Methods of biomolecular modelling - N143054
Title: Metody biomolekulárního modelování
Guaranteed by: Department of Informatics and Chemistry (143)
Faculty: Faculty of Chemical Technology
Actual: from 2019 to 2020
Semester: summer
Points: summer s.:4
E-Credits: summer s.:4
Examination process: summer s.:
Hours per week, examination: summer s.:2/1, C+Ex [HT]
Capacity: unknown / unknown (unknown)
Min. number of students: unlimited
State of the course: taught
Language: Czech
Teaching methods: full-time
Teaching methods: full-time
Is provided by: M143008
Guarantor: Lankaš Filip doc. Ing. Ph.D.
Is interchangeable with: M143008
Examination dates   Schedule   
Annotation -
The course is focused on computer modelling of biological macromolecules (nucleic acids and proteins) and their interactions. With increasing computer power and development of new algorithms, computer modelling now forms an integral part of research in molecular biology, genetics and biochemistry. The first part of the course comprises an introduction to probability theory and stochastic processes, more solid than usually taught in introductory courses. This knowledge is of broader use well outside the domain of biomolecular modelling. We then use the acquired theoretical background to formulate an important simulation method, Brownian dynamics. We finish by discussing its applications to specific biological problems such as protein-ligand interactions or macromolecular dynamics in the cell. The exercises include theoretical topics as well as simple computations which the students are supposed to programm themselves.
Last update: Lankaš Filip (28.06.2016)
Aim of the course -

Students will:

  • understand probability and stochastic processes at a more solid level
  • get insight into the theoretical formulation and algorithmic realization of Brownian dynamics simulations
  • obtain an overview of applications to specific problems at the border between molecular biology, genetics and bioinformatics

Last update: Lankaš Filip (28.06.2016)
Literature -

R: T. Schlick, Molecular Modeling and Simulation, Springer 2002

A: D. Frenkel, B. Smit, Understanding Molecular Simulation, Academic Press 2002

A: J. Šponer, F. Lankaš (eds.), Computational Studies of RNA and DNA, Springer 2006

Last update: Lankaš Filip (28.06.2016)
Learning resources -

Online materials for the course

Last update: Lankaš Filip (28.06.2016)
Requirements to the exam - Czech

Zápočet: aktivní účast na přednáškách a cvičeních

Zkouška: ústní

Last update: Lankaš Filip (28.06.2016)
Syllabus -

1. Introduction. Length and time scales in biomolecular modelling

2. Probability

3. Random variables

4. Characteristics of random variables

5. Probability distribution

6. Normal distribution

7. Stochastic processes

8. Langevin equation

9. Brownian motion

10. Brownian dynamics simulations

11. Application I: Diffusion-controlled protein-ligand binding

12. Application II: Dynamics of nucleosomes and of the chromatin fibre

13. Application III: Movement and interactions of biomolecules in the cell

Last update: Lankaš Filip (28.06.2016)
Registration requirements -

Essential bioinformatics, Molecular modelling

Last update: Lankaš Filip (28.06.2016)
Teaching methods
Activity Credits Hours
Účast na přednáškách 1 28
Příprava na přednášky, semináře, laboratoře, exkurzi nebo praxi 1 28
Příprava na zkoušku a její absolvování 2 56
4 / 4 112 / 112
Coursework assessment
Form Significance
Regular attendance 30
Oral examination 70