|
| Udgave: |
Efterår 2012 NAT |
| ECTS points: |
7,5 |
| Punkter: |
7,5 |
| Point: |
7,5 |
| Blokstruktur: |
2. blok |
| Skemagruppe: |
B |
| Institutter: |
Department of Biology |
| Uddannelsesdel: |
Kandidat niveau |
| Kontaktpersoner: |
Lektor Thomas Hamelryck, phone 3532 1278, thamelry@binf.ku.dk; Prof. Jan Gorodkin, phone 3533 3578, gorodkin@genome.ku.dk |
| Skema- oplysninger: |
Mondays 10-12, Tuesdays 13-15 and Fridays 10-12 |
| Skema- oplysninger: |
 Vis skema for kurset
Samlet oversigt over tid og sted for alle kurser inden for Lektionsplan for Det Naturvidenskabelige Fakultet Efterår 2012 NAT |
| Undervisnings- form: |
Lectures (4-6 pr week), exercises (2-4 hours pr. week) |
| Indhold: |
Overview of protein structure, experimental structure determination and structure analysis, calculation of RMSD and structure superposition, fold classification (CATH, SCOP, new methods), inference of function from structure, 1D prediction (secondary structure, solvent exposure, neural networks, HMMSTR) & sampling of protein conformations (TorusDBN, directional statistics), homology modelling & the loop closure problem, knowledge based energy functions, de novo prediction methods (ROSETTA, LINUS). RNA 2D and 3D structure prediction. Python based practicals using Biopython's Bio.PDB module. |
| Målbeskrivelse: |
To obtain the grade 12:
• The student must be able to explain the motivation, biological relevance and use of the methods covered in the course.
• The student must be able to present and explain the mathematical and algorithmic details of the methods covered in the course.
• The student must be able to suggest which methods and programs to apply for a given biological problem, and to point out problems and difficulties relating to such applications.
• The student must be able to implement standard algorithms to solve standard structural bioinformatics problems in Python and Bio.PDB, and to design and implement novel, related algorithms to solve related problems.
|
| Lærebøger: |
Tutor will provide slides, articles and tutorials. |
| Tilmelding: |
Course enrolment at selvbetjeningen at KUnet in the period 15 May - 1 June. |
| Faglige forudsætninger: |
Biological sequence analysis or similar. Linux and python programming or similar. |
| Eksamensform: |
The exam will consist of a take home programming task, that is, the development of a program that solves a specific structural bioinformatics problem. The program needs to be implemented in Phython using Bio.PDB (Biophython´s structural toolkit). You will have time for the take home assignment in week 3 and 4. Graded, 7-point scale, internal censor.
Re-exam: 3 day take home exam (54 hours). |
| Eksamen: |
Aflevering af rapport den 18. januar 2013.
Reeksamen: 54 timers opgave udleveres kl. 9.00 den 15. april og afleveres kl. 15.00 den 17. april 2013 |
| Kursus hjemmeside: |
 |
| Bemærkninger: |
The capacity is limited to 25 participants. The course is open to 3-year BSc students and MSc students in general, but prefence will be given to those enrolled in the bioinformatics graduate programme. Participants that are not enrolled in the bioinformatics graduate programme are expected to bring a laptop equipped with a network card to class. |
| Undervisnings- sprog: |
Engelsk
|
| Sidst redigeret: |
25/4-2012 |