Lecture and Exercise Protein Prediction II for Computational Biologists WiSe 2021/22



Lecture (4 SWS) + Exercise (2 SWS)




Burkhard Rost  (lecture)

tba (exercise)


Tuesday, 12:30 - 14:00
Thursday, 12:30 - 14:00
Thursday, (exercise), 14:00 - 15:00


Lecture: tba

Exercise: tba

Exam: tba




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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.




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).