Lecture and Exercise Protein Prediction II for Bioinformaticians WS18/19

Type:

Lecture (4 SWS) + Exercise (2 SWS)

Ects:

8.0

Lecturer

Burkhard Rost  (lecture)
Jonas Reeb (exercise)
Michael Bernhofer  (exercise)

Rotation:

Tuesday, 12:30 - 14:00 (lecture)
Thursday, 12:30 - 14:00 (lecture)
Thursday, 12:00 - 13:00 (exercise)

Place:

Lecture: 01.09.034

Exercise: 01.09.034

Exam: tba

Language:

English

Announcements:

 

Exam review on Monday, March 18, from 11:00 to 12:00 in room 01.09.034.

 

No exercise on 22.11.

No lecture on 13.11 (SVV).

The latest news are always on top!

Exam:

 

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

Exercise

25.10.

8.11.

15.11.  ml_sample_code.py  (updated NN paramters, and sample code for nested cross-validation)

29.11.

13.12.

10.11.

17.11. <<< An idea to consider for the final presentation

Lecture slides

Lecture 1 October 25th – Video

Lecture 2 November 15th – Video

Lecture 3 November 20th – Video

Lecture 4 November 27th – Video

Lecture 5 November 29th – Video

Lecture 6 December 4th – Video

Lecture 7 December 13th – Video

Lecture 8 December 18th – Video

Lecture 9 January 10th – Video

Lecture 10 January 15th – Video

Lecture 11 January 22th – Video

Lecture 12 January 24th – No Video