summary

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.

Syllabus

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

Literature

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)

VŠCHT Praha
Technická 5
166 28 Praha 6 – Dejvice
IČO: 60461373
DIČ: CZ60461373

Datová schránka: sp4j9ch

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