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Identical coursesBiomolecular Modelling (B-KUL-G0G79A)
Aims
Students should familiarize with several topics in the field of biomolecular modelling. The lectures are supplemented with hands-on sessions, which introduce the students to the solutions to modelling problems.
A compulsary part with evaluation via reports consists of the modelling and use of databases for the design of inhibitors to proteins making use of the commercial modelling package MOE.
After succesful completion of this course, the student:
- is able to creatively use simple unix-commands;
- has knowledge on bio-molecular dynamics;
- has sufficient capabilities of using any bio-molecular modelling program (graphic as well as command-line driven);
- has a basic knowledge of databases for biomolecular modelling and pharmacophore modelling.
Previous knowledge
This course is centered on several topics. The course is organized in such a way that some of the blocks may be used in other courses. Students that already followed a modelling course during the bachelor years may skip some of the study blocks and replace them by more in depth exercises.
Is included in these courses of study
- Master of Biophysics, Biochemistry and Biotechnology (Leuven) (Specialisation: Biochemistry and Biotechnology) 120 ects.
- Master of Biophysics, Biochemistry and Biotechnology (Leuven) (Specialisation: Biophysics) 120 ects.
- Courses for Exchange Students Faculty of Science (Leuven)
- Master of Chemistry (Leuven) 120 ects.
- Educatieve master in de wetenschappen en technologie (Leuven) 120 ects.
Activities
4.4 ects. Biomolecular Modelling (B-KUL-G0G79a)
Content
- Introduction to Molecular dynamics
- Introduction to Unix
- Introduction to programming in a modelling package
- Introduction to the modelling of biomolecular interactions; virtual recognition of small molecules in the context of macromolecules, like proteins (previously part of G0G77A Biomolecular Recognition)
Course material
1. The Brugel modelling package; Swiss-PDB-viewer; Pymol.
2. Carl-Ivar Branden & John Tooze: Introduction to protein structure, second edition. Publisher: Garland Publishing, 1999. ISBN 0-8153-2305-0
3. Tamar Schlick. Molecular modeling and simulation. Publisher: Springer ISBN: 0-387-95404-X.
Format: more information
Presentation based on recent modelling articles. Some demos are organized (molecular dynamics). Students also have to give a presentation on biomolecular recognition based on a recent modelling article.
1.6 ects. Biomolecular Modelling: Practical Course (B-KUL-G0G80a)
Content
See content of the lectures
Course material
Lecture handouts
Books
Excercises on topics seen during colleges
A selection of recent papers
Format: more information
- Some demos are organized (molecular dynamics).
- Students learn to use tools on how to select and exploit the properties of interacting molecules during hands-on excercises.
- Students give a presentation on biomolecular recognition based on a recent modelling article.
Evaluation
Evaluation: Biomolecular Modelling (B-KUL-G2G79a)
Explanation
The final exam is composed of:
- One question about Unix
- Theory questions
- One question concerning the student's presentation
The result of the examination is a weighed score of the assignments (presentation, 30%; detailed report, 40%) and the final exam (30%).
Failure for the report on CADD will result in a global failure (maximal score of 9/20).
Active participation during the presentations (asking questions) is a prerequisite to obtain a high grade.
Information about retaking exams
Oral examination with written preparation. Only the theory can be retaken as exam. Report and presentation cannot be retaken. In calculation of the final grade, the scores for report and presentation are taken from the first examination period.