C2150 Information processing and visualization in chemistry

Faculty of Science
Spring 2022
Extent and Intensity
0/2/0. 2 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).
Teacher(s)
Mgr. Martin Prokop, Ph.D. (lecturer)
Guaranteed by
Mgr. Martin Prokop, Ph.D.
National Centre for Biomolecular Research - Faculty of Science
Supplier department: National Centre for Biomolecular Research - Faculty of Science
Prerequisites
To be able to work in the UNIX operating system environment at the user level.
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
Course objectives
At the end of the course, student should be able to search databases of biomolecular structures, visualize chemical structures and prepare graphical outputs in the form of graphs and schemes.
Learning outcomes
On successful completion of the course, a learner will be able to: get a molecular structure data from database; visualize a structure using programs for visualization of molecules; use molecular structure data to solve simple scientific problems; visualize chemical data using simple graphs and schemes;
Syllabus
  • 1. Structural databases of the biomolecules, searching in databases. 2. Software for visualization of the molecules. 3. Visualization of molecules using the VMD software. 4. Movie preparation and advanced features of the VMD software. 5. Visualization of molecules using the Pymol software. 6. TRITON - visualization of the molecules. 7. TRITON - application in molecular modeling. 8. Data visualization using graphs - xmgrace software. 9. 2D and 3D molecular editors - MarvinSketch and Avogadro software. 10. Image editing a scheme design - GIMP and Inkscape software. 11. Other software for visualization of the molecules - Chimera, WHAT IF. 12. Transformation of structures from 2D to 3D - Corina software.
Literature
  • Molecular modeling of proteins. Edited by Andreas Kukol. Totowa, N.J.: Humana Press, 2008. xi, 390. ISBN 9781588298645. info
  • HÖLTJE, Hans-Dieter and Gerd FOLKERS. Molecular modelling :basic principles and applications. Edited by Thomas Beier - Wofgang Sippl - Didier Rognan. Weinheim: VCH Verlagsgesellschaft, 1997. xii, 194 s. ISBN 3-527-29384-1. info
  • Molecular modeling of nucleic acids. Edited by Neocles B. Leontis - John SantaLucia. Washington: American Chemical Society, 1998. x, 435 s. ISBN 0-8412-3541-4. info
  • http://www.ks.uiuc.edu/Research/vmd/
Teaching methods
Practical exercises using computer.
Assessment methods
Practical using of the VMD and Triton software. Visual presentation of text with graphs, video sequences and figures.
Language of instruction
Czech
Further Comments
The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week.
The course is also listed under the following terms Spring 2008 - for the purpose of the accreditation, 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 2020, Spring 2021.
  • Enrolment Statistics (Spring 2022, recent)
  • Permalink: https://is.muni.cz/course/sci/spring2022/C2150