C2150 Information processing and visualization in chemistry

Faculty of Science
Spring 2011
Extent and Intensity
0/2/0. 2 credit(s) (plus extra credits for completion). Type of Completion: k (colloquium).
Teacher(s)
Mgr. Zdeněk Kříž, Ph.D. (lecturer)
Mgr. Martin Prokop, Ph.D. (lecturer)
Guaranteed by
Mgr. Zdeněk Kříž, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Timetable
Tue 11:00–12:50 C04/211
Prerequisites
To be able to work in the UNIX operating system environment at the user level.
Course Enrolment Limitations
The course is only offered to the students of the study fields 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, validate obtained data, prepare the structures for molecular modeling procedures and to visualize obtained results in the form of presentation of poster. The objectives of this course is not to introduce molecular modeling methods.
Syllabus
  • 1. Visualization of molecules, transformation from 2D to 3D. 2. Software for visualization of the molecules. 3. Structural databases of the biomolecules, searching in databases. 4. Structure validation, software WHAT IF. 5. Visualization of molecules using the VMD software. 6. MD trajectories visualization using the VMD software. 7. MD data processing and its visualization - xmgrace and gnuplot software. 8. TRITON - visualization of the molecules. 9. TRITON - application in molecular modeling. 10. Graphical presentation - Open Office, Povray, Render3D and preparation of 3D figures. 11. Movie preparation and the possibilities of the VMD software extensions. 12. Other software for visualization of the molecules - Chimera, Pymol.
Literature
  • Molecular modeling of proteins. Edited by Andreas Kukol. Totowa: 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
Study Materials
The course is taught annually.
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 2012, spring 2012 - acreditation, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017, spring 2018, Spring 2019, Spring 2020, Spring 2021, Spring 2022, Spring 2023, Spring 2024, Spring 2025.
  • Enrolment Statistics (Spring 2011, recent)
  • Permalink: https://is.muni.cz/course/sci/spring2011/C2150