F8380 Basics of molecule modelling and bioniformatics

Faculty of Science
Spring 2011
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.
Timetable
Wed 17:00–17:50 BFU
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 in silico biomodel, used physical-chemical appriximations a calculations. 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.

The main objective of the course is to provide the students with the ability to
- list and describe computational steps in molecular dynamics (MD) and the physically-chemical approxiamtions used
- apply MD to model the biomolecules
- describe current bioinformatics tools.
Syllabus
  • 1. Force field definition
  • 2. Description of biomodel
  • 3. History of computational methods
  • 4. Molecular dynamics
  • 5. Analysis of MD results
  • 6. Other simulations
  • 7. Basis 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, oral
Language of instruction
Czech
Further Comments
Study Materials
The course is taught annually.
The course is also listed under the following terms Spring 2011 - only for the accreditation, Spring 2009, Spring 2010, Spring 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022.
  • Enrolment Statistics (Spring 2011, recent)
  • Permalink: https://is.muni.cz/course/sci/spring2011/F8380