F8380 Basics of molecule modelling and bioinformatics

Faculty of Science
Spring 2020
Extent and Intensity
1/0. 1 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).
Teacher(s)
Mgr. Kamila Réblová, Ph.D. (lecturer)
Mgr. Naděžda Špačková, Ph.D. (lecturer)
Guaranteed by
prof. RNDr. Josef Humlíček, CSc.
Department of Condensed Matter Physics – Physics Section – Faculty of Science
Contact Person: doc. Mgr. Karel Kubíček, PhD.
Supplier department: Department of Condensed Matter Physics – Physics Section – Faculty of Science
Course Enrolment Limitations
The course is also offered to the students of the fields other than those the course is directly associated with.
fields of study / plans the course is directly associated with
  • Biophysics (programme PřF, N-FY, specialization Molekulární biofyzika)
Course objectives
The course is focused to basics of molecular modelling of biomolecules using molecular dynamics (MD). It is concentrated on description of model systems, force fields, used physical-chemical approximations, biomolecular system preparations and MD simulations. It discusses analysis of MD results as well as other MD methods (i.e. LES, TMD, NEB nebo MMPBSA/MMGBSA). The lecture is aimed at current bioinformatics tools such as sequence alignment, databases, homology modelling and structure prediction.
Learning outcomes
The main objective of the course is to provide the students with the ability to
- list and describe basic principles of molecular dynamics (MD) and applied physically-chemical approximations
- apply MD to model the biomolecules
- analyze and characterize limits of MD methods
- describe current bioinformatics tools
Syllabus
  • 1. Atomic level methods for biomolecular studies, history of computational methods
  • 2. Force field and model system definition
  • 3. Basics of molecular dynamics (MD)
  • 4. Preparation of biomolecules for MD simulation
  • 5. Analysis of MD results
  • 6. Other simulation techniques
  • 7. Basics of bioinformatics
Literature
  • Andrew R. Leach, Molecular Modelling: Principles and Applications, second edition, Published by Pearson Education EMA, January 2001
Teaching methods
Lectures + class discussion
Assessment methods
colloquium, written test (including 10 short questions) followed by oral discussion of test results 70% of correct answers is needed to pass
Language of instruction
Czech
Further Comments
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2011 - only for the accreditation, Spring 2009, Spring 2010, Spring 2011, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2021, Spring 2022.
  • Enrolment Statistics (Spring 2020, recent)
  • Permalink: https://is.muni.cz/course/sci/spring2020/F8380