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| Semester | spring semester 2013 |
| Course frequency | Every spring sem. |
| Lecturers |
Simon Bernèche (simon.berneche@unibas.ch)
Hans-Joachim Böhm (hansjoachimboehm@aol.com) Markus Meuwly (m.meuwly@unibas.ch) Torsten Schwede (torsten.schwede@unibas.ch, Assessor) |
| Content | The course will cover concepts of protein structure bioinformatics, modelling and simulation methods, their application to protein structures and their interactions with other molecules. In particular: protein structure comparison and classification, principles of molecular interactions, molecular mechanics simulations, in silico and structure based drug design, de novo and comparative protein modelling techniques. During the course, the students will gain an overview of the theoretical concepts underlying modelling and simulation methods. The theoretical lectures are complemented by practical tasks, aiming to challenge the level of understanding of the students, e.g. by programming low‐level implementations of certain algorithms. Practical applications of modelling and simulation methods will involve critical evaluation and assessment of the reliability and accuracy of the applied methods. |
| Learning objectives | During the course, the students will gain in depth understanding of the theoretical concepts underlying modelling and simulation methods. The theoretical lectures are complemented by practical tasks, aiming to challenge the level of understanding of the students (e.g. programming low level implementations of certain algorithms without using specific libraries or tool kits). Experience in handling and manipulation of different three dimensional representations and concepts, including: atomic coordinates, atomistic and molecular physico chemical properties, molecular geometries, density maps, molecular descriptors. Experience in the practical applications of modelling and simulation methods, and their limitations. Practical exercises involve critical evaluation / assessment of the confidence and accuracy of the applied methods. |
| Comments | Lecture: Thursday 10-12, Klingelbergstrasse 61, Room 1201 Exercises: on agreement with exercise supervisors Schedule: 28.02. Introduction to programming in Python & OpenStructure 7.03. Working with crystal structures and computational assignment of oligomeric states 14.3. Protein structure comparison t.b.a. |
| Weblink | Workspace for materials and exercises |
| Admission requirements | Prerequisites: • Knowledge in structural biology, e.g. Bio4 ("Strukturbiologie") and Blockkurs or equivalent. • Basic programming skills (preferably in Python). |
| Language of instruction | English |
| Use of digital media | Online, optional |
| Interval | Weekday | Time | Room |
|---|
No dates available. Please contact the lecturer.
| Modules |
Cycle E: Computational and Systems Biology (Master Molecular Biology) Cycle E: Computational and Systems Biology (PhD subject: Biochemistry) Cycle E: Computational and Systems Biology (PhD subject: Neurobiology) Cycle E: Computational and Systems Biology (PhD subject: Bioinformatics) Cycle E: Computational and Systems Biology (PhD subject: Microbiology) Cycle E: Computational and Systems Biology (PhD subject: Cell Biology) Cycle E: Computational and Systems Biology (PhD subject: Pharmacology) Cycle E: Computational and Systems Biology (PhD subject: Genetics) Cycle E: Computational and Systems Biology (PhD subject: Biophysics) Cycle E: Computational and Systems Biology (PhD subject: Structural Biology) Module Specialisation: Molecular Biology (Master Nanosciences) |
| Assessment format | continuous assessment |
| Assessment details | The practical weekly exercises will be evaluated. |
| Assessment registration/deregistration | Reg.: course registration; dereg.: teaching staff |
| Repeat examination | no repeat examination |
| Scale | Pass / Fail |
| Repeated registration | as often as necessary |
| Responsible faculty | Faculty of Science, studiendekanat-philnat@unibas.ch |
| Offered by | Departement Biozentrum |