Molecular Modeling and Bioinformatics - D320060
Title: Molekulové modelování a bioinformatika
Guaranteed by: Department of Biochemistry and Microbiology (320)
Faculty: Faculty of Food and Biochemical Technology
Actual: from 2011
Semester: winter
Points: winter s.:0
E-Credits: winter s.:0
Examination process: winter s.:
Hours per week, examination: winter s.:0/0, other [HT]
Capacity: unknown / unknown (unknown)
Min. number of students: unlimited
Language: Czech
Teaching methods: full-time
Level:  
For type:  
Note: course is intended for doctoral students only
can be fulfilled in the future
Guarantor: Hrabal Richard prof. Ing. CSc.
Examination dates   Schedule   
Annotation -
Last update: Hrabal Richard prof. Ing. CSc. (20.10.2015)
The main goal of the course is to teach students the fundaments of modern instrumental techniques like mass spectrometry, nuclear magnetic resonance spectroscopy, X-ray crystallography, optical and electron microscopy, surface plasmon resonance and their applications in biochemistry. microbiology and other biological sciences. Introductory lectures cover methods of visualisation of biomolecules, computational methods and work with databases.
Aim of the course -
Last update: Hrabal Richard prof. Ing. CSc. (20.10.2015)

Students will be able to:

They will get an overview of modern analytical techniques common in biological sciences. They will learn the application field of each method, as well as their advantages and disadvantages. They will also be able to process and use experimental data from each instrumental method in their own work.

Literature -
Last update: Hrabal Richard prof. Ing. CSc. (20.10.2015)

R: http://www.vscht.cz/nmr/mol_model_bioinfo/

A: Karlík M., Úvod do transmisní elektronové mikroskopie, ČVUT Praha, 2011, 978-80-01-04729-3

A: H. Günther: NMR Spectrosocopy John Wileay and Sons, 2.vydání, 2001

A: Orsburn B.C., Handbook of basic mass spectrometry for biologists and medical technologists: What you really need to know to get started, Bench to Bedside Press, New York, 2010, 0615434983.

A: de Hoffmann E., Stroobant V., Mass spectrometry: Principles and Applications, Chichester, 2007, 978-0-470-03310-4.

A: A. Fiser, A. Sali. Modeller: generation and refinement of homology-based protein structure models. Methods Enzymol 374, 461-491, 2003.
Learning resources -
Last update: Hrabal Richard prof. Ing. CSc. (20.10.2015)

Computing methods: http://web.vscht.cz/spiwokv/modelovani/

EM: http://www.paru.cas.cz/lem/book/index.html

NMR: http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance

Syllabus -
Last update: Hrabal Richard prof. Ing. CSc. (20.10.2015)

1. Structural databases, basic operations with biomolecular structures, molecular electrostatics

2. Prediction of protein structures, docking, virtual screening

3. Molecular mechanics, QM/MM, molecular dynamics, protein folding

4. Bases of nuclear magnetic resonance spectroscopy, (NMR), chemical shift, coupling constant, instrumental equipment

5. Technology of structure determination of proteins and their complexes, study of dynamical behavior. Practical examples of using NMR

6. Introduction to X-ray crystallography, crystal preparation

7. Diffraction theory, collection of diffraction data, phase problem, structure determination. Model construction, structure validation

8. Principles and basic techniques of electron microscopy, TEM, SEM and their using in biological sciences

9. Atomic force microscopy AFM, scanning probe microscopy SPM, scanning tunneling microscopy STM

10. Introduction to protein mass spectrometry, ionizations techniques, detectors, fragmentation techniques

11. Applications of MS in biological sciences (molecular mass determination, protein identification, sequential analysis…. Practical examples of using MS)

12. Optical microscopy

13. Superresolution microscopy

14. Surface plasmon resonance
Registration requirements -
Last update: Hrabal Richard prof. Ing. CSc. (20.10.2015)

Students should have basic knowledge of mathematics, physics and chemistry, especially biochemistry and instrumental analysis.