Lecture and Exercise Protein Prediction I for Bioinformaticians SoSe2021

LECTURE WILL HAPPEN ONLINE! REGISTER NOW!

Due to current regulations, lecture and exercises will be available online starting mid-april. Please, register to Piazza as soon as you can to get the latest info.

Type:

Lecture (4 SWS) + Exercise (2 SWS)

ECTS:

8.0

Lecturer

Burkhard Rost  (lecture)
Maria Littmann, Kyra Erckert

We are using Piazza for communication. Please register at piazza.com/tum.de/spring2021/pp1cb and post your questions there.

Lectures:

Lecture material will be available via a YouTube playlist as soon as the course starts. This will include all lectures for the whole semester. The first lecture day (the first lecture Q&A will be on Thursday 29.4.2021).

Exercises (optional):

Exercises will take place via Big Blue Button (BBB) on Thursday, 14:00-15:30. Details on how to join the BBB call can be found on Piazza.

QAs (strongly encouraged!):

Lecture material, on a weekly basis: Tuesdays and Thursdays, 12:30 and 13:00.

Exam:

 

Language:

English

Announcements:

The first lecture will take place on April 29th

The first exercise will take place on April 29th

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. Intro 29th April - Video
  2. Intro merged live; Intro into protein structure1; Intro into protein structure2 May 4th - Video
  3. Sequence alignments May 6th – Video
  4. Sequence alignments 2 May 18th - Video
  5. Chalk Talk May 20th (No slides)
  6. Secondary structure prediction 2 May 27th – Video
  7. LIVE - 1D: Sec str pred 3 - Embeddings/Deep Learning June 1th - Video
  8. 1D: Transmembrane structure prediction June 8th - Video
  9. 1D: Transmembrane structure prediction 2 June 8th - Video
  10. 1D: Transmembrane str pred  - Embeddings Michael Bernhofer June 10th - (No video)
  11. 2D: Contact prediction - Deep Learning Konstantin Weissenow June 15th - Video
  12. Live - 3D: AlphaFold2 & Miscellaneous - Video

 

Exercise:

News/Important information

Slides