Lecture and Exercise Protein Prediction II for Bioinformaticians WS17/18


Lecture (4 SWS) + Exercise (2 SWS)




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


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


Lecture: 01.09.034

Exercise: 01.09.034

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




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February 1, 2018 12:00 – 13:30, LMU Hörsaal im Physik Werkstattgebäude, Am Coulombwall 1, ground floor, close to Mensa, Garching campus


This lecture continues the 'Protein Prediction' lecture. The attendance of this lecture is however not a mandatory requrement 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.


  • Redundancy reduced human proteome: CD-HIT, UniqueProt


02.11 Slides Phd thesis T. Goldberg (see Chapter 4 for LocNuclei, contact us for the Bachelor thesis on the topic).

09.11. Slides. Student presentations: iLoc-HumLocTree3, Hum-mPLoc3 

16.11. Slides. Student presentations: LocTree3Hum-mPLoc3 

23.11. Slides. Student presentations: DeepLocLocTree3, LucNuclei

30.11. Slides. Student presentations: DeepLoc, LocNuclei

07.12. Slides

14.12. Slides. Student presentations: DeepLoc, LocTree3 (Plots)

21.12. Slides. Student presentations: DeepLoc

11.01. Slides.

Lecture slides

02.11 Intro 1

14.11 Predict Sub-Cellular LocalizationVideo

21.11 Predict Sub-Cellular Localization 2Video

28.11 Predict Sub-Cellular Localization 3Video

30.11 Localization 4 (LocTree2/3)

12.12 Protein Interactions - Sites 2 – Video

14.12 Protein Interactions - Sites 3 – Video

09.01 Protein Interaction PairsVideo

11.01 Protein Interaction Pairs 2Video

16.01 Predict Effect of Sequence Variation