Protein Prediction II Bioinformaticians WS14/15

Type:

Lecture (4 SWS) + Exercise (2 SWS)

Ects:

8.0

Lecturer

Burkhard Rost  (lecture)
Tatyana Goldberg (exercise)

Rotation:

Tuesday, 12:45 - 14:15 (lecture)
Thursday, 12:45 - 14:15 (lecture)
Thursday, 14:15 - 15:15 (exercise)

Place:

Lecture: FMI 01.09.034

Exercise: FMI 01.09.034

Exam: January 22, 2015, 17:30-19:00, Interims Hörsaal 2

Language:

English

Announcements:

The latest news are always on top!

No exercise on Thursday Nov 20.

No lecture on Thursday Nov. 20.

No lecture on Tuesday Nov. 4 due to Student Assembly.

Fill in this form before lecture on Oct 30th.

We moved the exercises back to the time slot on Thursdays. Please note, the first exercise takes place on Thursday Oct 30th.

No lecture and no exercise on Tuesday Oct. 21 due to 'Protein Prediction I' make-up exam. The first exercise takes place on Tuesday Oct. 28.

No lectures on Tuesday Oct. 14 and Thursday Oct. 16 due to illness. The first exercise takes place on Tuesday Oct. 21 28 30.

Lecture starts on Oct. 9 and the exercise on Oct. 212830

Examen: January 22, 2015 (Important: Don't forget to register at TUMonline for the exam)

  • Makeup: tba

Content

This lecture continues the 'Protein Prediction' lecture. The attendance of this lecture is however not a mandatory requrement for 'Protein Prediction II'.Topics will include (but not be limited to):

  • Predicting protein function using sequence: sequence alignments, multiple sequence alignments, motifs, domain assignment, annotation transfer by homology, ab initio predictions.
  • Predicting protein function using structure: structural alignments, structural motifs, annotation transfer via structure similarity.
  • From structure prediction to function prediction: comparative modeling; prediction of: secondary structure, hydrophilicity profiles, solvent accessibility, transmembrane segments, disordered regions, contact maps, functional residues; template free modeling.
  • Machine learning.

Materials

20141023: Introduction to protein function 1 - Burkhard Rost - Slides Video (1080p)

20141023: Introduction to protein function 2 - Burkhard Rost - Slides Video (1080p)

20141028: Homology-based prediction of protein function 1 - Tobias Hamp - Slides Video (1080p)

20141030: Homology-based prediction of protein function 2 - Tobias Hamp - Slides Video (1080p)

20141106: Homology-based prediction of protein function 3 - Burkhard Rost - Slides No video (last year's)

20141111: Compute chemistry - enzyme function - Burkhard Rost - Slides Video (1080p)

20141113: Chalk talk, no video

20141118: Prediction of sub-cellular localization 1 - Burkhard Rost - Slides Video (1080p)

20141125: Prediction of sub-cellular localization 2 - Burkhard Rost - Slides Video (1080p)

20141127: Chalk talk, no video

20141202: Predict protein-protein interaction sites - Burkhard Rost - Slides Video (1080p)

20141209: Sequence motifs: Representing, matching and discovering -  Mikael Bodén - Slides Video (1080p)

20141211: Sequence motifs 2 -  Mikael Bodén - Slides cont'd from 9.12. Video (1080p)

20141216: 3D function prediction -  Andrea Schafferhans - Slides Video (1080p)

20141218: Protein-ligand interaction docking-  Andrea Schafferhans - Slides Video (1080p)

20140113: Predict effect of mutation on function - Burkhard Rost - Slides Video (1080p)

Exercise

Ebola virus - officially called EBOV - has caused at least 12 outbreaks in Central Africa and Gabon since 1976. It has never been recorded in West Africa, up to 2014. The current outbreak is exceptional in its size and emergence. Responding fast to this deadly outbreak, a team of researchers from the Broad Institute and Harvard University has sequenced dozens of EBOV genomes, and made them available in public databases.

In the exercises we will work with the nucleotide and protein data of EBOV. Looking at various functional and structures features of its genome, we might better understand this expanding epidemic.

For more details please refer to our wiki. The organisation, requirements and grading of the exercise are also explained there.The log in credentials will be announced in the exercise on Oct 21st2830th. 

Note: Interested students in developing a visualization software with JavaScript are welcome to attend the Protein Prediction II exercise for Computer Scientists. For more information look here.