Lecture and Exercise Protein Prediction II for Computer Scientists WS18/19

 

Type:

Lecture (4 SWS) + Exercise (2 SWS)

Ects:

8.0

Lecturer

Burkhard Rost  (lecture)

Jonas Reeb (exercise)

Michael Bernhofer (exercise)

Rotation:

Tuesday, 10:00 - 12:00
Thursday, 10:00 - 12:00
Thursday, (exercise), 12:00 - 13:00

Place:

Lecture:  01.09.034

Exercise: 01.09.034

Exam:

Language:

English

Announcements:

No exercise on 22.11.

No lecture on 13.11 (SVV).

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Exam tba

Content

This lecture continues the 'Protein Prediction I' lecture. The attendance of this lecture however is not a mandatory requirement 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.

 

Exercise slides

25.10.

8.11.

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

29.11.

Lecture slides

Lecture 1 October 25th – Video

Lecture 2 November 15th – Video

Lecture 3 November 20th – Video

Lecture 4 November 27th