Lecture and Exercise Protein Prediction II for Computer Scientists WiSe 2020/21



Lecture (4 SWS) + Exercise (2 SWS)




Burkhard Rost  (lecture)

Christian Dallago (exercise)


Tuesday, 10:30 - 12:00
Thursday, 10:30 - 12:00
Thursday, (exercise), 12:00 - 13:00


Lecture:  virtually

Exercise: virtually

Exam: tba




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First lecture on Tuesday, Nov 10. 10:15am CEST. 
Details in zoom-slides

Our lecture and exercise will be completely virtually.

12/01/21 and 14/01/21 are LIVE lectures starting at 10:30 and ending at 12:00!


The link for taking part in proctoring is  sent via email. If you do not have it by 01.02.2021, 10:00PM CET, please contact pp1ex@rostlab.org,





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.


  1. Zoom-Slides  Lecture Plan
  2. Lecture 1: Intro Nov 10th - Live Session
  3. Lecture 2: Intro to Protein Function Nov 11th - Video
  4. Lecture 3: Predict Localization Nov 19th  - Video
  5. Lecture 4: Localization1 Nov 24th - Video
  6. Lecture 5: Localization2 Dec 1st - Video
  7. Lecture 6: Protein Protein Interaction SItes Dec 8th - Video
  8. Lecture 7: Protein Protein Interaction Pairs Dec 10th - Video
  9. Lecture 8: Protein Protein Interaction Pairs + DNA Dec 15th - Video1 Video2(only until 15:20)
  10. Lecture 9: Representation Learning Jan 12th - Live on Zoom (start 10:30am CET)
  11. Lecture 10: Deep Learning  Jan 14th - Live on Zoom (start 10:30am CET)
  12. Lecture 11: SAV effect Jan 19th - Video Live on Zoom  (start 10:30am CET)  Website Issue. Slides temporarily hosted on LRZ Sync+Share
  13. Wrap Up: mock exam - start 10:30am CET
  14. Wrap Up: Live on Zoom (start 10:30am CET)



To successfully complete the exercise each group needs to fulfill the following requirements:

  • Give a presentation regarding their project that focuses either on the biological background, current state-of-the-art methods, or the provided data set.
  • Give a final presentation about their approach; e.g. architecture and performance.
  • Actively participate in the exercise. This primarily means attending all students' presentations and participating in the corresponding Q&A sessions.
  • Submit a working solution at the end of the semester. It should be able to make informed predictions based on new data and perform better than a random or very naive solution.

Presentations in general:

  • Attendance is mandatory for all students (not just the groups presenting) whenever there is a presentation by students.
  • For sessions without students' presentations, attendance is not mandatory.

Working in a group:

  • The workload within each group should be evenly split.
  • Not every student has to speak during their group's presentation (e.g. some could work on the presentations, the rest on the programming task).
  • If students in your group refuse to "carry their weight" or you are the only one doing any work, feel free to contact us (better early than late).