Lecture and Exercise Protein Prediction I for Computational Biologists SoSe2019

 

Type:

Lecture (4 SWS) + Exercise (2 SWS)

ECTS:

8.0

Lecturer

Burkhard Rost  (lecture)
Maria Schelling (exercise)

Lecture:

Tuesday, 12:30 - 14:00

  • Room: MI 01.09.034 (Rostlab seminar room)

Thursday, 12:30 - 14:00

  • Room: MI 01.09.034 (Rostlab seminar room)

Exercise:

Thursday, 14:00 - 15:30

  • Room: MI 01.09.034 (Rostlab seminar room)

Exam:

The exam takes place on Wedneday July 17th, 18.00-20.00 o'clock in MW2001. All computational biologists are seated on the gallery.

Make-up exam: no make-up

Language:

English

Announcements:

First lecture will be Thursday, 02.05.2019.
First exercise will be Thursday, 02.05.2019.

Content

Topics will include (but not be limited to):

  • Intro: what is protein function?
  • 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.

Slides:

  1. Lecture 1 May 7th – Video
  2. Lecture 2 May 9th – Video
  3. Lecture 3 May 14th (no video recording due to technical problems)
  4. Lecture 4 May 16th – Video
  5. Lecture 5 May 23rd (chalk talk → no video)
  6. Lecture 6 May 28th – Video
  7. Lecture 7 June 4th (no new slides) – Video
  8. Lecture 8 June 6th – Video
  9. Lecture 9 June 25th – Video
  10. Lecture 10 June 27th – Video
  11. Lecture 11 July 2nd – Video
  12. Recap 1 July 4th → no slides or video
  13. Recap 2 July 9th → no slides or video

Exercise:

News/Important information

  • Secondary structure and solvent accessibility predictions can be downloaded from http://rostlab.org/~bindpredict/sec_struct_predictions.tar.gz
  • SNAP calculations and binding site annotations have been updated. The dataset now consists of 769 proteins and each of them has binding site annotations
  • Students can earn a bonus of 0.3 for the final exam in the exercise. Requirements for the bonus are active participation in the exercise (working on one of the topics presented in the first exercise + regular attendance) and presentation of the results at the end of semester
  • Students who did not attend the first exercise on May 2, but still would like to participate have to write an email to Maria (maria.schelling@tum.de) until May 7 to get assigned to a group/topic. After that deadline, students can still join the exercise, but are no longer eligible for the bonus

Slides