Lecture and Exercise Protein Prediction II for Computer Scientists WS17/18



Lecture (4 SWS) + Exercise (2 SWS)




Burkhard Rost  (lecture)
Maria Schelling (exercise)
Michael Heinzinger  (exercise)
Jonas Reeb  (exercise)



Tuesday, 10:00 - 12:00
Thursday, 10:00 - 12:00
Thursday, (exercise), 12:30 - 15:00, room 019


Lecture:  01.09.034.

Exercise: LMU Hörsaal im Physik Werkstattgebäude, Am Coulombwall 1, ground floor, close to Mensa, Garching campus

Exam: LMU Hörsaal im Physik Werkstattgebäude, Am Coulombwall 1, ground floor, close to Mensa, Garching campus




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Exam February 1, 2018 12:00 – 13:30, LMU Hörsaal im Physik Werkstattgebäude, Am Coulombwall 1


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.






09.11 Slides (Note the changed start time for the exercises at 12:30​​)

16.11. Slides

23.11. Slides

  • Update 1: Now contains link to the full set of profiles

30.11. Slides 

07.12. Slides

14.12. Slides Student presentations: Group1

  • Watch this space for updates on the tasks

11.01. Slides

Final student presentations: Group 1


Lecture slides

02.11 Intro 1Video

14.11 Predict Localization (de novo)Video

21.11 Predict Localization (de novo) 2  – Video

28.11 Predict Localization (de novo) 3Video

30.11 Localization 4 – Video

12.12 Protein Protein Interactions: Sites 1 – Video

14.12 Protein Protein Interactions: Sites 2 – Video

09.01 Protein-Protein Interaction PairsVideo

11.01 Protein-Protein Interaction Pairs 2Video

16.01 Predict Effect of Sequence Variation – Video