Lecture and Exercise Protein Prediction I for Computer Scientists SoSe2021



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.


Lecture (4 SWS) + Exercise (2 SWS)




Burkhard Rost  (lecture)
Céline Marquet, Michael Bernhofer, Konstantin Weißenow, Tobias Olenyi

We are using Piazza for communication. Please register at piazza.com/tum.de/spring2021/pp1cs and post your questions there.


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 be made available on a weekly basis (on Thursday) and published on Piazza. On Thursday you will get: an exercise sheet, a presentation and a recording of one of the tutors going through the presentation. Additionally, on Mondays, tutors will hold a QA session for open ended exercise discussion (please FIRST ask on Piazza). The first exercise will be published on Thursday the 29.4.2021.

Quizzes (optional, 0.3 bonus):

Quizzes will be made available 30 minutes before the QA sessions of professor Rost (Tuesdays and Thursdays between 11:30 - 12:30) and remain open for a 30 minute period (e.g., 11:00 - 11:30am; see tentative schedule below). You have to answer the quiz during those 30 min to be awarded the points.

QAs (strongly encouraged!):

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


!!!!!!There will be no retake of the exam, you only have this one chance!!!!!!








  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 Michael Heinzinger June 1st - Video
  8. 1D: Transmembrane structure prediction 1 June 8th - Video
  9. Live - Transmembrane str pred 2 - Embeddings Michael Bernhofer June 10th - (No Video)
  10. Live - 2D: Contact prediction - Deep Learning Konstantin Weissenow June 15th - Video
  11. Live - 3D: AlphaFold2 & Miscellaneous June 17th - Video


  1. Exercise 0 - Worksheet
  2. Exercise 1 - Worksheet
  3. Exercise 2Worksheet
  4. Exercise 3Worksheet
  5. Exercise 4 - Worksheet
  6. Exercise 5 - Worksheet
  7. Exercise 6 - Worksheet
  8. Exercise 7 - Worksheet