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24169-01 - Vorlesung mit Übungen: Computational Structural Biology (6 KP)
| Semester | Frühjahrsemester 2013 |
| Angebotsmuster | Jedes Frühjahrsem. |
| Dozierende |
Simon Bernèche (simon.berneche@unibas.ch)
Hans-Joachim Böhm (hansjoachimboehm@aol.com) Markus Meuwly (m.meuwly@unibas.ch) Torsten Schwede (torsten.schwede@unibas.ch, BeurteilerIn) |
| Inhalt | 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. |
| Lernziele | 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. |
| Bemerkungen | 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 |
| Teilnahmevoraussetzungen | Prerequisites: • Knowledge in structural biology, e.g. Bio4 ("Strukturbiologie") and Blockkurs or equivalent. • Basic programming skills (preferably in Python). |
| Unterrichtssprache | Englisch |
| Einsatz digitaler Medien | Online-Angebot fakultativ |
| Intervall | Wochentag | Zeit | Raum |
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Keine Einzeltermine verfügbar, bitte informieren Sie sich direkt bei den Dozierenden.
| Module |
Cycle E: Computational and Systems Biology (Promotionsfach: Biochemie) Cycle E: Computational and Systems Biology (Promotionsfach: Biophysik) Cycle E: Computational and Systems Biology (Promotionsfach: Genetik) Cycle E: Computational and Systems Biology (Promotionsfach: Mikrobiologie) Cycle E: Computational and Systems Biology (Promotionsfach: Zellbiologie) Cycle E: Computational and Systems Biology (Promotionsfach: Pharmakologie) Cycle E: Computational and Systems Biology (Promotionsfach: Neurobiologie) Cycle E: Computational and Systems Biology (Promotionsfach: Bioinformatik) Cycle E: Computational and Systems Biology (Promotionsfach: Strukturbiologie) Cycle E: Computational and Systems Biology (Master Molekularbiologie) Modul Vertiefungsfach Molekularbiologie (Master Nanowissenschaften) |
| Prüfung | Lehrveranst.-begleitend |
| Hinweise zur Prüfung | The practical weekly exercises will be evaluated. |
| An-/Abmeldung zur Prüfung | Anmelden: Belegen; Abmelden: Dozierende |
| Wiederholungsprüfung | keine Wiederholungsprüfung |
| Skala | Pass / Fail |
| Belegen bei Nichtbestehen | beliebig wiederholbar |
| Zuständige Fakultät | Philosophisch-Naturwissenschaftliche Fakultät, studiendekanat-philnat@unibas.ch |
| Anbietende Organisationseinheit | Departement Biozentrum |