Lecture and Exercise Protein Prediction II for Bioinformaticians WiSe 2019/20

Lecture and Exercise Protein Prediction II for Bioinformaticians WS18/19

Type:

Lecture (4 SWS) + Exercise (2 SWS)

Ects:

8.0

Lecturer

Burkhard Rost  (lecture)

Christian Dallago (exercise)
Michael Bernhofer (exercise)
Michael Heinzinger (exercise)

Rotation:

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

Place:

Lecture: 01.09.034

Exercise: 01.09.034

Exam: 019, LMU Physics building at the other end of the Garching campus

Language:

English

Announcements:

Lecture on Tuesday 10.12.19 cancelled due to illness!

The exercise will be in room 01.09.034 (Informatics building) from 12:00 to 13:00.

The latest news are always on top!

Exam:

Thursday, January 30, 2020. 11:00 - 13:00, room 019

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

Group

Topic for group project

Topic and date for intermediate presentation

Final Talk
1 Signal Peptides Data set (Nov 28) Jan 23
2 NLS / NES Biological background (Nov 14) Jan 16
10 Binding Residues Biological background (Nov 14) Jan 16
11 Signal Peptides State-of-the-art (Nov 28) Jan 23
12 NLS / NES Data set (Nov 28) Jan 16
13 Signal Peptides Biological background (Nov 14) Jan 23
14 Binding Residues State-of-the-art (Nov 28) Jan 16

Data sets & ELMo embeddings:
- Binding site residues, br_seqvec.tar.gz (462MB)
- Signal peptides, sp_seqvec.tar.gz (5.5GB)
- NES/NLS, ns_seqvec.tar.gz (2.0GB)

Intermediate Student Presentations:
- Biological Background:
- State of the Art:
- Data Set: NES/NLS  Signal Peptides

 

  1. Exercise 1, Oct 31
  2. Exercise 2, Nov 7
  3. Exercise 4, Dec 12
  4. Exercise 6, Jan 9

 

Lecture slides

  1. Lecture 1 October 29th       - Video
  2. Lecture 2 November 5th    - Video
  3. Lecture 3 November 7th    - Video
  4. Lecture 4 November 14th  - Video
  5. Lecture 5 November 19th - Video
  6. Lecture 6 November 21th - Video
  7. Lecture 7 November 26th (no new slides) - Video
  8. Lecture 8 December 3rd - Chalk Talk (No slides, No recording)
  9. Lecture 9 December 10th - Cancelled due to illness
  10. Lecture 10 December 12th Part1 Part2 - Video
  11. Lecture 11 December 17th - Video
  12. Lecture 12 January 9th - Video
  13. Lecture 13 January 14th - Video
  14. Lecture 14 January 16th - Video